From a3422f7a453696a13a1a54ca21c684433529bf26 Mon Sep 17 00:00:00 2001 From: oriolfornes Date: Mon, 4 Oct 2021 09:11:16 -0700 Subject: [PATCH] updated files --- README.md | 18 +- environment.yml => conda/environment.yml | 1 + genomes/get-genomes.sh | 2 +- profiles/fungi/MA0265.1.pwm | 16 ++ profiles/fungi/MA0265.2.pwm | 20 ++ profiles/fungi/MA0266.1.pwm | 7 + profiles/fungi/MA0267.1.pwm | 14 +- profiles/fungi/MA0268.1.pwm | 14 +- profiles/fungi/MA0269.1.pwm | 21 ++ profiles/fungi/MA0270.1.pwm | 8 + profiles/fungi/MA0271.1.pwm | 6 + profiles/fungi/MA0272.1.pwm | 16 +- profiles/fungi/MA0273.1.pwm | 42 ++-- profiles/fungi/MA0274.1.pwm | 8 + profiles/fungi/MA0275.1.pwm | 6 + profiles/fungi/MA0276.1.pwm | 10 + profiles/fungi/MA0277.1.pwm | 9 + profiles/fungi/MA0278.1.pwm | 21 ++ profiles/fungi/MA0279.1.pwm | 20 +- profiles/fungi/MA0279.2.pwm | 16 ++ profiles/fungi/MA0280.1.pwm | 12 +- profiles/fungi/MA0281.1.pwm | 8 + profiles/fungi/MA0281.2.pwm | 15 ++ profiles/fungi/MA0282.1.pwm | 16 +- profiles/fungi/MA0283.1.pwm | 8 + profiles/fungi/MA0284.1.pwm | 10 + profiles/fungi/MA0284.2.pwm | 28 +-- profiles/fungi/MA0285.1.pwm | 9 + profiles/fungi/MA0286.1.pwm | 18 +- profiles/fungi/MA0287.1.pwm | 22 +- profiles/fungi/MA0288.1.pwm | 9 + profiles/fungi/MA0289.1.pwm | 7 + profiles/fungi/MA0290.1.pwm | 19 ++ profiles/fungi/MA0291.1.pwm | 9 + profiles/fungi/MA0292.1.pwm | 7 + profiles/fungi/MA0293.1.pwm | 11 + profiles/fungi/MA0294.1.pwm | 18 +- profiles/fungi/MA0295.1.pwm | 16 +- profiles/fungi/MA0296.1.pwm | 20 ++ profiles/fungi/MA0297.1.pwm | 14 +- profiles/fungi/MA0299.1.pwm | 15 ++ profiles/fungi/MA0300.1.pwm | 16 +- profiles/fungi/MA0301.1.pwm | 9 + profiles/fungi/MA0302.1.pwm | 22 +- profiles/fungi/MA0303.1.pwm | 21 ++ profiles/fungi/MA0303.2.pwm | 22 +- profiles/fungi/MA0304.1.pwm | 16 +- profiles/fungi/MA0305.1.pwm | 7 + profiles/fungi/MA0306.1.pwm | 18 +- profiles/fungi/MA0307.1.pwm | 5 + profiles/fungi/MA0308.1.pwm | 21 ++ profiles/fungi/MA0309.1.pwm | 8 + profiles/fungi/MA0310.1.pwm | 8 + profiles/fungi/MA0311.1.pwm | 10 +- profiles/fungi/MA0312.1.pwm | 8 + profiles/fungi/MA0312.2.pwm | 20 +- profiles/fungi/MA0313.1.pwm | 5 + profiles/fungi/MA0314.1.pwm | 15 ++ profiles/fungi/MA0314.2.pwm | 12 ++ profiles/fungi/MA0316.1.pwm | 30 +-- profiles/fungi/MA0317.1.pwm | 16 +- profiles/fungi/MA0318.1.pwm | 8 + profiles/fungi/MA0319.1.pwm | 16 +- profiles/fungi/MA0320.1.pwm | 16 +- profiles/fungi/MA0321.1.pwm | 18 +- profiles/fungi/MA0322.1.pwm | 9 + profiles/fungi/MA0323.1.pwm | 15 ++ profiles/fungi/MA0324.1.pwm | 10 + profiles/fungi/MA0325.1.pwm | 8 + profiles/fungi/MA0326.1.pwm | 8 + profiles/fungi/MA0327.1.pwm | 14 +- profiles/fungi/MA0328.1.pwm | 18 +- profiles/fungi/MA0328.2.pwm | 8 + profiles/fungi/MA0329.1.pwm | 7 + profiles/fungi/MA0330.1.pwm | 14 +- profiles/fungi/MA0331.1.pwm | 12 ++ profiles/fungi/MA0332.1.pwm | 6 + profiles/fungi/MA0333.1.pwm | 18 +- profiles/fungi/MA0334.1.pwm | 7 + profiles/fungi/MA0335.1.pwm | 8 + profiles/fungi/MA0336.1.pwm | 42 ++-- profiles/fungi/MA0337.1.pwm | 14 +- profiles/fungi/MA0338.1.pwm | 7 + profiles/fungi/MA0339.1.pwm | 14 +- profiles/fungi/MA0340.1.pwm | 12 +- profiles/fungi/MA0341.1.pwm | 5 + profiles/fungi/MA0342.1.pwm | 5 + profiles/fungi/MA0343.1.pwm | 42 ++-- profiles/fungi/MA0344.1.pwm | 16 +- profiles/fungi/MA0347.1.pwm | 20 ++ profiles/fungi/MA0347.2.pwm | 26 +-- profiles/fungi/MA0348.1.pwm | 9 + profiles/fungi/MA0349.1.pwm | 14 +- profiles/fungi/MA0350.1.pwm | 42 ++-- profiles/fungi/MA0351.1.pwm | 21 ++ profiles/fungi/MA0352.1.pwm | 16 +- profiles/fungi/MA0352.2.pwm | 28 +-- profiles/fungi/MA0353.1.pwm | 16 +- profiles/fungi/MA0354.1.pwm | 8 + profiles/fungi/MA0355.1.pwm | 20 +- profiles/fungi/MA0356.1.pwm | 6 + profiles/fungi/MA0357.1.pwm | 16 +- profiles/fungi/MA0358.1.pwm | 16 +- profiles/fungi/MA0359.1.pwm | 20 +- profiles/fungi/MA0359.2.pwm | 15 ++ profiles/fungi/MA0360.1.pwm | 8 + profiles/fungi/MA0361.1.pwm | 7 + profiles/fungi/MA0362.1.pwm | 14 +- profiles/fungi/MA0363.1.pwm | 18 +- profiles/fungi/MA0363.2.pwm | 30 +-- profiles/fungi/MA0364.1.pwm | 14 +- profiles/fungi/MA0365.1.pwm | 16 +- profiles/fungi/MA0366.1.pwm | 10 +- profiles/fungi/MA0367.1.pwm | 11 + profiles/fungi/MA0368.1.pwm | 7 + profiles/fungi/MA0369.1.pwm | 18 ++ profiles/fungi/MA0370.1.pwm | 10 + profiles/fungi/MA0371.1.pwm | 12 ++ profiles/fungi/MA0372.1.pwm | 16 +- profiles/fungi/MA0373.1.pwm | 14 +- profiles/fungi/MA0374.1.pwm | 14 +- profiles/fungi/MA0375.1.pwm | 16 +- profiles/fungi/MA0376.1.pwm | 20 ++ profiles/fungi/MA0377.1.pwm | 21 ++ profiles/fungi/MA0378.1.pwm | 21 ++ profiles/fungi/MA0379.1.pwm | 5 + profiles/fungi/MA0380.1.pwm | 14 +- profiles/fungi/MA0381.1.pwm | 12 +- profiles/fungi/MA0382.1.pwm | 16 +- profiles/fungi/MA0382.2.pwm | 34 +-- profiles/fungi/MA0384.1.pwm | 11 + profiles/fungi/MA0385.1.pwm | 11 + profiles/fungi/MA0386.1.pwm | 21 ++ profiles/fungi/MA0387.1.pwm | 10 + profiles/fungi/MA0388.1.pwm | 16 +- profiles/fungi/MA0389.1.pwm | 16 +- profiles/fungi/MA0390.1.pwm | 42 ++-- profiles/fungi/MA0391.1.pwm | 7 + profiles/fungi/MA0392.1.pwm | 16 +- profiles/fungi/MA0393.1.pwm | 14 +- profiles/fungi/MA0394.1.pwm | 8 + profiles/fungi/MA0395.1.pwm | 20 ++ profiles/fungi/MA0396.1.pwm | 18 +- profiles/fungi/MA0397.1.pwm | 9 + profiles/fungi/MA0398.1.pwm | 9 + profiles/fungi/MA0399.1.pwm | 7 + profiles/fungi/MA0400.1.pwm | 40 ++-- profiles/fungi/MA0401.1.pwm | 16 +- profiles/fungi/MA0402.1.pwm | 8 + profiles/fungi/MA0403.1.pwm | 8 + profiles/fungi/MA0403.2.pwm | 16 ++ profiles/fungi/MA0404.1.pwm | 16 +- profiles/fungi/MA0405.1.pwm | 16 +- profiles/fungi/MA0406.1.pwm | 16 +- profiles/fungi/MA0407.1.pwm | 30 +-- profiles/fungi/MA0408.1.pwm | 16 +- profiles/fungi/MA0409.1.pwm | 7 + profiles/fungi/MA0410.1.pwm | 16 +- profiles/fungi/MA0411.1.pwm | 7 + profiles/fungi/MA0412.1.pwm | 26 +-- profiles/fungi/MA0412.2.pwm | 30 +-- profiles/fungi/MA0413.1.pwm | 40 ++-- profiles/fungi/MA0414.1.pwm | 7 + profiles/fungi/MA0415.1.pwm | 40 ++-- profiles/fungi/MA0416.1.pwm | 16 +- profiles/fungi/MA0417.1.pwm | 12 +- profiles/fungi/MA0418.1.pwm | 20 ++ profiles/fungi/MA0419.1.pwm | 11 + profiles/fungi/MA0420.1.pwm | 16 +- profiles/fungi/MA0421.1.pwm | 10 + profiles/fungi/MA0422.1.pwm | 20 +- profiles/fungi/MA0423.1.pwm | 9 + profiles/fungi/MA0424.1.pwm | 8 + profiles/fungi/MA0425.1.pwm | 28 +-- profiles/fungi/MA0426.1.pwm | 12 +- profiles/fungi/MA0428.1.pwm | 18 +- profiles/fungi/MA0429.1.pwm | 14 +- profiles/fungi/MA0430.1.pwm | 16 +- profiles/fungi/MA0431.1.pwm | 18 +- profiles/fungi/MA0432.1.pwm | 16 +- profiles/fungi/MA0433.1.pwm | 8 + profiles/fungi/MA0434.1.pwm | 18 +- profiles/fungi/MA0435.1.pwm | 20 ++ profiles/fungi/MA0436.1.pwm | 14 +- profiles/fungi/MA0437.1.pwm | 9 + profiles/fungi/MA0438.1.pwm | 8 + profiles/fungi/MA0439.1.pwm | 11 + profiles/fungi/MA0440.1.pwm | 15 ++ profiles/fungi/MA0441.1.pwm | 18 +- profiles/fungi/MA0929.1.pwm | 12 ++ profiles/fungi/MA1431.1.pwm | 10 + profiles/fungi/MA1432.1.pwm | 8 + profiles/fungi/MA1433.1.pwm | 16 +- profiles/fungi/MA1434.1.pwm | 14 +- profiles/fungi/MA1435.1.pwm | 10 + profiles/fungi/MA1436.1.pwm | 16 +- profiles/fungi/MA1437.1.pwm | 16 +- profiles/get-profiles.py | 104 ++++------ profiles/insects/MA0010.1.pwm | 14 ++ profiles/insects/MA0011.1.pwm | 16 +- profiles/insects/MA0012.1.pwm | 22 +- profiles/insects/MA0013.1.pwm | 22 +- profiles/insects/MA0015.1.pwm | 10 + profiles/insects/MA0016.1.pwm | 20 +- profiles/insects/MA0022.1.pwm | 24 +-- profiles/insects/MA0023.1.pwm | 20 +- profiles/insects/MA0026.1.pwm | 14 +- profiles/insects/MA0049.1.pwm | 10 + profiles/insects/MA0085.1.pwm | 16 ++ profiles/insects/MA0086.1.pwm | 6 + profiles/insects/MA0086.2.pwm | 26 +-- profiles/insects/MA0094.1.pwm | 4 + profiles/insects/MA0094.2.pwm | 16 +- profiles/insects/MA0126.1.pwm | 18 +- profiles/insects/MA0165.1.pwm | 7 + profiles/insects/MA0166.1.pwm | 7 + profiles/insects/MA0167.1.pwm | 7 + profiles/insects/MA0168.1.pwm | 7 + profiles/insects/MA0169.1.pwm | 7 + profiles/insects/MA0170.1.pwm | 14 +- profiles/insects/MA0171.1.pwm | 7 + profiles/insects/MA0172.1.pwm | 7 + profiles/insects/MA0173.1.pwm | 14 +- profiles/insects/MA0174.1.pwm | 7 + profiles/insects/MA0175.1.pwm | 14 +- profiles/insects/MA0176.1.pwm | 14 +- profiles/insects/MA0177.1.pwm | 14 +- profiles/insects/MA0178.1.pwm | 14 +- profiles/insects/MA0179.1.pwm | 7 + profiles/insects/MA0180.1.pwm | 18 +- profiles/insects/MA0181.1.pwm | 14 +- profiles/insects/MA0182.1.pwm | 14 +- profiles/insects/MA0183.1.pwm | 8 + profiles/insects/MA0184.1.pwm | 14 +- profiles/insects/MA0185.1.pwm | 6 + profiles/insects/MA0186.1.pwm | 7 + profiles/insects/MA0187.1.pwm | 7 + profiles/insects/MA0188.1.pwm | 7 + profiles/insects/MA0189.1.pwm | 14 +- profiles/insects/MA0190.1.pwm | 12 +- profiles/insects/MA0191.1.pwm | 14 +- profiles/insects/MA0192.1.pwm | 7 + profiles/insects/MA0193.1.pwm | 14 +- profiles/insects/MA0194.1.pwm | 7 + profiles/insects/MA0195.1.pwm | 14 +- profiles/insects/MA0196.1.pwm | 7 + profiles/insects/MA0197.1.pwm | 8 + profiles/insects/MA0197.2.pwm | 24 +-- profiles/insects/MA0198.1.pwm | 7 + profiles/insects/MA0199.1.pwm | 5 + profiles/insects/MA0200.1.pwm | 7 + profiles/insects/MA0201.1.pwm | 7 + profiles/insects/MA0202.1.pwm | 14 +- profiles/insects/MA0203.1.pwm | 14 +- profiles/insects/MA0204.1.pwm | 6 + profiles/insects/MA0205.1.pwm | 20 +- profiles/insects/MA0205.2.pwm | 12 ++ profiles/insects/MA0206.1.pwm | 7 + profiles/insects/MA0207.1.pwm | 6 + profiles/insects/MA0208.1.pwm | 14 +- profiles/insects/MA0209.1.pwm | 7 + profiles/insects/MA0210.1.pwm | 10 +- profiles/insects/MA0211.1.pwm | 7 + profiles/insects/MA0212.1.pwm | 12 +- profiles/insects/MA0213.1.pwm | 8 + profiles/insects/MA0214.1.pwm | 14 +- profiles/insects/MA0215.1.pwm | 7 + profiles/insects/MA0216.1.pwm | 7 + profiles/insects/MA0216.2.pwm | 11 + profiles/insects/MA0217.1.pwm | 10 +- profiles/insects/MA0218.1.pwm | 12 +- profiles/insects/MA0219.1.pwm | 14 +- profiles/insects/MA0220.1.pwm | 14 +- profiles/insects/MA0221.1.pwm | 14 +- profiles/insects/MA0222.1.pwm | 8 + profiles/insects/MA0224.1.pwm | 14 +- profiles/insects/MA0225.1.pwm | 14 +- profiles/insects/MA0226.1.pwm | 7 + profiles/insects/MA0227.1.pwm | 12 +- profiles/insects/MA0228.1.pwm | 14 +- profiles/insects/MA0229.1.pwm | 8 + profiles/insects/MA0230.1.pwm | 7 + profiles/insects/MA0231.1.pwm | 6 + profiles/insects/MA0232.1.pwm | 6 + profiles/insects/MA0233.1.pwm | 10 +- profiles/insects/MA0234.1.pwm | 12 +- profiles/insects/MA0235.1.pwm | 7 + profiles/insects/MA0236.1.pwm | 14 +- profiles/insects/MA0237.1.pwm | 8 + profiles/insects/MA0237.2.pwm | 28 +-- profiles/insects/MA0238.1.pwm | 14 +- profiles/insects/MA0239.1.pwm | 18 +- profiles/insects/MA0240.1.pwm | 7 + profiles/insects/MA0241.1.pwm | 7 + profiles/insects/MA0242.1.pwm | 9 + profiles/insects/MA0243.1.pwm | 12 ++ profiles/insects/MA0244.1.pwm | 16 +- profiles/insects/MA0245.1.pwm | 7 + profiles/insects/MA0246.1.pwm | 6 + profiles/insects/MA0247.1.pwm | 16 +- profiles/insects/MA0247.2.pwm | 20 +- profiles/insects/MA0248.1.pwm | 7 + profiles/insects/MA0249.1.pwm | 24 +-- profiles/insects/MA0249.2.pwm | 11 + profiles/insects/MA0250.1.pwm | 14 +- profiles/insects/MA0251.1.pwm | 14 +- profiles/insects/MA0252.1.pwm | 12 +- profiles/insects/MA0253.1.pwm | 9 + profiles/insects/MA0254.1.pwm | 12 +- profiles/insects/MA0255.1.pwm | 10 + profiles/insects/MA0256.1.pwm | 14 +- profiles/insects/MA0257.1.pwm | 14 +- profiles/insects/MA0443.1.pwm | 20 +- profiles/insects/MA0444.1.pwm | 14 +- profiles/insects/MA0445.1.pwm | 22 +- profiles/insects/MA0446.1.pwm | 22 +- profiles/insects/MA0447.1.pwm | 10 + profiles/insects/MA0448.1.pwm | 14 +- profiles/insects/MA0449.1.pwm | 10 + profiles/insects/MA0450.1.pwm | 18 +- profiles/insects/MA0451.1.pwm | 12 ++ profiles/insects/MA0452.1.pwm | 22 +- profiles/insects/MA0452.2.pwm | 28 +-- profiles/insects/MA0454.1.pwm | 22 +- profiles/insects/MA0456.1.pwm | 24 +-- profiles/insects/MA0457.1.pwm | 7 + profiles/insects/MA0458.1.pwm | 11 + profiles/insects/MA0459.1.pwm | 20 +- profiles/insects/MA0460.1.pwm | 9 + profiles/insects/MA0529.1.pwm | 30 +-- profiles/insects/MA0529.2.pwm | 12 ++ profiles/insects/MA0530.1.pwm | 30 +-- profiles/insects/MA0531.1.pwm | 30 +-- profiles/insects/MA0532.1.pwm | 15 ++ profiles/insects/MA0533.1.pwm | 21 ++ profiles/insects/MA0534.1.pwm | 15 ++ profiles/insects/MA0535.1.pwm | 15 ++ profiles/insects/MA0536.1.pwm | 22 +- profiles/insects/MA0915.1.pwm | 8 + profiles/insects/MA0916.1.pwm | 8 + profiles/insects/MA0917.1.pwm | 8 + profiles/insects/MA1455.1.pwm | 34 +-- profiles/insects/MA1456.1.pwm | 10 + profiles/insects/MA1457.1.pwm | 26 +-- profiles/insects/MA1458.1.pwm | 24 +-- profiles/insects/MA1459.1.pwm | 18 ++ profiles/insects/MA1460.1.pwm | 11 + profiles/insects/MA1461.1.pwm | 34 +-- profiles/insects/MA1462.1.pwm | 24 +-- profiles/insects/MA1700.1.pwm | 28 +-- profiles/insects/MA1702.1.pwm | 24 +-- profiles/insects/MA1836.1.pwm | 22 +- profiles/insects/MA1837.1.pwm | 22 +- profiles/insects/MA1838.1.pwm | 11 + profiles/insects/MA1839.1.pwm | 11 + profiles/insects/MA1840.1.pwm | 13 ++ profiles/insects/MA1841.1.pwm | 36 ++-- profiles/insects/MA1842.1.pwm | 10 + profiles/nematodes/MA0260.1.pwm | 12 +- profiles/nematodes/MA0261.1.pwm | 12 +- profiles/nematodes/MA0262.1.pwm | 13 ++ profiles/nematodes/MA0263.1.pwm | 28 +-- profiles/nematodes/MA0264.1.pwm | 22 +- profiles/nematodes/MA0537.1.pwm | 22 +- profiles/nematodes/MA0538.1.pwm | 30 +-- profiles/nematodes/MA0540.1.pwm | 16 ++ profiles/nematodes/MA0541.1.pwm | 15 ++ profiles/nematodes/MA0542.1.pwm | 8 + profiles/nematodes/MA0543.1.pwm | 30 +-- profiles/nematodes/MA0544.1.pwm | 24 +-- profiles/nematodes/MA0545.1.pwm | 11 + profiles/nematodes/MA0546.1.pwm | 10 + profiles/nematodes/MA0547.1.pwm | 15 ++ profiles/nematodes/MA0918.1.pwm | 24 +-- profiles/nematodes/MA0919.1.pwm | 10 + profiles/nematodes/MA0920.1.pwm | 8 + profiles/nematodes/MA0921.1.pwm | 9 + profiles/nematodes/MA0922.1.pwm | 9 + profiles/nematodes/MA0923.1.pwm | 18 +- profiles/nematodes/MA0924.1.pwm | 16 +- profiles/nematodes/MA0925.1.pwm | 11 + profiles/nematodes/MA0926.1.pwm | 8 + profiles/nematodes/MA0927.1.pwm | 16 +- profiles/nematodes/MA0928.1.pwm | 22 +- profiles/nematodes/MA1438.1.pwm | 10 + profiles/nematodes/MA1439.1.pwm | 8 + profiles/nematodes/MA1440.1.pwm | 8 + profiles/nematodes/MA1441.1.pwm | 11 + profiles/nematodes/MA1442.1.pwm | 8 + profiles/nematodes/MA1443.1.pwm | 8 + profiles/nematodes/MA1444.1.pwm | 12 ++ profiles/nematodes/MA1445.1.pwm | 20 +- profiles/nematodes/MA1446.1.pwm | 12 ++ profiles/nematodes/MA1448.1.pwm | 7 + profiles/nematodes/MA1449.1.pwm | 24 +-- profiles/nematodes/MA1450.1.pwm | 28 +-- profiles/nematodes/MA1451.1.pwm | 16 +- profiles/nematodes/MA1699.1.pwm | 16 ++ profiles/nematodes/MA1701.1.pwm | 20 +- profiles/nematodes/MA1703.1.pwm | 22 +- profiles/nematodes/MA1704.1.pwm | 11 + profiles/plants/MA0001.1.pwm | 20 +- profiles/plants/MA0001.2.pwm | 18 ++ profiles/plants/MA0005.1.pwm | 22 +- profiles/plants/MA0005.2.pwm | 36 ++-- profiles/plants/MA0008.1.pwm | 16 +- profiles/plants/MA0008.2.pwm | 12 ++ profiles/plants/MA0020.1.pwm | 6 + profiles/plants/MA0021.1.pwm | 6 + profiles/plants/MA0034.1.pwm | 10 + profiles/plants/MA0053.1.pwm | 10 +- profiles/plants/MA0054.1.pwm | 9 + profiles/plants/MA0064.1.pwm | 5 + profiles/plants/MA0082.1.pwm | 14 ++ profiles/plants/MA0096.1.pwm | 7 + profiles/plants/MA0097.1.pwm | 24 +-- profiles/plants/MA0110.1.pwm | 9 + profiles/plants/MA0110.2.pwm | 13 ++ profiles/plants/MA0110.3.pwm | 12 ++ profiles/plants/MA0121.1.pwm | 16 +- profiles/plants/MA0123.1.pwm | 20 +- profiles/plants/MA0127.1.pwm | 20 +- profiles/plants/MA0128.1.pwm | 16 +- profiles/plants/MA0129.1.pwm | 14 +- profiles/plants/MA0548.1.pwm | 15 ++ profiles/plants/MA0548.2.pwm | 38 ++-- profiles/plants/MA0549.1.pwm | 22 +- profiles/plants/MA0550.1.pwm | 28 +-- profiles/plants/MA0550.2.pwm | 40 ++-- profiles/plants/MA0551.1.pwm | 16 ++ profiles/plants/MA0552.1.pwm | 28 +-- profiles/plants/MA0553.1.pwm | 16 +- profiles/plants/MA0554.1.pwm | 15 ++ profiles/plants/MA0555.1.pwm | 20 ++ profiles/plants/MA0556.1.pwm | 30 +-- profiles/plants/MA0557.1.pwm | 12 ++ profiles/plants/MA0558.1.pwm | 21 ++ profiles/plants/MA0559.1.pwm | 14 ++ profiles/plants/MA0560.1.pwm | 20 +- profiles/plants/MA0561.1.pwm | 16 +- profiles/plants/MA0562.1.pwm | 16 +- profiles/plants/MA0563.1.pwm | 11 + profiles/plants/MA0564.1.pwm | 9 + profiles/plants/MA0565.1.pwm | 18 +- profiles/plants/MA0565.2.pwm | 20 +- profiles/plants/MA0566.1.pwm | 16 +- profiles/plants/MA0567.1.pwm | 8 + profiles/plants/MA0568.1.pwm | 16 +- profiles/plants/MA0569.1.pwm | 8 + profiles/plants/MA0570.1.pwm | 19 ++ profiles/plants/MA0570.2.pwm | 24 +-- profiles/plants/MA0571.1.pwm | 42 ++-- profiles/plants/MA0573.1.pwm | 38 ++-- profiles/plants/MA0574.1.pwm | 26 +-- profiles/plants/MA0575.1.pwm | 13 ++ profiles/plants/MA0576.1.pwm | 13 ++ profiles/plants/MA0577.1.pwm | 16 ++ profiles/plants/MA0577.2.pwm | 16 +- profiles/plants/MA0578.1.pwm | 16 ++ profiles/plants/MA0579.1.pwm | 22 +- profiles/plants/MA0580.1.pwm | 14 ++ profiles/plants/MA0581.1.pwm | 11 + profiles/plants/MA0582.1.pwm | 24 +-- profiles/plants/MA0583.1.pwm | 24 +-- profiles/plants/MA0584.1.pwm | 18 ++ profiles/plants/MA0585.1.pwm | 18 ++ profiles/plants/MA0586.1.pwm | 19 ++ profiles/plants/MA0586.2.pwm | 22 +- profiles/plants/MA0587.1.pwm | 10 + profiles/plants/MA0588.1.pwm | 22 +- profiles/plants/MA0589.1.pwm | 11 + profiles/plants/MA0590.1.pwm | 19 ++ profiles/plants/MA0930.1.pwm | 16 +- profiles/plants/MA0931.1.pwm | 10 + profiles/plants/MA0932.1.pwm | 8 + profiles/plants/MA0933.1.pwm | 8 + profiles/plants/MA0934.1.pwm | 16 +- profiles/plants/MA0935.1.pwm | 16 +- profiles/plants/MA0936.1.pwm | 16 +- profiles/plants/MA0937.1.pwm | 16 +- profiles/plants/MA0938.1.pwm | 8 + profiles/plants/MA0939.1.pwm | 8 + profiles/plants/MA0940.1.pwm | 26 +-- profiles/plants/MA0941.1.pwm | 26 +-- profiles/plants/MA0942.1.pwm | 8 + profiles/plants/MA0943.1.pwm | 16 +- profiles/plants/MA0944.1.pwm | 9 + profiles/plants/MA0945.1.pwm | 10 + profiles/plants/MA0946.1.pwm | 16 +- profiles/plants/MA0947.1.pwm | 16 +- profiles/plants/MA0948.1.pwm | 13 ++ profiles/plants/MA0949.1.pwm | 20 +- profiles/plants/MA0950.1.pwm | 16 +- profiles/plants/MA0951.1.pwm | 8 + profiles/plants/MA0952.1.pwm | 8 + profiles/plants/MA0953.1.pwm | 9 + profiles/plants/MA0954.1.pwm | 10 + profiles/plants/MA0954.2.pwm | 13 ++ profiles/plants/MA0955.1.pwm | 14 +- profiles/plants/MA0956.1.pwm | 20 +- profiles/plants/MA0957.1.pwm | 8 + profiles/plants/MA0958.1.pwm | 16 +- profiles/plants/MA0959.1.pwm | 16 +- profiles/plants/MA0960.1.pwm | 10 + profiles/plants/MA0961.1.pwm | 18 +- profiles/plants/MA0962.1.pwm | 8 + profiles/plants/MA0963.1.pwm | 16 +- profiles/plants/MA0964.1.pwm | 10 + profiles/plants/MA0965.1.pwm | 10 + profiles/plants/MA0966.1.pwm | 20 +- profiles/plants/MA0967.1.pwm | 16 +- profiles/plants/MA0968.1.pwm | 18 +- profiles/plants/MA0968.2.pwm | 15 ++ profiles/plants/MA0969.1.pwm | 18 +- profiles/plants/MA0970.1.pwm | 9 + profiles/plants/MA0971.1.pwm | 10 + profiles/plants/MA0972.1.pwm | 16 +- profiles/plants/MA0973.1.pwm | 20 +- profiles/plants/MA0974.1.pwm | 9 + profiles/plants/MA0974.2.pwm | 12 ++ profiles/plants/MA0975.1.pwm | 8 + profiles/plants/MA0976.1.pwm | 16 +- profiles/plants/MA0976.2.pwm | 24 +-- profiles/plants/MA0977.1.pwm | 16 +- profiles/plants/MA0978.1.pwm | 8 + profiles/plants/MA0979.1.pwm | 16 +- profiles/plants/MA0980.1.pwm | 16 +- profiles/plants/MA0980.2.pwm | 12 ++ profiles/plants/MA0981.1.pwm | 10 + profiles/plants/MA0982.1.pwm | 14 +- profiles/plants/MA0983.1.pwm | 8 + profiles/plants/MA0984.1.pwm | 8 + profiles/plants/MA0986.1.pwm | 16 +- profiles/plants/MA0987.1.pwm | 10 + profiles/plants/MA0988.1.pwm | 20 +- profiles/plants/MA0989.1.pwm | 18 +- profiles/plants/MA0990.1.pwm | 20 +- profiles/plants/MA0992.1.pwm | 16 +- profiles/plants/MA0992.2.pwm | 12 ++ profiles/plants/MA0993.1.pwm | 10 + profiles/plants/MA0994.1.pwm | 20 +- profiles/plants/MA0995.1.pwm | 10 + profiles/plants/MA0995.2.pwm | 11 + profiles/plants/MA0997.1.pwm | 18 +- profiles/plants/MA0998.1.pwm | 10 + profiles/plants/MA1000.1.pwm | 16 +- profiles/plants/MA1000.2.pwm | 30 +-- profiles/plants/MA1001.1.pwm | 10 + profiles/plants/MA1001.2.pwm | 24 +-- profiles/plants/MA1004.1.pwm | 8 + profiles/plants/MA1005.1.pwm | 8 + profiles/plants/MA1005.2.pwm | 11 + profiles/plants/MA1006.1.pwm | 10 + profiles/plants/MA1007.1.pwm | 8 + profiles/plants/MA1008.1.pwm | 20 +- profiles/plants/MA1009.1.pwm | 16 +- profiles/plants/MA1010.1.pwm | 26 +-- profiles/plants/MA1011.1.pwm | 20 +- profiles/plants/MA1012.1.pwm | 28 +-- profiles/plants/MA1013.1.pwm | 8 + profiles/plants/MA1014.1.pwm | 8 + profiles/plants/MA1015.1.pwm | 16 +- profiles/plants/MA1016.1.pwm | 18 +- profiles/plants/MA1017.1.pwm | 9 + profiles/plants/MA1018.1.pwm | 11 + profiles/plants/MA1019.1.pwm | 9 + profiles/plants/MA1020.1.pwm | 8 + profiles/plants/MA1021.1.pwm | 8 + profiles/plants/MA1022.1.pwm | 10 + profiles/plants/MA1023.1.pwm | 16 +- profiles/plants/MA1024.1.pwm | 10 + profiles/plants/MA1025.1.pwm | 24 +-- profiles/plants/MA1026.1.pwm | 8 + profiles/plants/MA1026.2.pwm | 30 +-- profiles/plants/MA1027.1.pwm | 16 +- profiles/plants/MA1028.1.pwm | 16 +- profiles/plants/MA1030.1.pwm | 10 + profiles/plants/MA1031.1.pwm | 20 +- profiles/plants/MA1032.1.pwm | 20 +- profiles/plants/MA1033.1.pwm | 8 + profiles/plants/MA1034.1.pwm | 8 + profiles/plants/MA1035.1.pwm | 8 + profiles/plants/MA1036.1.pwm | 16 +- profiles/plants/MA1037.1.pwm | 9 + profiles/plants/MA1038.1.pwm | 11 + profiles/plants/MA1039.1.pwm | 16 +- profiles/plants/MA1040.1.pwm | 16 +- profiles/plants/MA1041.1.pwm | 8 + profiles/plants/MA1042.1.pwm | 8 + profiles/plants/MA1043.1.pwm | 20 +- profiles/plants/MA1044.1.pwm | 12 ++ profiles/plants/MA1045.1.pwm | 10 + profiles/plants/MA1046.1.pwm | 9 + profiles/plants/MA1047.1.pwm | 16 +- profiles/plants/MA1047.2.pwm | 30 +-- profiles/plants/MA1048.1.pwm | 8 + profiles/plants/MA1049.1.pwm | 16 +- profiles/plants/MA1050.1.pwm | 8 + profiles/plants/MA1051.1.pwm | 16 +- profiles/plants/MA1053.1.pwm | 16 +- profiles/plants/MA1054.1.pwm | 10 + profiles/plants/MA1055.1.pwm | 16 +- profiles/plants/MA1056.1.pwm | 12 ++ profiles/plants/MA1057.1.pwm | 8 + profiles/plants/MA1058.1.pwm | 9 + profiles/plants/MA1059.1.pwm | 18 +- profiles/plants/MA1059.2.pwm | 12 ++ profiles/plants/MA1060.1.pwm | 16 +- profiles/plants/MA1061.1.pwm | 18 +- profiles/plants/MA1062.1.pwm | 8 + profiles/plants/MA1062.2.pwm | 19 ++ profiles/plants/MA1063.1.pwm | 20 +- profiles/plants/MA1064.1.pwm | 20 +- profiles/plants/MA1065.1.pwm | 10 + profiles/plants/MA1065.2.pwm | 19 ++ profiles/plants/MA1066.1.pwm | 8 + profiles/plants/MA1067.1.pwm | 16 +- profiles/plants/MA1068.1.pwm | 8 + profiles/plants/MA1069.1.pwm | 10 + profiles/plants/MA1070.1.pwm | 20 +- profiles/plants/MA1071.1.pwm | 14 +- profiles/plants/MA1074.1.pwm | 8 + profiles/plants/MA1075.1.pwm | 8 + profiles/plants/MA1076.1.pwm | 10 + profiles/plants/MA1076.2.pwm | 16 ++ profiles/plants/MA1077.1.pwm | 10 + profiles/plants/MA1078.1.pwm | 16 +- profiles/plants/MA1079.1.pwm | 10 + profiles/plants/MA1080.1.pwm | 16 +- profiles/plants/MA1081.1.pwm | 8 + profiles/plants/MA1083.1.pwm | 20 +- profiles/plants/MA1084.1.pwm | 8 + profiles/plants/MA1085.1.pwm | 8 + profiles/plants/MA1085.2.pwm | 10 + profiles/plants/MA1086.1.pwm | 10 + profiles/plants/MA1087.1.pwm | 8 + profiles/plants/MA1088.1.pwm | 20 +- profiles/plants/MA1089.1.pwm | 20 +- profiles/plants/MA1090.1.pwm | 11 + profiles/plants/MA1091.1.pwm | 8 + profiles/plants/MA1092.1.pwm | 8 + profiles/plants/MA1093.1.pwm | 8 + profiles/plants/MA1094.1.pwm | 18 +- profiles/plants/MA1095.1.pwm | 16 +- profiles/plants/MA1096.1.pwm | 8 + profiles/plants/MA1097.1.pwm | 8 + profiles/plants/MA1098.1.pwm | 8 + profiles/plants/MA1156.1.pwm | 20 ++ profiles/plants/MA1157.1.pwm | 40 ++-- profiles/plants/MA1158.1.pwm | 20 ++ profiles/plants/MA1159.1.pwm | 15 ++ profiles/plants/MA1160.1.pwm | 20 ++ profiles/plants/MA1161.1.pwm | 15 ++ profiles/plants/MA1162.1.pwm | 15 ++ profiles/plants/MA1163.1.pwm | 14 ++ profiles/plants/MA1164.1.pwm | 11 + profiles/plants/MA1165.1.pwm | 11 + profiles/plants/MA1166.1.pwm | 28 +-- profiles/plants/MA1167.1.pwm | 22 +- profiles/plants/MA1168.1.pwm | 14 ++ profiles/plants/MA1169.1.pwm | 26 +-- profiles/plants/MA1170.1.pwm | 17 ++ profiles/plants/MA1171.1.pwm | 22 +- profiles/plants/MA1172.1.pwm | 30 +-- profiles/plants/MA1173.1.pwm | 15 ++ profiles/plants/MA1174.1.pwm | 30 +-- profiles/plants/MA1175.1.pwm | 11 + profiles/plants/MA1176.1.pwm | 22 +- profiles/plants/MA1177.1.pwm | 13 ++ profiles/plants/MA1178.1.pwm | 30 +-- profiles/plants/MA1179.1.pwm | 19 ++ profiles/plants/MA1180.1.pwm | 15 ++ profiles/plants/MA1181.1.pwm | 11 + profiles/plants/MA1182.1.pwm | 12 ++ profiles/plants/MA1183.1.pwm | 11 + profiles/plants/MA1184.1.pwm | 14 ++ profiles/plants/MA1185.1.pwm | 20 +- profiles/plants/MA1186.1.pwm | 30 +-- profiles/plants/MA1187.1.pwm | 10 + profiles/plants/MA1188.1.pwm | 14 ++ profiles/plants/MA1189.1.pwm | 15 ++ profiles/plants/MA1190.1.pwm | 11 + profiles/plants/MA1191.1.pwm | 30 +-- profiles/plants/MA1192.1.pwm | 30 +-- profiles/plants/MA1193.1.pwm | 42 ++-- profiles/plants/MA1194.1.pwm | 30 +-- profiles/plants/MA1195.1.pwm | 30 +-- profiles/plants/MA1196.1.pwm | 30 +-- profiles/plants/MA1197.1.pwm | 24 +-- profiles/plants/MA1198.1.pwm | 22 +- profiles/plants/MA1199.1.pwm | 15 ++ profiles/plants/MA1200.1.pwm | 18 ++ profiles/plants/MA1201.1.pwm | 14 +- profiles/plants/MA1202.1.pwm | 12 +- profiles/plants/MA1203.1.pwm | 30 +-- profiles/plants/MA1204.1.pwm | 36 ++-- profiles/plants/MA1205.1.pwm | 19 ++ profiles/plants/MA1206.1.pwm | 20 +- profiles/plants/MA1207.1.pwm | 34 +-- profiles/plants/MA1208.1.pwm | 28 +-- profiles/plants/MA1209.1.pwm | 11 + profiles/plants/MA1210.1.pwm | 20 +- profiles/plants/MA1211.1.pwm | 11 + profiles/plants/MA1212.1.pwm | 11 + profiles/plants/MA1213.1.pwm | 28 +-- profiles/plants/MA1214.1.pwm | 42 ++-- profiles/plants/MA1215.1.pwm | 11 + profiles/plants/MA1218.1.pwm | 26 +-- profiles/plants/MA1219.1.pwm | 15 ++ profiles/plants/MA1220.1.pwm | 30 +-- profiles/plants/MA1221.1.pwm | 30 +-- profiles/plants/MA1222.1.pwm | 30 +-- profiles/plants/MA1223.1.pwm | 28 +-- profiles/plants/MA1225.1.pwm | 30 +-- profiles/plants/MA1226.1.pwm | 30 +-- profiles/plants/MA1227.1.pwm | 42 ++-- profiles/plants/MA1227.2.pwm | 15 ++ profiles/plants/MA1228.1.pwm | 17 ++ profiles/plants/MA1229.1.pwm | 15 ++ profiles/plants/MA1230.1.pwm | 14 ++ profiles/plants/MA1231.1.pwm | 15 ++ profiles/plants/MA1232.1.pwm | 40 ++-- profiles/plants/MA1233.1.pwm | 40 ++-- profiles/plants/MA1233.2.pwm | 30 +-- profiles/plants/MA1234.1.pwm | 28 +-- profiles/plants/MA1235.1.pwm | 22 +- profiles/plants/MA1236.1.pwm | 19 ++ profiles/plants/MA1238.1.pwm | 15 ++ profiles/plants/MA1238.2.pwm | 26 +-- profiles/plants/MA1239.1.pwm | 19 ++ profiles/plants/MA1240.1.pwm | 42 ++-- profiles/plants/MA1241.1.pwm | 32 +-- profiles/plants/MA1242.1.pwm | 11 + profiles/plants/MA1243.1.pwm | 34 +-- profiles/plants/MA1244.1.pwm | 19 ++ profiles/plants/MA1245.1.pwm | 30 +-- profiles/plants/MA1245.2.pwm | 11 + profiles/plants/MA1246.1.pwm | 42 ++-- profiles/plants/MA1247.1.pwm | 30 +-- profiles/plants/MA1248.1.pwm | 40 ++-- profiles/plants/MA1250.1.pwm | 30 +-- profiles/plants/MA1251.1.pwm | 38 ++-- profiles/plants/MA1252.1.pwm | 30 +-- profiles/plants/MA1253.1.pwm | 28 +-- profiles/plants/MA1256.1.pwm | 21 ++ profiles/plants/MA1257.1.pwm | 42 ++-- profiles/plants/MA1258.1.pwm | 42 ++-- profiles/plants/MA1259.1.pwm | 15 ++ profiles/plants/MA1260.1.pwm | 42 ++-- profiles/plants/MA1261.1.pwm | 30 +-- profiles/plants/MA1262.1.pwm | 42 ++-- profiles/plants/MA1263.1.pwm | 14 ++ profiles/plants/MA1264.1.pwm | 30 +-- profiles/plants/MA1265.1.pwm | 20 ++ profiles/plants/MA1265.2.pwm | 24 +-- profiles/plants/MA1266.1.pwm | 30 +-- profiles/plants/MA1267.1.pwm | 58 +++--- profiles/plants/MA1268.1.pwm | 27 +++ profiles/plants/MA1269.1.pwm | 28 +-- profiles/plants/MA1270.1.pwm | 19 ++ profiles/plants/MA1272.1.pwm | 21 ++ profiles/plants/MA1273.1.pwm | 38 ++-- profiles/plants/MA1274.1.pwm | 42 ++-- profiles/plants/MA1275.1.pwm | 11 + profiles/plants/MA1276.1.pwm | 22 +- profiles/plants/MA1277.1.pwm | 42 ++-- profiles/plants/MA1278.1.pwm | 42 ++-- profiles/plants/MA1279.1.pwm | 42 ++-- profiles/plants/MA1280.1.pwm | 28 +-- profiles/plants/MA1281.1.pwm | 21 ++ profiles/plants/MA1282.1.pwm | 26 +-- profiles/plants/MA1283.1.pwm | 20 ++ profiles/plants/MA1284.1.pwm | 60 +++--- profiles/plants/MA1285.1.pwm | 21 ++ profiles/plants/MA1286.1.pwm | 12 ++ profiles/plants/MA1287.1.pwm | 14 ++ profiles/plants/MA1288.1.pwm | 13 ++ profiles/plants/MA1289.1.pwm | 13 ++ profiles/plants/MA1290.1.pwm | 22 +- profiles/plants/MA1291.1.pwm | 11 + profiles/plants/MA1292.1.pwm | 30 +-- profiles/plants/MA1293.1.pwm | 14 ++ profiles/plants/MA1294.1.pwm | 30 +-- profiles/plants/MA1295.1.pwm | 13 ++ profiles/plants/MA1296.1.pwm | 11 + profiles/plants/MA1297.1.pwm | 13 ++ profiles/plants/MA1298.1.pwm | 11 + profiles/plants/MA1299.1.pwm | 14 ++ profiles/plants/MA1300.1.pwm | 38 ++-- profiles/plants/MA1301.1.pwm | 22 +- profiles/plants/MA1302.1.pwm | 22 +- profiles/plants/MA1303.1.pwm | 13 ++ profiles/plants/MA1304.1.pwm | 24 +-- profiles/plants/MA1305.1.pwm | 12 ++ profiles/plants/MA1306.1.pwm | 14 ++ profiles/plants/MA1307.1.pwm | 19 ++ profiles/plants/MA1308.1.pwm | 13 ++ profiles/plants/MA1309.1.pwm | 11 + profiles/plants/MA1310.1.pwm | 21 ++ profiles/plants/MA1311.1.pwm | 13 ++ profiles/plants/MA1311.2.pwm | 11 + profiles/plants/MA1312.1.pwm | 14 ++ profiles/plants/MA1313.1.pwm | 28 +-- profiles/plants/MA1314.1.pwm | 26 +-- profiles/plants/MA1315.1.pwm | 14 ++ profiles/plants/MA1316.1.pwm | 22 +- profiles/plants/MA1317.1.pwm | 26 +-- profiles/plants/MA1318.1.pwm | 26 +-- profiles/plants/MA1320.1.pwm | 14 ++ profiles/plants/MA1321.1.pwm | 11 + profiles/plants/MA1322.1.pwm | 11 + profiles/plants/MA1323.1.pwm | 22 +- profiles/plants/MA1324.1.pwm | 8 + profiles/plants/MA1325.1.pwm | 15 ++ profiles/plants/MA1326.1.pwm | 22 +- profiles/plants/MA1327.1.pwm | 44 ++-- profiles/plants/MA1327.2.pwm | 20 +- profiles/plants/MA1328.1.pwm | 30 +-- profiles/plants/MA1329.1.pwm | 15 ++ profiles/plants/MA1329.2.pwm | 26 +-- profiles/plants/MA1330.1.pwm | 15 ++ profiles/plants/MA1331.1.pwm | 11 + profiles/plants/MA1332.1.pwm | 22 +- profiles/plants/MA1333.1.pwm | 22 +- profiles/plants/MA1334.1.pwm | 30 +-- profiles/plants/MA1335.1.pwm | 22 +- profiles/plants/MA1336.1.pwm | 28 +-- profiles/plants/MA1337.1.pwm | 15 ++ profiles/plants/MA1338.1.pwm | 15 ++ profiles/plants/MA1339.1.pwm | 24 +-- profiles/plants/MA1340.1.pwm | 15 ++ profiles/plants/MA1341.1.pwm | 15 ++ profiles/plants/MA1343.1.pwm | 14 ++ profiles/plants/MA1344.1.pwm | 30 +-- profiles/plants/MA1345.1.pwm | 28 +-- profiles/plants/MA1346.1.pwm | 15 ++ profiles/plants/MA1348.1.pwm | 22 +- profiles/plants/MA1349.1.pwm | 15 ++ profiles/plants/MA1350.1.pwm | 12 ++ profiles/plants/MA1351.1.pwm | 30 +-- profiles/plants/MA1352.1.pwm | 21 ++ profiles/plants/MA1353.1.pwm | 15 ++ profiles/plants/MA1354.1.pwm | 29 +++ profiles/plants/MA1355.1.pwm | 30 +-- profiles/plants/MA1356.1.pwm | 21 ++ profiles/plants/MA1357.1.pwm | 11 + profiles/plants/MA1358.1.pwm | 22 +- profiles/plants/MA1359.1.pwm | 42 ++-- profiles/plants/MA1360.1.pwm | 42 ++-- profiles/plants/MA1361.1.pwm | 34 +-- profiles/plants/MA1362.1.pwm | 30 +-- profiles/plants/MA1363.1.pwm | 30 +-- profiles/plants/MA1364.1.pwm | 15 ++ profiles/plants/MA1365.1.pwm | 30 +-- profiles/plants/MA1365.2.pwm | 11 + profiles/plants/MA1366.1.pwm | 32 +-- profiles/plants/MA1367.1.pwm | 28 +-- profiles/plants/MA1368.1.pwm | 42 ++-- profiles/plants/MA1368.2.pwm | 28 +-- profiles/plants/MA1369.1.pwm | 22 +- profiles/plants/MA1370.1.pwm | 32 +-- profiles/plants/MA1371.1.pwm | 17 ++ profiles/plants/MA1372.1.pwm | 22 +- profiles/plants/MA1373.1.pwm | 15 ++ profiles/plants/MA1374.1.pwm | 36 ++-- profiles/plants/MA1375.1.pwm | 11 + profiles/plants/MA1376.1.pwm | 34 +-- profiles/plants/MA1377.1.pwm | 19 ++ profiles/plants/MA1378.1.pwm | 30 +-- profiles/plants/MA1379.1.pwm | 30 +-- profiles/plants/MA1380.1.pwm | 30 +-- profiles/plants/MA1381.1.pwm | 30 +-- profiles/plants/MA1382.1.pwm | 15 ++ profiles/plants/MA1383.1.pwm | 15 ++ profiles/plants/MA1384.1.pwm | 26 +-- profiles/plants/MA1385.1.pwm | 15 ++ profiles/plants/MA1386.1.pwm | 22 +- profiles/plants/MA1387.1.pwm | 15 ++ profiles/plants/MA1388.1.pwm | 8 + profiles/plants/MA1389.1.pwm | 15 ++ profiles/plants/MA1390.1.pwm | 13 ++ profiles/plants/MA1391.1.pwm | 11 + profiles/plants/MA1391.2.pwm | 13 ++ profiles/plants/MA1392.1.pwm | 30 +-- profiles/plants/MA1393.1.pwm | 14 ++ profiles/plants/MA1393.2.pwm | 11 + profiles/plants/MA1394.1.pwm | 22 +- profiles/plants/MA1394.2.pwm | 12 ++ profiles/plants/MA1396.1.pwm | 13 ++ profiles/plants/MA1397.1.pwm | 11 + profiles/plants/MA1398.1.pwm | 30 +-- profiles/plants/MA1398.2.pwm | 11 + profiles/plants/MA1400.1.pwm | 28 +-- profiles/plants/MA1401.1.pwm | 12 ++ profiles/plants/MA1402.1.pwm | 21 ++ profiles/plants/MA1403.1.pwm | 30 +++ profiles/plants/MA1404.1.pwm | 48 ++--- profiles/plants/MA1405.1.pwm | 20 +- profiles/plants/MA1406.1.pwm | 10 + profiles/plants/MA1408.1.pwm | 20 +- profiles/plants/MA1409.1.pwm | 20 +- profiles/plants/MA1410.1.pwm | 20 +- profiles/plants/MA1411.1.pwm | 10 + profiles/plants/MA1412.1.pwm | 10 + profiles/plants/MA1414.1.pwm | 10 + profiles/plants/MA1415.1.pwm | 11 + profiles/plants/MA1416.1.pwm | 14 ++ profiles/plants/MA1417.1.pwm | 13 ++ profiles/plants/MA1424.1.pwm | 15 ++ profiles/plants/MA1425.1.pwm | 24 +-- profiles/plants/MA1426.1.pwm | 20 +- profiles/plants/MA1427.1.pwm | 9 + profiles/plants/MA1428.1.pwm | 9 + profiles/plants/MA1430.1.pwm | 10 + profiles/plants/MA1659.1.pwm | 24 +-- profiles/plants/MA1660.1.pwm | 48 ++--- profiles/plants/MA1661.1.pwm | 12 ++ profiles/plants/MA1662.1.pwm | 13 ++ profiles/plants/MA1663.1.pwm | 16 ++ profiles/plants/MA1664.1.pwm | 30 +-- profiles/plants/MA1665.1.pwm | 12 ++ profiles/plants/MA1666.1.pwm | 14 ++ profiles/plants/MA1667.1.pwm | 11 + profiles/plants/MA1669.1.pwm | 28 +-- profiles/plants/MA1670.1.pwm | 15 ++ profiles/plants/MA1671.1.pwm | 22 +- profiles/plants/MA1672.1.pwm | 26 +-- profiles/plants/MA1673.1.pwm | 24 +-- profiles/plants/MA1674.1.pwm | 24 +++ profiles/plants/MA1675.1.pwm | 26 +-- profiles/plants/MA1676.1.pwm | 24 +++ profiles/plants/MA1677.1.pwm | 12 ++ profiles/plants/MA1678.1.pwm | 48 ++--- profiles/plants/MA1679.1.pwm | 15 ++ profiles/plants/MA1681.1.pwm | 28 +-- profiles/plants/MA1682.1.pwm | 28 +-- profiles/plants/MA1685.1.pwm | 30 +-- profiles/plants/MA1686.1.pwm | 28 +-- profiles/plants/MA1687.1.pwm | 32 +-- profiles/plants/MA1688.1.pwm | 28 +-- profiles/plants/MA1689.1.pwm | 26 +-- profiles/plants/MA1690.1.pwm | 15 ++ profiles/plants/MA1691.1.pwm | 26 +-- profiles/plants/MA1692.1.pwm | 15 ++ profiles/plants/MA1693.1.pwm | 26 +-- profiles/plants/MA1694.1.pwm | 28 +-- profiles/plants/MA1695.1.pwm | 28 +-- profiles/plants/MA1696.1.pwm | 12 ++ profiles/plants/MA1697.1.pwm | 12 ++ profiles/plants/MA1698.1.pwm | 28 +-- profiles/plants/MA1706.1.pwm | 10 + profiles/plants/MA1732.1.pwm | 30 +-- profiles/plants/MA1733.1.pwm | 28 +-- profiles/plants/MA1734.1.pwm | 16 ++ profiles/plants/MA1735.1.pwm | 11 + profiles/plants/MA1736.1.pwm | 22 +- profiles/plants/MA1737.1.pwm | 22 +- profiles/plants/MA1738.1.pwm | 30 +-- profiles/plants/MA1739.1.pwm | 28 +-- profiles/plants/MA1740.1.pwm | 10 + profiles/plants/MA1741.1.pwm | 16 ++ profiles/plants/MA1742.1.pwm | 22 +- profiles/plants/MA1743.1.pwm | 30 +-- profiles/plants/MA1744.1.pwm | 10 + profiles/plants/MA1745.1.pwm | 12 ++ profiles/plants/MA1746.1.pwm | 22 +- profiles/plants/MA1747.1.pwm | 14 ++ profiles/plants/MA1748.1.pwm | 18 +- profiles/plants/MA1749.1.pwm | 30 +-- profiles/plants/MA1750.1.pwm | 15 ++ profiles/plants/MA1751.1.pwm | 22 +- profiles/plants/MA1752.1.pwm | 30 +-- profiles/plants/MA1753.1.pwm | 30 +-- profiles/plants/MA1754.1.pwm | 21 ++ profiles/plants/MA1755.1.pwm | 20 +- profiles/plants/MA1756.1.pwm | 15 ++ profiles/plants/MA1757.1.pwm | 11 + profiles/plants/MA1758.1.pwm | 15 ++ profiles/plants/MA1759.1.pwm | 19 ++ profiles/plants/MA1760.1.pwm | 26 +-- profiles/plants/MA1761.1.pwm | 26 +-- profiles/plants/MA1762.1.pwm | 28 +-- profiles/plants/MA1763.1.pwm | 28 +-- profiles/plants/MA1764.1.pwm | 26 +-- profiles/plants/MA1765.1.pwm | 14 ++ profiles/plants/MA1766.1.pwm | 30 +-- profiles/plants/MA1767.1.pwm | 11 + profiles/plants/MA1768.1.pwm | 15 ++ profiles/plants/MA1769.1.pwm | 28 +-- profiles/plants/MA1770.1.pwm | 26 +-- profiles/plants/MA1771.1.pwm | 15 ++ profiles/plants/MA1772.1.pwm | 26 +-- profiles/plants/MA1773.1.pwm | 21 ++ profiles/plants/MA1774.1.pwm | 19 ++ profiles/plants/MA1775.1.pwm | 26 +-- profiles/plants/MA1776.1.pwm | 42 ++-- profiles/plants/MA1777.1.pwm | 28 +-- profiles/plants/MA1778.1.pwm | 30 +-- profiles/plants/MA1779.1.pwm | 11 + profiles/plants/MA1780.1.pwm | 10 + profiles/plants/MA1781.1.pwm | 38 ++-- profiles/plants/MA1782.1.pwm | 26 +-- profiles/plants/MA1783.1.pwm | 19 ++ profiles/plants/MA1784.1.pwm | 21 ++ profiles/plants/MA1785.1.pwm | 22 +- profiles/plants/MA1786.1.pwm | 10 + profiles/plants/MA1787.1.pwm | 15 ++ profiles/plants/MA1788.1.pwm | 38 ++-- profiles/plants/MA1789.1.pwm | 30 +-- profiles/plants/MA1790.1.pwm | 15 ++ profiles/plants/MA1791.1.pwm | 38 ++-- profiles/plants/MA1792.1.pwm | 32 +-- profiles/plants/MA1793.1.pwm | 20 +- profiles/plants/MA1794.1.pwm | 15 ++ profiles/plants/MA1795.1.pwm | 10 + profiles/plants/MA1796.1.pwm | 16 +- profiles/plants/MA1797.1.pwm | 16 +- profiles/plants/MA1798.1.pwm | 21 ++ profiles/plants/MA1799.1.pwm | 10 + profiles/plants/MA1800.1.pwm | 16 +- profiles/plants/MA1801.1.pwm | 11 + profiles/plants/MA1802.1.pwm | 10 + profiles/plants/MA1803.1.pwm | 28 +-- profiles/plants/MA1804.1.pwm | 10 + profiles/plants/MA1805.1.pwm | 18 +- profiles/plants/MA1806.1.pwm | 11 + profiles/plants/MA1807.1.pwm | 11 + profiles/plants/MA1808.1.pwm | 11 + profiles/plants/MA1809.1.pwm | 11 + profiles/plants/MA1810.1.pwm | 28 +-- profiles/plants/MA1811.1.pwm | 11 + profiles/plants/MA1812.1.pwm | 30 +-- profiles/plants/MA1813.1.pwm | 22 +- profiles/plants/MA1814.1.pwm | 30 +-- profiles/plants/MA1815.1.pwm | 13 ++ profiles/plants/MA1816.1.pwm | 24 +-- profiles/plants/MA1817.1.pwm | 26 +-- profiles/plants/MA1818.1.pwm | 20 +- profiles/plants/MA1819.1.pwm | 12 ++ profiles/plants/MA1820.1.pwm | 13 ++ profiles/plants/MA1821.1.pwm | 11 + profiles/plants/MA1822.1.pwm | 13 ++ profiles/plants/MA1823.1.pwm | 12 ++ profiles/plants/MA1824.1.pwm | 24 +-- profiles/plants/MA1825.1.pwm | 22 +- profiles/plants/MA1826.1.pwm | 28 +-- profiles/plants/MA1827.1.pwm | 11 + profiles/plants/MA1828.1.pwm | 12 ++ profiles/plants/MA1829.1.pwm | 26 +-- profiles/plants/MA1830.1.pwm | 46 ++--- profiles/plants/MA1831.1.pwm | 12 ++ profiles/plants/MA1832.1.pwm | 11 + profiles/plants/MA1833.1.pwm | 16 ++ profiles/plants/MA1834.1.pwm | 11 + profiles/plants/MA1835.1.pwm | 13 ++ profiles/urochordates/MA0118.1.pwm | 18 +- profiles/urochordates/MA1843.1.pwm | 20 ++ profiles/urochordates/MA1844.1.pwm | 40 ++-- profiles/urochordates/MA1845.1.pwm | 40 ++-- profiles/urochordates/MA1846.1.pwm | 22 ++ profiles/urochordates/MA1847.1.pwm | 40 ++-- profiles/urochordates/MA1848.1.pwm | 20 ++ profiles/urochordates/MA1849.1.pwm | 22 ++ profiles/urochordates/MA1850.1.pwm | 44 ++-- profiles/urochordates/MA1851.1.pwm | 44 ++-- profiles/urochordates/MA1852.1.pwm | 40 ++-- profiles/urochordates/MA1853.1.pwm | 20 ++ profiles/urochordates/MA1854.1.pwm | 20 ++ profiles/urochordates/MA1855.1.pwm | 40 ++-- profiles/urochordates/MA1856.1.pwm | 44 ++-- profiles/urochordates/MA1857.1.pwm | 20 ++ profiles/urochordates/MA1858.1.pwm | 40 ++-- profiles/urochordates/MA1859.1.pwm | 20 ++ profiles/urochordates/MA1860.1.pwm | 22 ++ profiles/urochordates/MA1861.1.pwm | 22 ++ profiles/urochordates/MA1862.1.pwm | 20 ++ profiles/urochordates/MA1863.1.pwm | 40 ++-- profiles/urochordates/MA1864.1.pwm | 40 ++-- profiles/urochordates/MA1865.1.pwm | 40 ++-- profiles/urochordates/MA1866.1.pwm | 20 ++ profiles/urochordates/MA1867.1.pwm | 20 ++ profiles/urochordates/MA1868.1.pwm | 20 ++ profiles/urochordates/MA1869.1.pwm | 40 ++-- profiles/urochordates/MA1870.1.pwm | 40 ++-- profiles/urochordates/MA1871.1.pwm | 40 ++-- profiles/urochordates/MA1872.1.pwm | 20 ++ profiles/urochordates/MA1873.1.pwm | 40 ++-- profiles/urochordates/MA1874.1.pwm | 20 ++ profiles/urochordates/MA1875.1.pwm | 40 ++-- profiles/urochordates/MA1876.1.pwm | 40 ++-- profiles/urochordates/MA1877.1.pwm | 22 ++ profiles/urochordates/MA1878.1.pwm | 44 ++-- profiles/urochordates/MA1879.1.pwm | 20 ++ profiles/urochordates/MA1880.1.pwm | 22 ++ profiles/urochordates/MA1881.1.pwm | 40 ++-- profiles/urochordates/MA1882.1.pwm | 20 ++ profiles/urochordates/MA1883.1.pwm | 20 ++ profiles/urochordates/MA1884.1.pwm | 20 ++ profiles/urochordates/MA1885.1.pwm | 40 ++-- profiles/urochordates/MA1886.1.pwm | 20 ++ profiles/urochordates/MA1887.1.pwm | 40 ++-- profiles/urochordates/MA1888.1.pwm | 44 ++-- profiles/urochordates/MA1889.1.pwm | 40 ++-- profiles/urochordates/MA1890.1.pwm | 44 ++-- profiles/urochordates/MA1891.1.pwm | 40 ++-- profiles/urochordates/MA1892.1.pwm | 20 ++ profiles/urochordates/MA1893.1.pwm | 40 ++-- profiles/urochordates/MA1894.1.pwm | 40 ++-- profiles/urochordates/MA1895.1.pwm | 20 ++ profiles/urochordates/MA1896.1.pwm | 40 ++-- profiles/urochordates/MA1897.1.pwm | 20 ++ profiles/urochordates/MA1898.1.pwm | 20 ++ profiles/urochordates/MA1899.1.pwm | 20 ++ profiles/urochordates/MA1900.1.pwm | 40 ++-- profiles/urochordates/MA1901.1.pwm | 20 ++ profiles/urochordates/MA1902.1.pwm | 44 ++-- profiles/urochordates/MA1903.1.pwm | 40 ++-- profiles/urochordates/MA1904.1.pwm | 40 ++-- profiles/urochordates/MA1905.1.pwm | 40 ++-- profiles/urochordates/MA1906.1.pwm | 40 ++-- profiles/urochordates/MA1907.1.pwm | 20 ++ profiles/urochordates/MA1908.1.pwm | 44 ++-- profiles/urochordates/MA1909.1.pwm | 20 ++ profiles/urochordates/MA1910.1.pwm | 20 ++ profiles/urochordates/MA1911.1.pwm | 20 ++ profiles/urochordates/MA1912.1.pwm | 20 ++ profiles/urochordates/MA1913.1.pwm | 40 ++-- profiles/urochordates/MA1914.1.pwm | 20 ++ profiles/urochordates/MA1915.1.pwm | 40 ++-- profiles/urochordates/MA1916.1.pwm | 20 ++ profiles/urochordates/MA1917.1.pwm | 20 ++ profiles/urochordates/MA1918.1.pwm | 20 ++ profiles/urochordates/MA1919.1.pwm | 44 ++-- profiles/urochordates/MA1920.1.pwm | 22 ++ profiles/urochordates/MA1921.1.pwm | 22 ++ profiles/urochordates/MA1922.1.pwm | 40 ++-- profiles/urochordates/MA1923.1.pwm | 20 ++ profiles/urochordates/MA1924.1.pwm | 20 ++ profiles/urochordates/MA1925.1.pwm | 40 ++-- profiles/urochordates/MA1926.1.pwm | 20 ++ profiles/urochordates/MA1927.1.pwm | 44 ++-- profiles/vertebrates/MA0002.1.pwm | 22 +- profiles/vertebrates/MA0002.2.pwm | 22 +- profiles/vertebrates/MA0003.1.pwm | 9 + profiles/vertebrates/MA0003.2.pwm | 30 +-- profiles/vertebrates/MA0003.3.pwm | 22 +- profiles/vertebrates/MA0003.4.pwm | 28 +-- profiles/vertebrates/MA0004.1.pwm | 6 + profiles/vertebrates/MA0006.1.pwm | 6 + profiles/vertebrates/MA0007.1.pwm | 44 ++-- profiles/vertebrates/MA0007.2.pwm | 30 +-- profiles/vertebrates/MA0007.3.pwm | 34 +-- profiles/vertebrates/MA0009.1.pwm | 22 +- profiles/vertebrates/MA0009.2.pwm | 32 +-- profiles/vertebrates/MA0014.1.pwm | 40 ++-- profiles/vertebrates/MA0014.2.pwm | 38 ++-- profiles/vertebrates/MA0014.3.pwm | 24 +-- profiles/vertebrates/MA0017.1.pwm | 14 ++ profiles/vertebrates/MA0017.2.pwm | 13 ++ profiles/vertebrates/MA0018.1.pwm | 24 +-- profiles/vertebrates/MA0018.2.pwm | 8 + profiles/vertebrates/MA0018.3.pwm | 12 ++ profiles/vertebrates/MA0018.4.pwm | 13 ++ profiles/vertebrates/MA0019.1.pwm | 24 +-- profiles/vertebrates/MA0024.1.pwm | 16 +- profiles/vertebrates/MA0024.2.pwm | 11 + profiles/vertebrates/MA0024.3.pwm | 24 +-- profiles/vertebrates/MA0025.1.pwm | 22 +- profiles/vertebrates/MA0025.2.pwm | 13 ++ profiles/vertebrates/MA0027.1.pwm | 22 +- profiles/vertebrates/MA0027.2.pwm | 8 + profiles/vertebrates/MA0028.1.pwm | 20 +- profiles/vertebrates/MA0028.2.pwm | 20 +- profiles/vertebrates/MA0029.1.pwm | 28 +-- profiles/vertebrates/MA0030.1.pwm | 28 +-- profiles/vertebrates/MA0031.1.pwm | 8 + profiles/vertebrates/MA0032.1.pwm | 16 +- profiles/vertebrates/MA0032.2.pwm | 11 + profiles/vertebrates/MA0033.1.pwm | 16 +- profiles/vertebrates/MA0033.2.pwm | 7 + profiles/vertebrates/MA0035.1.pwm | 12 +- profiles/vertebrates/MA0035.2.pwm | 22 +- profiles/vertebrates/MA0035.3.pwm | 11 + profiles/vertebrates/MA0035.4.pwm | 11 + profiles/vertebrates/MA0036.1.pwm | 10 +- profiles/vertebrates/MA0036.2.pwm | 14 ++ profiles/vertebrates/MA0036.3.pwm | 11 + profiles/vertebrates/MA0037.1.pwm | 6 + profiles/vertebrates/MA0037.2.pwm | 8 + profiles/vertebrates/MA0037.3.pwm | 8 + profiles/vertebrates/MA0037.4.pwm | 24 +-- profiles/vertebrates/MA0038.1.pwm | 10 + profiles/vertebrates/MA0038.2.pwm | 24 +-- profiles/vertebrates/MA0039.1.pwm | 20 +- profiles/vertebrates/MA0039.2.pwm | 20 +- profiles/vertebrates/MA0039.3.pwm | 11 + profiles/vertebrates/MA0039.4.pwm | 12 ++ profiles/vertebrates/MA0040.1.pwm | 11 + profiles/vertebrates/MA0041.1.pwm | 24 +-- profiles/vertebrates/MA0041.2.pwm | 32 +-- profiles/vertebrates/MA0042.1.pwm | 24 +-- profiles/vertebrates/MA0042.2.pwm | 14 +- profiles/vertebrates/MA0043.1.pwm | 24 +-- profiles/vertebrates/MA0043.2.pwm | 24 +-- profiles/vertebrates/MA0043.3.pwm | 14 ++ profiles/vertebrates/MA0046.1.pwm | 14 ++ profiles/vertebrates/MA0046.2.pwm | 15 ++ profiles/vertebrates/MA0047.1.pwm | 24 +-- profiles/vertebrates/MA0047.2.pwm | 12 ++ profiles/vertebrates/MA0047.3.pwm | 22 +- profiles/vertebrates/MA0048.1.pwm | 12 ++ profiles/vertebrates/MA0048.2.pwm | 10 + profiles/vertebrates/MA0050.1.pwm | 24 +-- profiles/vertebrates/MA0050.2.pwm | 42 ++-- profiles/vertebrates/MA0050.3.pwm | 15 ++ profiles/vertebrates/MA0051.1.pwm | 36 ++-- profiles/vertebrates/MA0052.1.pwm | 10 + profiles/vertebrates/MA0052.2.pwm | 30 +-- profiles/vertebrates/MA0052.3.pwm | 24 +-- profiles/vertebrates/MA0052.4.pwm | 15 ++ profiles/vertebrates/MA0056.1.pwm | 12 +- profiles/vertebrates/MA0056.2.pwm | 26 +-- profiles/vertebrates/MA0058.1.pwm | 20 +- profiles/vertebrates/MA0058.2.pwm | 10 + profiles/vertebrates/MA0058.3.pwm | 20 +- profiles/vertebrates/MA0059.1.pwm | 11 + profiles/vertebrates/MA0060.1.pwm | 32 +-- profiles/vertebrates/MA0060.2.pwm | 36 ++-- profiles/vertebrates/MA0060.3.pwm | 22 +- profiles/vertebrates/MA0062.1.pwm | 20 +- profiles/vertebrates/MA0062.2.pwm | 11 + profiles/vertebrates/MA0062.3.pwm | 14 ++ profiles/vertebrates/MA0063.1.pwm | 14 +- profiles/vertebrates/MA0063.2.pwm | 11 + profiles/vertebrates/MA0065.1.pwm | 20 ++ profiles/vertebrates/MA0065.2.pwm | 15 ++ profiles/vertebrates/MA0066.1.pwm | 20 ++ profiles/vertebrates/MA0067.1.pwm | 8 + profiles/vertebrates/MA0067.2.pwm | 34 +-- profiles/vertebrates/MA0068.1.pwm | 30 +++ profiles/vertebrates/MA0068.2.pwm | 8 + profiles/vertebrates/MA0069.1.pwm | 14 ++ profiles/vertebrates/MA0070.1.pwm | 24 +-- profiles/vertebrates/MA0071.1.pwm | 10 + profiles/vertebrates/MA0072.1.pwm | 14 ++ profiles/vertebrates/MA0073.1.pwm | 20 ++ profiles/vertebrates/MA0074.1.pwm | 15 ++ profiles/vertebrates/MA0075.1.pwm | 5 + profiles/vertebrates/MA0075.2.pwm | 8 + profiles/vertebrates/MA0075.3.pwm | 8 + profiles/vertebrates/MA0076.1.pwm | 18 +- profiles/vertebrates/MA0076.2.pwm | 22 +- profiles/vertebrates/MA0077.1.pwm | 18 +- profiles/vertebrates/MA0078.1.pwm | 9 + profiles/vertebrates/MA0078.2.pwm | 14 ++ profiles/vertebrates/MA0079.1.pwm | 10 + profiles/vertebrates/MA0079.2.pwm | 10 + profiles/vertebrates/MA0079.3.pwm | 11 + profiles/vertebrates/MA0079.4.pwm | 30 +-- profiles/vertebrates/MA0079.5.pwm | 9 + profiles/vertebrates/MA0080.1.pwm | 12 +- profiles/vertebrates/MA0080.2.pwm | 14 +- profiles/vertebrates/MA0080.3.pwm | 15 ++ profiles/vertebrates/MA0080.4.pwm | 14 ++ profiles/vertebrates/MA0080.5.pwm | 20 ++ profiles/vertebrates/MA0080.6.pwm | 34 +-- profiles/vertebrates/MA0081.1.pwm | 14 +- profiles/vertebrates/MA0081.2.pwm | 32 +-- profiles/vertebrates/MA0083.1.pwm | 12 ++ profiles/vertebrates/MA0083.2.pwm | 36 ++-- profiles/vertebrates/MA0083.3.pwm | 16 ++ profiles/vertebrates/MA0084.1.pwm | 18 +- profiles/vertebrates/MA0087.1.pwm | 14 +- profiles/vertebrates/MA0087.2.pwm | 13 ++ profiles/vertebrates/MA0088.1.pwm | 20 ++ profiles/vertebrates/MA0088.2.pwm | 16 ++ profiles/vertebrates/MA0089.1.pwm | 12 +- profiles/vertebrates/MA0089.2.pwm | 32 +-- profiles/vertebrates/MA0090.1.pwm | 24 +-- profiles/vertebrates/MA0090.2.pwm | 20 +- profiles/vertebrates/MA0090.3.pwm | 26 +-- profiles/vertebrates/MA0091.1.pwm | 24 +-- profiles/vertebrates/MA0092.1.pwm | 20 +- profiles/vertebrates/MA0093.1.pwm | 7 + profiles/vertebrates/MA0093.2.pwm | 22 +- profiles/vertebrates/MA0093.3.pwm | 28 +-- profiles/vertebrates/MA0095.1.pwm | 12 +- profiles/vertebrates/MA0095.2.pwm | 24 +-- profiles/vertebrates/MA0095.3.pwm | 24 +-- profiles/vertebrates/MA0098.1.pwm | 12 +- profiles/vertebrates/MA0098.2.pwm | 15 ++ profiles/vertebrates/MA0098.3.pwm | 20 +- profiles/vertebrates/MA0099.1.pwm | 16 +- profiles/vertebrates/MA0099.2.pwm | 14 +- profiles/vertebrates/MA0099.3.pwm | 20 +- profiles/vertebrates/MA0100.1.pwm | 8 + profiles/vertebrates/MA0100.2.pwm | 10 + profiles/vertebrates/MA0100.3.pwm | 10 + profiles/vertebrates/MA0101.1.pwm | 20 +- profiles/vertebrates/MA0102.1.pwm | 12 ++ profiles/vertebrates/MA0102.2.pwm | 9 + profiles/vertebrates/MA0102.3.pwm | 11 + profiles/vertebrates/MA0102.4.pwm | 28 +-- profiles/vertebrates/MA0103.1.pwm | 12 +- profiles/vertebrates/MA0103.2.pwm | 9 + profiles/vertebrates/MA0103.3.pwm | 11 + profiles/vertebrates/MA0104.1.pwm | 12 +- profiles/vertebrates/MA0104.2.pwm | 20 +- profiles/vertebrates/MA0104.3.pwm | 16 +- profiles/vertebrates/MA0104.4.pwm | 24 +-- profiles/vertebrates/MA0105.1.pwm | 10 + profiles/vertebrates/MA0105.2.pwm | 22 +- profiles/vertebrates/MA0105.3.pwm | 11 + profiles/vertebrates/MA0105.4.pwm | 13 ++ profiles/vertebrates/MA0106.1.pwm | 40 ++-- profiles/vertebrates/MA0106.2.pwm | 30 +-- profiles/vertebrates/MA0106.3.pwm | 36 ++-- profiles/vertebrates/MA0107.1.pwm | 20 +- profiles/vertebrates/MA0108.1.pwm | 30 +-- profiles/vertebrates/MA0108.2.pwm | 15 ++ profiles/vertebrates/MA0111.1.pwm | 11 + profiles/vertebrates/MA0112.1.pwm | 36 ++-- profiles/vertebrates/MA0112.2.pwm | 20 ++ profiles/vertebrates/MA0112.3.pwm | 17 ++ profiles/vertebrates/MA0113.1.pwm | 18 ++ profiles/vertebrates/MA0113.2.pwm | 15 ++ profiles/vertebrates/MA0113.3.pwm | 17 ++ profiles/vertebrates/MA0114.1.pwm | 13 ++ profiles/vertebrates/MA0114.2.pwm | 30 +-- profiles/vertebrates/MA0114.3.pwm | 16 ++ profiles/vertebrates/MA0114.4.pwm | 26 +-- profiles/vertebrates/MA0115.1.pwm | 34 +-- profiles/vertebrates/MA0116.1.pwm | 30 +-- profiles/vertebrates/MA0117.1.pwm | 8 + profiles/vertebrates/MA0117.2.pwm | 24 +-- profiles/vertebrates/MA0119.1.pwm | 28 +-- profiles/vertebrates/MA0122.1.pwm | 9 + profiles/vertebrates/MA0122.2.pwm | 18 +- profiles/vertebrates/MA0122.3.pwm | 26 +-- profiles/vertebrates/MA0124.1.pwm | 14 +- profiles/vertebrates/MA0124.2.pwm | 18 +- profiles/vertebrates/MA0125.1.pwm | 8 + profiles/vertebrates/MA0130.1.pwm | 12 +- profiles/vertebrates/MA0131.1.pwm | 20 +- profiles/vertebrates/MA0131.2.pwm | 12 ++ profiles/vertebrates/MA0132.1.pwm | 12 +- profiles/vertebrates/MA0132.2.pwm | 8 + profiles/vertebrates/MA0132.3.pwm | 16 +- profiles/vertebrates/MA0135.1.pwm | 13 ++ profiles/vertebrates/MA0136.1.pwm | 18 +- profiles/vertebrates/MA0136.2.pwm | 11 + profiles/vertebrates/MA0136.3.pwm | 24 +-- profiles/vertebrates/MA0137.1.pwm | 28 +-- profiles/vertebrates/MA0137.2.pwm | 30 +-- profiles/vertebrates/MA0137.3.pwm | 11 + profiles/vertebrates/MA0138.1.pwm | 38 ++-- profiles/vertebrates/MA0138.2.pwm | 21 ++ profiles/vertebrates/MA0139.1.pwm | 19 ++ profiles/vertebrates/MA0140.1.pwm | 36 ++-- profiles/vertebrates/MA0140.2.pwm | 36 ++-- profiles/vertebrates/MA0141.1.pwm | 24 +-- profiles/vertebrates/MA0141.2.pwm | 12 ++ profiles/vertebrates/MA0141.3.pwm | 22 +- profiles/vertebrates/MA0142.1.pwm | 30 +-- profiles/vertebrates/MA0143.1.pwm | 30 +-- profiles/vertebrates/MA0143.2.pwm | 15 ++ profiles/vertebrates/MA0143.3.pwm | 8 + profiles/vertebrates/MA0143.4.pwm | 11 + profiles/vertebrates/MA0144.1.pwm | 10 + profiles/vertebrates/MA0144.2.pwm | 11 + profiles/vertebrates/MA0145.1.pwm | 14 ++ profiles/vertebrates/MA0145.2.pwm | 14 ++ profiles/vertebrates/MA0146.1.pwm | 28 +-- profiles/vertebrates/MA0146.2.pwm | 14 ++ profiles/vertebrates/MA0147.1.pwm | 20 +- profiles/vertebrates/MA0147.2.pwm | 20 +- profiles/vertebrates/MA0147.3.pwm | 12 ++ profiles/vertebrates/MA0148.1.pwm | 22 +- profiles/vertebrates/MA0148.2.pwm | 22 +- profiles/vertebrates/MA0148.3.pwm | 30 +-- profiles/vertebrates/MA0148.4.pwm | 12 ++ profiles/vertebrates/MA0149.1.pwm | 18 ++ profiles/vertebrates/MA0150.1.pwm | 22 +- profiles/vertebrates/MA0150.2.pwm | 30 +-- profiles/vertebrates/MA0151.1.pwm | 6 + profiles/vertebrates/MA0152.1.pwm | 14 +- profiles/vertebrates/MA0152.2.pwm | 16 ++ profiles/vertebrates/MA0153.1.pwm | 24 +-- profiles/vertebrates/MA0153.2.pwm | 13 ++ profiles/vertebrates/MA0154.1.pwm | 20 +- profiles/vertebrates/MA0154.2.pwm | 11 + profiles/vertebrates/MA0154.3.pwm | 14 ++ profiles/vertebrates/MA0154.4.pwm | 30 +-- profiles/vertebrates/MA0155.1.pwm | 12 ++ profiles/vertebrates/MA0156.1.pwm | 16 +- profiles/vertebrates/MA0156.2.pwm | 10 + profiles/vertebrates/MA0156.3.pwm | 24 +-- profiles/vertebrates/MA0157.1.pwm | 8 + profiles/vertebrates/MA0157.2.pwm | 16 +- profiles/vertebrates/MA0157.3.pwm | 12 ++ profiles/vertebrates/MA0158.1.pwm | 8 + profiles/vertebrates/MA0158.2.pwm | 16 +- profiles/vertebrates/MA0159.1.pwm | 17 ++ profiles/vertebrates/MA0160.1.pwm | 16 +- profiles/vertebrates/MA0160.2.pwm | 10 + profiles/vertebrates/MA0161.1.pwm | 6 + profiles/vertebrates/MA0161.2.pwm | 11 + profiles/vertebrates/MA0162.1.pwm | 22 +- profiles/vertebrates/MA0162.2.pwm | 14 ++ profiles/vertebrates/MA0162.3.pwm | 28 +-- profiles/vertebrates/MA0162.4.pwm | 14 ++ profiles/vertebrates/MA0163.1.pwm | 28 +-- profiles/vertebrates/MA0164.1.pwm | 7 + profiles/vertebrates/MA0258.1.pwm | 36 ++-- profiles/vertebrates/MA0258.2.pwm | 30 +-- profiles/vertebrates/MA0259.1.pwm | 8 + profiles/vertebrates/MA0442.1.pwm | 6 + profiles/vertebrates/MA0442.2.pwm | 22 +- profiles/vertebrates/MA0461.1.pwm | 16 +- profiles/vertebrates/MA0461.2.pwm | 10 + profiles/vertebrates/MA0462.1.pwm | 11 + profiles/vertebrates/MA0462.2.pwm | 22 +- profiles/vertebrates/MA0463.1.pwm | 14 ++ profiles/vertebrates/MA0463.2.pwm | 16 ++ profiles/vertebrates/MA0464.1.pwm | 22 +- profiles/vertebrates/MA0464.2.pwm | 10 + profiles/vertebrates/MA0465.1.pwm | 11 + profiles/vertebrates/MA0465.2.pwm | 24 +-- profiles/vertebrates/MA0466.1.pwm | 11 + profiles/vertebrates/MA0466.2.pwm | 10 + profiles/vertebrates/MA0466.3.pwm | 12 ++ profiles/vertebrates/MA0467.1.pwm | 11 + profiles/vertebrates/MA0467.2.pwm | 20 +- profiles/vertebrates/MA0468.1.pwm | 11 + profiles/vertebrates/MA0469.1.pwm | 30 +-- profiles/vertebrates/MA0469.2.pwm | 36 ++-- profiles/vertebrates/MA0469.3.pwm | 16 ++ profiles/vertebrates/MA0470.1.pwm | 22 +- profiles/vertebrates/MA0470.2.pwm | 28 +-- profiles/vertebrates/MA0471.1.pwm | 11 + profiles/vertebrates/MA0471.2.pwm | 13 ++ profiles/vertebrates/MA0472.1.pwm | 30 +-- profiles/vertebrates/MA0472.2.pwm | 11 + profiles/vertebrates/MA0473.1.pwm | 13 ++ profiles/vertebrates/MA0473.2.pwm | 12 ++ profiles/vertebrates/MA0473.3.pwm | 28 +-- profiles/vertebrates/MA0474.1.pwm | 11 + profiles/vertebrates/MA0474.2.pwm | 10 + profiles/vertebrates/MA0474.3.pwm | 14 ++ profiles/vertebrates/MA0475.1.pwm | 11 + profiles/vertebrates/MA0475.2.pwm | 10 + profiles/vertebrates/MA0476.1.pwm | 22 +- profiles/vertebrates/MA0477.1.pwm | 22 +- profiles/vertebrates/MA0477.2.pwm | 13 ++ profiles/vertebrates/MA0478.1.pwm | 22 +- profiles/vertebrates/MA0479.1.pwm | 11 + profiles/vertebrates/MA0480.1.pwm | 11 + profiles/vertebrates/MA0480.2.pwm | 11 + profiles/vertebrates/MA0481.1.pwm | 30 +-- profiles/vertebrates/MA0481.2.pwm | 24 +-- profiles/vertebrates/MA0481.3.pwm | 22 +- profiles/vertebrates/MA0482.1.pwm | 22 +- profiles/vertebrates/MA0482.2.pwm | 24 +-- profiles/vertebrates/MA0483.1.pwm | 11 + profiles/vertebrates/MA0484.1.pwm | 15 ++ profiles/vertebrates/MA0484.2.pwm | 26 +-- profiles/vertebrates/MA0485.1.pwm | 13 ++ profiles/vertebrates/MA0485.2.pwm | 20 +- profiles/vertebrates/MA0486.1.pwm | 30 +-- profiles/vertebrates/MA0486.2.pwm | 13 ++ profiles/vertebrates/MA0488.1.pwm | 13 ++ profiles/vertebrates/MA0489.1.pwm | 28 +-- profiles/vertebrates/MA0489.2.pwm | 12 ++ profiles/vertebrates/MA0490.1.pwm | 22 +- profiles/vertebrates/MA0490.2.pwm | 13 ++ profiles/vertebrates/MA0491.1.pwm | 11 + profiles/vertebrates/MA0491.2.pwm | 13 ++ profiles/vertebrates/MA0492.1.pwm | 15 ++ profiles/vertebrates/MA0493.1.pwm | 22 +- profiles/vertebrates/MA0493.2.pwm | 18 +- profiles/vertebrates/MA0494.1.pwm | 38 ++-- profiles/vertebrates/MA0495.1.pwm | 18 ++ profiles/vertebrates/MA0495.2.pwm | 42 ++-- profiles/vertebrates/MA0495.3.pwm | 32 +-- profiles/vertebrates/MA0496.1.pwm | 30 +-- profiles/vertebrates/MA0496.2.pwm | 38 ++-- profiles/vertebrates/MA0496.3.pwm | 15 ++ profiles/vertebrates/MA0497.1.pwm | 30 +-- profiles/vertebrates/MA0498.1.pwm | 15 ++ profiles/vertebrates/MA0498.2.pwm | 7 + profiles/vertebrates/MA0499.1.pwm | 13 ++ profiles/vertebrates/MA0499.2.pwm | 13 ++ profiles/vertebrates/MA0500.1.pwm | 11 + profiles/vertebrates/MA0500.2.pwm | 12 ++ profiles/vertebrates/MA0501.1.pwm | 15 ++ profiles/vertebrates/MA0502.1.pwm | 30 +-- profiles/vertebrates/MA0502.2.pwm | 24 +-- profiles/vertebrates/MA0504.1.pwm | 30 +-- profiles/vertebrates/MA0505.1.pwm | 15 ++ profiles/vertebrates/MA0505.2.pwm | 13 ++ profiles/vertebrates/MA0506.1.pwm | 11 + profiles/vertebrates/MA0506.2.pwm | 15 ++ profiles/vertebrates/MA0507.1.pwm | 13 ++ profiles/vertebrates/MA0507.2.pwm | 14 ++ profiles/vertebrates/MA0508.1.pwm | 15 ++ profiles/vertebrates/MA0508.2.pwm | 10 + profiles/vertebrates/MA0508.3.pwm | 11 + profiles/vertebrates/MA0509.1.pwm | 28 +-- profiles/vertebrates/MA0509.2.pwm | 28 +-- profiles/vertebrates/MA0509.3.pwm | 32 +-- profiles/vertebrates/MA0510.1.pwm | 30 +-- profiles/vertebrates/MA0510.2.pwm | 32 +-- profiles/vertebrates/MA0511.1.pwm | 30 +-- profiles/vertebrates/MA0511.2.pwm | 9 + profiles/vertebrates/MA0512.1.pwm | 22 +- profiles/vertebrates/MA0512.2.pwm | 28 +-- profiles/vertebrates/MA0513.1.pwm | 26 +-- profiles/vertebrates/MA0514.1.pwm | 20 +- profiles/vertebrates/MA0514.2.pwm | 22 +- profiles/vertebrates/MA0515.1.pwm | 20 +- profiles/vertebrates/MA0516.1.pwm | 15 ++ profiles/vertebrates/MA0516.2.pwm | 17 ++ profiles/vertebrates/MA0516.3.pwm | 18 +- profiles/vertebrates/MA0517.1.pwm | 30 +-- profiles/vertebrates/MA0518.1.pwm | 14 ++ profiles/vertebrates/MA0519.1.pwm | 11 + profiles/vertebrates/MA0520.1.pwm | 30 +-- profiles/vertebrates/MA0521.1.pwm | 11 + profiles/vertebrates/MA0521.2.pwm | 12 ++ profiles/vertebrates/MA0522.1.pwm | 22 +- profiles/vertebrates/MA0522.2.pwm | 10 + profiles/vertebrates/MA0522.3.pwm | 22 +- profiles/vertebrates/MA0523.1.pwm | 14 ++ profiles/vertebrates/MA0524.1.pwm | 15 ++ profiles/vertebrates/MA0524.2.pwm | 12 ++ profiles/vertebrates/MA0525.1.pwm | 40 ++-- profiles/vertebrates/MA0525.2.pwm | 36 ++-- profiles/vertebrates/MA0526.1.pwm | 11 + profiles/vertebrates/MA0526.2.pwm | 16 ++ profiles/vertebrates/MA0526.3.pwm | 28 +-- profiles/vertebrates/MA0526.4.pwm | 12 ++ profiles/vertebrates/MA0527.1.pwm | 30 +-- profiles/vertebrates/MA0528.1.pwm | 21 ++ profiles/vertebrates/MA0528.2.pwm | 24 +-- profiles/vertebrates/MA0591.1.pwm | 30 +-- profiles/vertebrates/MA0592.1.pwm | 22 +- profiles/vertebrates/MA0592.2.pwm | 11 + profiles/vertebrates/MA0592.3.pwm | 26 +-- profiles/vertebrates/MA0593.1.pwm | 11 + profiles/vertebrates/MA0594.1.pwm | 22 +- profiles/vertebrates/MA0594.2.pwm | 10 + profiles/vertebrates/MA0595.1.pwm | 10 + profiles/vertebrates/MA0596.1.pwm | 10 + profiles/vertebrates/MA0597.1.pwm | 9 + profiles/vertebrates/MA0598.1.pwm | 16 +- profiles/vertebrates/MA0598.2.pwm | 24 +-- profiles/vertebrates/MA0598.3.pwm | 30 +-- profiles/vertebrates/MA0599.1.pwm | 10 + profiles/vertebrates/MA0600.1.pwm | 38 ++-- profiles/vertebrates/MA0600.2.pwm | 16 ++ profiles/vertebrates/MA0601.1.pwm | 22 +- profiles/vertebrates/MA0602.1.pwm | 28 +-- profiles/vertebrates/MA0603.1.pwm | 20 +- profiles/vertebrates/MA0604.1.pwm | 16 +- profiles/vertebrates/MA0605.1.pwm | 8 + profiles/vertebrates/MA0605.2.pwm | 24 +-- profiles/vertebrates/MA0606.1.pwm | 20 +- profiles/vertebrates/MA0606.2.pwm | 24 +-- profiles/vertebrates/MA0607.1.pwm | 8 + profiles/vertebrates/MA0607.2.pwm | 20 +- profiles/vertebrates/MA0608.1.pwm | 9 + profiles/vertebrates/MA0609.1.pwm | 20 +- profiles/vertebrates/MA0609.2.pwm | 16 ++ profiles/vertebrates/MA0610.1.pwm | 22 +- profiles/vertebrates/MA0611.1.pwm | 8 + profiles/vertebrates/MA0611.2.pwm | 16 ++ profiles/vertebrates/MA0612.1.pwm | 20 +- profiles/vertebrates/MA0612.2.pwm | 8 + profiles/vertebrates/MA0613.1.pwm | 8 + profiles/vertebrates/MA0614.1.pwm | 8 + profiles/vertebrates/MA0615.1.pwm | 17 ++ profiles/vertebrates/MA0616.1.pwm | 13 ++ profiles/vertebrates/MA0616.2.pwm | 20 +- profiles/vertebrates/MA0618.1.pwm | 16 +- profiles/vertebrates/MA0619.1.pwm | 9 + profiles/vertebrates/MA0620.1.pwm | 10 + profiles/vertebrates/MA0620.2.pwm | 18 ++ profiles/vertebrates/MA0620.3.pwm | 36 ++-- profiles/vertebrates/MA0621.1.pwm | 22 +- profiles/vertebrates/MA0622.1.pwm | 16 +- profiles/vertebrates/MA0623.1.pwm | 10 + profiles/vertebrates/MA0623.2.pwm | 10 + profiles/vertebrates/MA0624.1.pwm | 10 + profiles/vertebrates/MA0624.2.pwm | 12 ++ profiles/vertebrates/MA0625.1.pwm | 20 +- profiles/vertebrates/MA0625.2.pwm | 18 +- profiles/vertebrates/MA0626.1.pwm | 10 + profiles/vertebrates/MA0627.1.pwm | 32 +-- profiles/vertebrates/MA0627.2.pwm | 13 ++ profiles/vertebrates/MA0628.1.pwm | 10 + profiles/vertebrates/MA0629.1.pwm | 34 +-- profiles/vertebrates/MA0630.1.pwm | 8 + profiles/vertebrates/MA0631.1.pwm | 17 ++ profiles/vertebrates/MA0632.1.pwm | 10 + profiles/vertebrates/MA0632.2.pwm | 10 + profiles/vertebrates/MA0633.1.pwm | 10 + profiles/vertebrates/MA0633.2.pwm | 20 +- profiles/vertebrates/MA0634.1.pwm | 10 + profiles/vertebrates/MA0635.1.pwm | 20 +- profiles/vertebrates/MA0636.1.pwm | 10 + profiles/vertebrates/MA0638.1.pwm | 14 ++ profiles/vertebrates/MA0639.1.pwm | 24 +-- profiles/vertebrates/MA0640.1.pwm | 13 ++ profiles/vertebrates/MA0640.2.pwm | 28 +-- profiles/vertebrates/MA0641.1.pwm | 12 ++ profiles/vertebrates/MA0642.1.pwm | 20 +- profiles/vertebrates/MA0642.2.pwm | 8 + profiles/vertebrates/MA0643.1.pwm | 20 +- profiles/vertebrates/MA0644.1.pwm | 20 +- profiles/vertebrates/MA0644.2.pwm | 16 +- profiles/vertebrates/MA0645.1.pwm | 10 + profiles/vertebrates/MA0646.1.pwm | 11 + profiles/vertebrates/MA0647.1.pwm | 24 +-- profiles/vertebrates/MA0648.1.pwm | 20 +- profiles/vertebrates/MA0649.1.pwm | 10 + profiles/vertebrates/MA0650.1.pwm | 20 +- profiles/vertebrates/MA0650.2.pwm | 22 +- profiles/vertebrates/MA0650.3.pwm | 24 +-- profiles/vertebrates/MA0651.1.pwm | 11 + profiles/vertebrates/MA0651.2.pwm | 24 +-- profiles/vertebrates/MA0652.1.pwm | 14 ++ profiles/vertebrates/MA0653.1.pwm | 30 +-- profiles/vertebrates/MA0654.1.pwm | 16 +- profiles/vertebrates/MA0655.1.pwm | 9 + profiles/vertebrates/MA0656.1.pwm | 24 +-- profiles/vertebrates/MA0657.1.pwm | 36 ++-- profiles/vertebrates/MA0658.1.pwm | 10 + profiles/vertebrates/MA0659.1.pwm | 42 ++-- profiles/vertebrates/MA0659.2.pwm | 15 ++ profiles/vertebrates/MA0659.3.pwm | 30 +-- profiles/vertebrates/MA0660.1.pwm | 12 ++ profiles/vertebrates/MA0661.1.pwm | 20 +- profiles/vertebrates/MA0662.1.pwm | 10 + profiles/vertebrates/MA0663.1.pwm | 10 + profiles/vertebrates/MA0664.1.pwm | 10 + profiles/vertebrates/MA0665.1.pwm | 10 + profiles/vertebrates/MA0666.1.pwm | 8 + profiles/vertebrates/MA0666.2.pwm | 16 +- profiles/vertebrates/MA0667.1.pwm | 10 + profiles/vertebrates/MA0668.1.pwm | 10 + profiles/vertebrates/MA0668.2.pwm | 30 +-- profiles/vertebrates/MA0669.1.pwm | 10 + profiles/vertebrates/MA0670.1.pwm | 20 +- profiles/vertebrates/MA0671.1.pwm | 18 +- profiles/vertebrates/MA0672.1.pwm | 20 +- profiles/vertebrates/MA0673.1.pwm | 9 + profiles/vertebrates/MA0674.1.pwm | 8 + profiles/vertebrates/MA0675.1.pwm | 16 +- profiles/vertebrates/MA0676.1.pwm | 9 + profiles/vertebrates/MA0677.1.pwm | 14 ++ profiles/vertebrates/MA0678.1.pwm | 10 + profiles/vertebrates/MA0679.1.pwm | 14 ++ profiles/vertebrates/MA0679.2.pwm | 32 +-- profiles/vertebrates/MA0680.1.pwm | 20 +- profiles/vertebrates/MA0680.2.pwm | 15 ++ profiles/vertebrates/MA0681.1.pwm | 11 + profiles/vertebrates/MA0681.2.pwm | 32 +-- profiles/vertebrates/MA0682.1.pwm | 8 + profiles/vertebrates/MA0682.2.pwm | 16 +- profiles/vertebrates/MA0683.1.pwm | 16 ++ profiles/vertebrates/MA0684.1.pwm | 10 + profiles/vertebrates/MA0684.2.pwm | 12 ++ profiles/vertebrates/MA0685.1.pwm | 34 +-- profiles/vertebrates/MA0685.2.pwm | 18 +- profiles/vertebrates/MA0686.1.pwm | 11 + profiles/vertebrates/MA0687.1.pwm | 14 ++ profiles/vertebrates/MA0688.1.pwm | 11 + profiles/vertebrates/MA0689.1.pwm | 11 + profiles/vertebrates/MA0690.1.pwm | 10 + profiles/vertebrates/MA0690.2.pwm | 11 + profiles/vertebrates/MA0691.1.pwm | 20 +- profiles/vertebrates/MA0692.1.pwm | 20 +- profiles/vertebrates/MA0693.1.pwm | 16 ++ profiles/vertebrates/MA0693.2.pwm | 16 +- profiles/vertebrates/MA0693.3.pwm | 11 + profiles/vertebrates/MA0694.1.pwm | 24 +-- profiles/vertebrates/MA0695.1.pwm | 12 ++ profiles/vertebrates/MA0696.1.pwm | 14 ++ profiles/vertebrates/MA0697.1.pwm | 30 +-- profiles/vertebrates/MA0697.2.pwm | 26 +-- profiles/vertebrates/MA0698.1.pwm | 26 +-- profiles/vertebrates/MA0699.1.pwm | 10 + profiles/vertebrates/MA0700.1.pwm | 20 +- profiles/vertebrates/MA0700.2.pwm | 22 +- profiles/vertebrates/MA0701.1.pwm | 16 +- profiles/vertebrates/MA0701.2.pwm | 8 + profiles/vertebrates/MA0702.1.pwm | 16 +- profiles/vertebrates/MA0702.2.pwm | 16 +- profiles/vertebrates/MA0703.1.pwm | 8 + profiles/vertebrates/MA0703.2.pwm | 22 +- profiles/vertebrates/MA0704.1.pwm | 8 + profiles/vertebrates/MA0705.1.pwm | 16 +- profiles/vertebrates/MA0706.1.pwm | 20 +- profiles/vertebrates/MA0707.1.pwm | 10 + profiles/vertebrates/MA0707.2.pwm | 16 +- profiles/vertebrates/MA0708.1.pwm | 8 + profiles/vertebrates/MA0708.2.pwm | 8 + profiles/vertebrates/MA0709.1.pwm | 16 +- profiles/vertebrates/MA0710.1.pwm | 20 +- profiles/vertebrates/MA0711.1.pwm | 16 +- profiles/vertebrates/MA0712.1.pwm | 8 + profiles/vertebrates/MA0712.2.pwm | 12 ++ profiles/vertebrates/MA0713.1.pwm | 22 +- profiles/vertebrates/MA0714.1.pwm | 18 +- profiles/vertebrates/MA0715.1.pwm | 11 + profiles/vertebrates/MA0716.1.pwm | 16 +- profiles/vertebrates/MA0717.1.pwm | 8 + profiles/vertebrates/MA0718.1.pwm | 20 +- profiles/vertebrates/MA0719.1.pwm | 16 +- profiles/vertebrates/MA0720.1.pwm | 16 +- profiles/vertebrates/MA0721.1.pwm | 16 +- profiles/vertebrates/MA0722.1.pwm | 16 +- profiles/vertebrates/MA0723.1.pwm | 16 +- profiles/vertebrates/MA0723.2.pwm | 16 +- profiles/vertebrates/MA0724.1.pwm | 9 + profiles/vertebrates/MA0725.1.pwm | 8 + profiles/vertebrates/MA0726.1.pwm | 8 + profiles/vertebrates/MA0727.1.pwm | 17 ++ profiles/vertebrates/MA0728.1.pwm | 30 +-- profiles/vertebrates/MA0729.1.pwm | 36 ++-- profiles/vertebrates/MA0730.1.pwm | 34 +-- profiles/vertebrates/MA0731.1.pwm | 17 ++ profiles/vertebrates/MA0732.1.pwm | 30 +-- profiles/vertebrates/MA0733.1.pwm | 16 ++ profiles/vertebrates/MA0734.1.pwm | 24 +-- profiles/vertebrates/MA0734.2.pwm | 30 +-- profiles/vertebrates/MA0734.3.pwm | 13 ++ profiles/vertebrates/MA0735.1.pwm | 32 +-- profiles/vertebrates/MA0736.1.pwm | 28 +-- profiles/vertebrates/MA0737.1.pwm | 14 ++ profiles/vertebrates/MA0738.1.pwm | 18 +- profiles/vertebrates/MA0739.1.pwm | 9 + profiles/vertebrates/MA0740.1.pwm | 28 +-- profiles/vertebrates/MA0740.2.pwm | 9 + profiles/vertebrates/MA0741.1.pwm | 22 +- profiles/vertebrates/MA0742.1.pwm | 15 ++ profiles/vertebrates/MA0742.2.pwm | 9 + profiles/vertebrates/MA0743.1.pwm | 15 ++ profiles/vertebrates/MA0743.2.pwm | 32 +-- profiles/vertebrates/MA0744.1.pwm | 13 ++ profiles/vertebrates/MA0744.2.pwm | 16 ++ profiles/vertebrates/MA0745.1.pwm | 18 +- profiles/vertebrates/MA0745.2.pwm | 26 +-- profiles/vertebrates/MA0746.1.pwm | 11 + profiles/vertebrates/MA0746.2.pwm | 26 +-- profiles/vertebrates/MA0747.1.pwm | 24 +-- profiles/vertebrates/MA0748.1.pwm | 11 + profiles/vertebrates/MA0748.2.pwm | 11 + profiles/vertebrates/MA0749.1.pwm | 26 +-- profiles/vertebrates/MA0750.1.pwm | 24 +-- profiles/vertebrates/MA0750.2.pwm | 26 +-- profiles/vertebrates/MA0751.1.pwm | 30 +-- profiles/vertebrates/MA0752.1.pwm | 34 +-- profiles/vertebrates/MA0753.1.pwm | 20 +- profiles/vertebrates/MA0753.2.pwm | 26 +-- profiles/vertebrates/MA0754.1.pwm | 10 + profiles/vertebrates/MA0754.2.pwm | 10 + profiles/vertebrates/MA0755.1.pwm | 20 +- profiles/vertebrates/MA0756.1.pwm | 28 +-- profiles/vertebrates/MA0756.2.pwm | 18 +- profiles/vertebrates/MA0757.1.pwm | 28 +-- profiles/vertebrates/MA0758.1.pwm | 14 ++ profiles/vertebrates/MA0759.1.pwm | 20 +- profiles/vertebrates/MA0759.2.pwm | 22 +- profiles/vertebrates/MA0760.1.pwm | 10 + profiles/vertebrates/MA0761.1.pwm | 10 + profiles/vertebrates/MA0761.2.pwm | 28 +-- profiles/vertebrates/MA0762.1.pwm | 22 +- profiles/vertebrates/MA0763.1.pwm | 10 + profiles/vertebrates/MA0764.1.pwm | 20 +- profiles/vertebrates/MA0764.2.pwm | 10 + profiles/vertebrates/MA0764.3.pwm | 10 + profiles/vertebrates/MA0765.1.pwm | 10 + profiles/vertebrates/MA0765.2.pwm | 22 +- profiles/vertebrates/MA0765.3.pwm | 20 +- profiles/vertebrates/MA0766.1.pwm | 16 +- profiles/vertebrates/MA0766.2.pwm | 10 + profiles/vertebrates/MA0767.1.pwm | 20 +- profiles/vertebrates/MA0768.1.pwm | 30 +-- profiles/vertebrates/MA0768.2.pwm | 14 ++ profiles/vertebrates/MA0769.1.pwm | 12 ++ profiles/vertebrates/MA0769.2.pwm | 11 + profiles/vertebrates/MA0770.1.pwm | 13 ++ profiles/vertebrates/MA0771.1.pwm | 26 +-- profiles/vertebrates/MA0772.1.pwm | 14 ++ profiles/vertebrates/MA0773.1.pwm | 12 ++ profiles/vertebrates/MA0774.1.pwm | 16 +- profiles/vertebrates/MA0775.1.pwm | 8 + profiles/vertebrates/MA0776.1.pwm | 12 ++ profiles/vertebrates/MA0777.1.pwm | 15 ++ profiles/vertebrates/MA0778.1.pwm | 26 +-- profiles/vertebrates/MA0779.1.pwm | 34 +-- profiles/vertebrates/MA0780.1.pwm | 20 +- profiles/vertebrates/MA0781.1.pwm | 34 +-- profiles/vertebrates/MA0782.1.pwm | 12 ++ profiles/vertebrates/MA0782.2.pwm | 15 ++ profiles/vertebrates/MA0783.1.pwm | 24 +-- profiles/vertebrates/MA0784.1.pwm | 14 ++ profiles/vertebrates/MA0784.2.pwm | 32 +-- profiles/vertebrates/MA0785.1.pwm | 12 ++ profiles/vertebrates/MA0786.1.pwm | 24 +-- profiles/vertebrates/MA0787.1.pwm | 12 ++ profiles/vertebrates/MA0788.1.pwm | 13 ++ profiles/vertebrates/MA0789.1.pwm | 9 + profiles/vertebrates/MA0790.1.pwm | 14 ++ profiles/vertebrates/MA0791.1.pwm | 32 +-- profiles/vertebrates/MA0792.1.pwm | 9 + profiles/vertebrates/MA0793.1.pwm | 20 +- profiles/vertebrates/MA0794.1.pwm | 12 ++ profiles/vertebrates/MA0795.1.pwm | 10 + profiles/vertebrates/MA0796.1.pwm | 24 +-- profiles/vertebrates/MA0797.1.pwm | 24 +-- profiles/vertebrates/MA0798.1.pwm | 32 +-- profiles/vertebrates/MA0798.2.pwm | 14 ++ profiles/vertebrates/MA0798.3.pwm | 32 +-- profiles/vertebrates/MA0799.1.pwm | 16 ++ profiles/vertebrates/MA0799.2.pwm | 17 ++ profiles/vertebrates/MA0800.1.pwm | 13 ++ profiles/vertebrates/MA0801.1.pwm | 8 + profiles/vertebrates/MA0802.1.pwm | 20 +- profiles/vertebrates/MA0803.1.pwm | 16 +- profiles/vertebrates/MA0804.1.pwm | 20 ++ profiles/vertebrates/MA0805.1.pwm | 16 +- profiles/vertebrates/MA0806.1.pwm | 16 +- profiles/vertebrates/MA0807.1.pwm | 8 + profiles/vertebrates/MA0808.1.pwm | 16 +- profiles/vertebrates/MA0809.1.pwm | 10 + profiles/vertebrates/MA0809.2.pwm | 24 +-- profiles/vertebrates/MA0810.1.pwm | 12 ++ profiles/vertebrates/MA0811.1.pwm | 24 +-- profiles/vertebrates/MA0812.1.pwm | 11 + profiles/vertebrates/MA0813.1.pwm | 13 ++ profiles/vertebrates/MA0814.1.pwm | 11 + profiles/vertebrates/MA0814.2.pwm | 14 ++ profiles/vertebrates/MA0815.1.pwm | 26 +-- profiles/vertebrates/MA0816.1.pwm | 20 +- profiles/vertebrates/MA0817.1.pwm | 24 +-- profiles/vertebrates/MA0818.1.pwm | 10 + profiles/vertebrates/MA0818.2.pwm | 10 + profiles/vertebrates/MA0819.1.pwm | 10 + profiles/vertebrates/MA0819.2.pwm | 10 + profiles/vertebrates/MA0820.1.pwm | 10 + profiles/vertebrates/MA0821.1.pwm | 24 +-- profiles/vertebrates/MA0821.2.pwm | 10 + profiles/vertebrates/MA0822.1.pwm | 12 ++ profiles/vertebrates/MA0823.1.pwm | 10 + profiles/vertebrates/MA0825.1.pwm | 10 + profiles/vertebrates/MA0826.1.pwm | 20 +- profiles/vertebrates/MA0827.1.pwm | 10 + profiles/vertebrates/MA0828.1.pwm | 20 +- profiles/vertebrates/MA0828.2.pwm | 28 +-- profiles/vertebrates/MA0829.1.pwm | 20 +- profiles/vertebrates/MA0829.2.pwm | 14 ++ profiles/vertebrates/MA0830.1.pwm | 10 + profiles/vertebrates/MA0830.2.pwm | 13 ++ profiles/vertebrates/MA0831.1.pwm | 10 + profiles/vertebrates/MA0831.2.pwm | 16 +- profiles/vertebrates/MA0831.3.pwm | 20 +- profiles/vertebrates/MA0832.1.pwm | 14 ++ profiles/vertebrates/MA0833.1.pwm | 26 +-- profiles/vertebrates/MA0833.2.pwm | 28 +-- profiles/vertebrates/MA0834.1.pwm | 28 +-- profiles/vertebrates/MA0835.2.pwm | 11 + profiles/vertebrates/MA0836.1.pwm | 20 +- profiles/vertebrates/MA0836.2.pwm | 26 +-- profiles/vertebrates/MA0837.1.pwm | 10 + profiles/vertebrates/MA0837.2.pwm | 12 ++ profiles/vertebrates/MA0838.1.pwm | 10 + profiles/vertebrates/MA0839.1.pwm | 28 +-- profiles/vertebrates/MA0840.1.pwm | 12 ++ profiles/vertebrates/MA0841.1.pwm | 11 + profiles/vertebrates/MA0842.1.pwm | 11 + profiles/vertebrates/MA0842.2.pwm | 26 +-- profiles/vertebrates/MA0843.1.pwm | 24 +-- profiles/vertebrates/MA0844.1.pwm | 14 ++ profiles/vertebrates/MA0845.1.pwm | 11 + profiles/vertebrates/MA0846.1.pwm | 12 ++ profiles/vertebrates/MA0847.1.pwm | 7 + profiles/vertebrates/MA0847.2.pwm | 26 +-- profiles/vertebrates/MA0847.3.pwm | 12 ++ profiles/vertebrates/MA0848.1.pwm | 7 + profiles/vertebrates/MA0849.1.pwm | 14 +- profiles/vertebrates/MA0850.1.pwm | 14 +- profiles/vertebrates/MA0851.1.pwm | 34 +-- profiles/vertebrates/MA0852.1.pwm | 17 ++ profiles/vertebrates/MA0852.2.pwm | 14 ++ profiles/vertebrates/MA0853.1.pwm | 34 +-- profiles/vertebrates/MA0854.1.pwm | 34 +-- profiles/vertebrates/MA0855.1.pwm | 14 ++ profiles/vertebrates/MA0856.1.pwm | 14 ++ profiles/vertebrates/MA0857.1.pwm | 16 ++ profiles/vertebrates/MA0858.1.pwm | 34 +-- profiles/vertebrates/MA0859.1.pwm | 32 +-- profiles/vertebrates/MA0860.1.pwm | 17 ++ profiles/vertebrates/MA0861.1.pwm | 18 ++ profiles/vertebrates/MA0862.1.pwm | 8 + profiles/vertebrates/MA0863.1.pwm | 14 ++ profiles/vertebrates/MA0864.1.pwm | 16 ++ profiles/vertebrates/MA0864.2.pwm | 32 +-- profiles/vertebrates/MA0865.1.pwm | 24 +-- profiles/vertebrates/MA0865.2.pwm | 24 +-- profiles/vertebrates/MA0866.1.pwm | 15 ++ profiles/vertebrates/MA0867.1.pwm | 16 ++ profiles/vertebrates/MA0867.2.pwm | 10 + profiles/vertebrates/MA0868.1.pwm | 32 +-- profiles/vertebrates/MA0868.2.pwm | 10 + profiles/vertebrates/MA0869.1.pwm | 30 +-- profiles/vertebrates/MA0869.2.pwm | 24 +-- profiles/vertebrates/MA0870.1.pwm | 30 +-- profiles/vertebrates/MA0871.1.pwm | 20 +- profiles/vertebrates/MA0871.2.pwm | 11 + profiles/vertebrates/MA0872.1.pwm | 26 +-- profiles/vertebrates/MA0873.1.pwm | 11 + profiles/vertebrates/MA0874.1.pwm | 17 ++ profiles/vertebrates/MA0875.1.pwm | 8 + profiles/vertebrates/MA0876.1.pwm | 16 +- profiles/vertebrates/MA0877.1.pwm | 10 + profiles/vertebrates/MA0877.2.pwm | 16 +- profiles/vertebrates/MA0877.3.pwm | 16 +- profiles/vertebrates/MA0878.1.pwm | 9 + profiles/vertebrates/MA0878.2.pwm | 22 +- profiles/vertebrates/MA0878.3.pwm | 20 +- profiles/vertebrates/MA0879.1.pwm | 10 + profiles/vertebrates/MA0879.2.pwm | 16 +- profiles/vertebrates/MA0880.1.pwm | 16 +- profiles/vertebrates/MA0881.1.pwm | 8 + profiles/vertebrates/MA0882.1.pwm | 8 + profiles/vertebrates/MA0883.1.pwm | 17 ++ profiles/vertebrates/MA0884.1.pwm | 26 +-- profiles/vertebrates/MA0884.2.pwm | 26 +-- profiles/vertebrates/MA0885.1.pwm | 16 +- profiles/vertebrates/MA0885.2.pwm | 12 ++ profiles/vertebrates/MA0886.1.pwm | 10 + profiles/vertebrates/MA0887.1.pwm | 20 +- profiles/vertebrates/MA0888.1.pwm | 10 + profiles/vertebrates/MA0889.1.pwm | 20 +- profiles/vertebrates/MA0890.1.pwm | 10 + profiles/vertebrates/MA0891.1.pwm | 20 +- profiles/vertebrates/MA0892.1.pwm | 20 +- profiles/vertebrates/MA0893.1.pwm | 20 +- profiles/vertebrates/MA0893.2.pwm | 8 + profiles/vertebrates/MA0894.1.pwm | 10 + profiles/vertebrates/MA0895.1.pwm | 20 +- profiles/vertebrates/MA0896.1.pwm | 17 ++ profiles/vertebrates/MA0897.1.pwm | 17 ++ profiles/vertebrates/MA0898.1.pwm | 34 +-- profiles/vertebrates/MA0899.1.pwm | 22 +- profiles/vertebrates/MA0900.1.pwm | 10 + profiles/vertebrates/MA0900.2.pwm | 8 + profiles/vertebrates/MA0901.1.pwm | 10 + profiles/vertebrates/MA0901.2.pwm | 14 ++ profiles/vertebrates/MA0902.1.pwm | 10 + profiles/vertebrates/MA0902.2.pwm | 16 +- profiles/vertebrates/MA0903.1.pwm | 20 +- profiles/vertebrates/MA0904.1.pwm | 32 +-- profiles/vertebrates/MA0904.2.pwm | 8 + profiles/vertebrates/MA0905.1.pwm | 10 + profiles/vertebrates/MA0906.1.pwm | 11 + profiles/vertebrates/MA0907.1.pwm | 11 + profiles/vertebrates/MA0908.1.pwm | 10 + profiles/vertebrates/MA0909.1.pwm | 10 + profiles/vertebrates/MA0909.2.pwm | 11 + profiles/vertebrates/MA0909.3.pwm | 10 + profiles/vertebrates/MA0910.1.pwm | 34 +-- profiles/vertebrates/MA0910.2.pwm | 8 + profiles/vertebrates/MA0911.1.pwm | 12 ++ profiles/vertebrates/MA0912.1.pwm | 16 ++ profiles/vertebrates/MA0912.2.pwm | 16 +- profiles/vertebrates/MA0913.1.pwm | 10 + profiles/vertebrates/MA0913.2.pwm | 20 +- profiles/vertebrates/MA0914.1.pwm | 8 + profiles/vertebrates/MA1099.1.pwm | 20 +- profiles/vertebrates/MA1099.2.pwm | 10 + profiles/vertebrates/MA1100.1.pwm | 26 +-- profiles/vertebrates/MA1100.2.pwm | 20 +- profiles/vertebrates/MA1101.1.pwm | 14 ++ profiles/vertebrates/MA1101.2.pwm | 38 ++-- profiles/vertebrates/MA1102.1.pwm | 28 +-- profiles/vertebrates/MA1102.2.pwm | 12 ++ profiles/vertebrates/MA1103.1.pwm | 22 +- profiles/vertebrates/MA1103.2.pwm | 22 +- profiles/vertebrates/MA1104.1.pwm | 26 +-- profiles/vertebrates/MA1104.2.pwm | 13 ++ profiles/vertebrates/MA1105.1.pwm | 15 ++ profiles/vertebrates/MA1105.2.pwm | 24 +-- profiles/vertebrates/MA1106.1.pwm | 10 + profiles/vertebrates/MA1107.1.pwm | 13 ++ profiles/vertebrates/MA1107.2.pwm | 32 +-- profiles/vertebrates/MA1108.1.pwm | 26 +-- profiles/vertebrates/MA1108.2.pwm | 10 + profiles/vertebrates/MA1109.1.pwm | 13 ++ profiles/vertebrates/MA1110.1.pwm | 22 +- profiles/vertebrates/MA1110.2.pwm | 20 +- profiles/vertebrates/MA1111.1.pwm | 11 + profiles/vertebrates/MA1112.1.pwm | 20 +- profiles/vertebrates/MA1112.2.pwm | 24 +-- profiles/vertebrates/MA1113.1.pwm | 24 +-- profiles/vertebrates/MA1113.2.pwm | 13 ++ profiles/vertebrates/MA1114.1.pwm | 17 ++ profiles/vertebrates/MA1115.1.pwm | 11 + profiles/vertebrates/MA1116.1.pwm | 20 +- profiles/vertebrates/MA1117.1.pwm | 22 +- profiles/vertebrates/MA1118.1.pwm | 11 + profiles/vertebrates/MA1119.1.pwm | 32 +-- profiles/vertebrates/MA1120.1.pwm | 22 +- profiles/vertebrates/MA1121.1.pwm | 13 ++ profiles/vertebrates/MA1122.1.pwm | 22 +- profiles/vertebrates/MA1123.1.pwm | 13 ++ profiles/vertebrates/MA1123.2.pwm | 26 +-- profiles/vertebrates/MA1124.1.pwm | 13 ++ profiles/vertebrates/MA1125.1.pwm | 12 ++ profiles/vertebrates/MA1126.1.pwm | 16 ++ profiles/vertebrates/MA1127.1.pwm | 22 +- profiles/vertebrates/MA1128.1.pwm | 13 ++ profiles/vertebrates/MA1129.1.pwm | 10 + profiles/vertebrates/MA1130.1.pwm | 24 +-- profiles/vertebrates/MA1131.1.pwm | 11 + profiles/vertebrates/MA1132.1.pwm | 10 + profiles/vertebrates/MA1133.1.pwm | 12 ++ profiles/vertebrates/MA1134.1.pwm | 12 ++ profiles/vertebrates/MA1135.1.pwm | 10 + profiles/vertebrates/MA1136.1.pwm | 10 + profiles/vertebrates/MA1137.1.pwm | 13 ++ profiles/vertebrates/MA1138.1.pwm | 20 +- profiles/vertebrates/MA1139.1.pwm | 12 ++ profiles/vertebrates/MA1140.1.pwm | 20 +- profiles/vertebrates/MA1140.2.pwm | 24 +-- profiles/vertebrates/MA1141.1.pwm | 13 ++ profiles/vertebrates/MA1142.1.pwm | 20 +- profiles/vertebrates/MA1143.1.pwm | 10 + profiles/vertebrates/MA1144.1.pwm | 10 + profiles/vertebrates/MA1145.1.pwm | 15 ++ profiles/vertebrates/MA1146.1.pwm | 15 ++ profiles/vertebrates/MA1147.1.pwm | 15 ++ profiles/vertebrates/MA1148.1.pwm | 36 ++-- profiles/vertebrates/MA1149.1.pwm | 36 ++-- profiles/vertebrates/MA1150.1.pwm | 11 + profiles/vertebrates/MA1151.1.pwm | 24 +-- profiles/vertebrates/MA1152.1.pwm | 10 + profiles/vertebrates/MA1153.1.pwm | 16 +- profiles/vertebrates/MA1154.1.pwm | 34 +-- profiles/vertebrates/MA1155.1.pwm | 30 +-- profiles/vertebrates/MA1418.1.pwm | 21 ++ profiles/vertebrates/MA1419.1.pwm | 15 ++ profiles/vertebrates/MA1420.1.pwm | 28 +-- profiles/vertebrates/MA1421.1.pwm | 12 ++ profiles/vertebrates/MA1463.1.pwm | 20 +- profiles/vertebrates/MA1464.1.pwm | 20 +- profiles/vertebrates/MA1466.1.pwm | 28 +-- profiles/vertebrates/MA1467.1.pwm | 10 + profiles/vertebrates/MA1467.2.pwm | 22 +- profiles/vertebrates/MA1468.1.pwm | 20 +- profiles/vertebrates/MA1470.1.pwm | 20 ++ profiles/vertebrates/MA1471.1.pwm | 24 +-- profiles/vertebrates/MA1472.1.pwm | 20 +- profiles/vertebrates/MA1472.2.pwm | 24 +-- profiles/vertebrates/MA1473.1.pwm | 22 +- profiles/vertebrates/MA1474.1.pwm | 24 +-- profiles/vertebrates/MA1475.1.pwm | 12 ++ profiles/vertebrates/MA1476.1.pwm | 8 + profiles/vertebrates/MA1476.2.pwm | 24 +-- profiles/vertebrates/MA1478.1.pwm | 24 +-- profiles/vertebrates/MA1479.1.pwm | 24 +-- profiles/vertebrates/MA1480.1.pwm | 10 + profiles/vertebrates/MA1481.1.pwm | 16 +- profiles/vertebrates/MA1483.1.pwm | 24 +-- profiles/vertebrates/MA1483.2.pwm | 24 +-- profiles/vertebrates/MA1484.1.pwm | 10 + profiles/vertebrates/MA1485.1.pwm | 28 +-- profiles/vertebrates/MA1487.1.pwm | 30 +-- profiles/vertebrates/MA1487.2.pwm | 14 ++ profiles/vertebrates/MA1489.1.pwm | 8 + profiles/vertebrates/MA1491.1.pwm | 30 +-- profiles/vertebrates/MA1491.2.pwm | 32 +-- profiles/vertebrates/MA1493.1.pwm | 10 + profiles/vertebrates/MA1494.1.pwm | 15 ++ profiles/vertebrates/MA1495.1.pwm | 16 +- profiles/vertebrates/MA1496.1.pwm | 8 + profiles/vertebrates/MA1497.1.pwm | 20 +- profiles/vertebrates/MA1498.1.pwm | 8 + profiles/vertebrates/MA1498.2.pwm | 8 + profiles/vertebrates/MA1499.1.pwm | 16 +- profiles/vertebrates/MA1500.1.pwm | 16 +- profiles/vertebrates/MA1501.1.pwm | 20 +- profiles/vertebrates/MA1502.1.pwm | 16 +- profiles/vertebrates/MA1503.1.pwm | 10 + profiles/vertebrates/MA1504.1.pwm | 16 +- profiles/vertebrates/MA1505.1.pwm | 16 +- profiles/vertebrates/MA1506.1.pwm | 11 + profiles/vertebrates/MA1507.1.pwm | 8 + profiles/vertebrates/MA1508.1.pwm | 12 ++ profiles/vertebrates/MA1509.1.pwm | 9 + profiles/vertebrates/MA1511.1.pwm | 11 + profiles/vertebrates/MA1511.2.pwm | 9 + profiles/vertebrates/MA1512.1.pwm | 22 +- profiles/vertebrates/MA1513.1.pwm | 22 +- profiles/vertebrates/MA1514.1.pwm | 30 +-- profiles/vertebrates/MA1515.1.pwm | 11 + profiles/vertebrates/MA1516.1.pwm | 22 +- profiles/vertebrates/MA1517.1.pwm | 11 + profiles/vertebrates/MA1518.1.pwm | 16 +- profiles/vertebrates/MA1518.2.pwm | 36 ++-- profiles/vertebrates/MA1519.1.pwm | 16 +- profiles/vertebrates/MA1520.1.pwm | 30 +-- profiles/vertebrates/MA1521.1.pwm | 30 +-- profiles/vertebrates/MA1522.1.pwm | 11 + profiles/vertebrates/MA1523.1.pwm | 10 + profiles/vertebrates/MA1524.1.pwm | 12 ++ profiles/vertebrates/MA1524.2.pwm | 32 +-- profiles/vertebrates/MA1525.1.pwm | 10 + profiles/vertebrates/MA1525.2.pwm | 10 + profiles/vertebrates/MA1527.1.pwm | 17 ++ profiles/vertebrates/MA1528.1.pwm | 34 +-- profiles/vertebrates/MA1529.1.pwm | 18 ++ profiles/vertebrates/MA1530.1.pwm | 9 + profiles/vertebrates/MA1531.1.pwm | 30 +-- profiles/vertebrates/MA1532.1.pwm | 15 ++ profiles/vertebrates/MA1532.2.pwm | 30 +-- profiles/vertebrates/MA1533.1.pwm | 17 ++ profiles/vertebrates/MA1534.1.pwm | 9 + profiles/vertebrates/MA1535.1.pwm | 9 + profiles/vertebrates/MA1536.1.pwm | 16 +- profiles/vertebrates/MA1537.1.pwm | 15 ++ profiles/vertebrates/MA1538.1.pwm | 30 +-- profiles/vertebrates/MA1539.1.pwm | 15 ++ profiles/vertebrates/MA1540.1.pwm | 11 + profiles/vertebrates/MA1541.1.pwm | 34 +-- profiles/vertebrates/MA1542.1.pwm | 20 +- profiles/vertebrates/MA1544.1.pwm | 14 ++ profiles/vertebrates/MA1545.1.pwm | 26 +-- profiles/vertebrates/MA1546.1.pwm | 16 ++ profiles/vertebrates/MA1547.1.pwm | 16 +- profiles/vertebrates/MA1547.2.pwm | 16 +- profiles/vertebrates/MA1548.1.pwm | 20 +- profiles/vertebrates/MA1549.1.pwm | 20 +- profiles/vertebrates/MA1550.1.pwm | 16 ++ profiles/vertebrates/MA1552.1.pwm | 28 +-- profiles/vertebrates/MA1553.1.pwm | 14 ++ profiles/vertebrates/MA1554.1.pwm | 9 + profiles/vertebrates/MA1555.1.pwm | 28 +-- profiles/vertebrates/MA1556.1.pwm | 14 ++ profiles/vertebrates/MA1557.1.pwm | 10 + profiles/vertebrates/MA1558.1.pwm | 10 + profiles/vertebrates/MA1559.1.pwm | 10 + profiles/vertebrates/MA1560.1.pwm | 20 +- profiles/vertebrates/MA1561.1.pwm | 22 +- profiles/vertebrates/MA1562.1.pwm | 10 + profiles/vertebrates/MA1563.1.pwm | 8 + profiles/vertebrates/MA1563.2.pwm | 16 +- profiles/vertebrates/MA1564.1.pwm | 12 ++ profiles/vertebrates/MA1565.1.pwm | 12 ++ profiles/vertebrates/MA1566.1.pwm | 20 +- profiles/vertebrates/MA1566.2.pwm | 11 + profiles/vertebrates/MA1567.1.pwm | 10 + profiles/vertebrates/MA1567.2.pwm | 24 +-- profiles/vertebrates/MA1568.1.pwm | 12 ++ profiles/vertebrates/MA1569.1.pwm | 11 + profiles/vertebrates/MA1570.1.pwm | 20 +- profiles/vertebrates/MA1571.1.pwm | 24 +-- profiles/vertebrates/MA1572.1.pwm | 12 ++ profiles/vertebrates/MA1573.1.pwm | 38 ++-- profiles/vertebrates/MA1573.2.pwm | 28 +-- profiles/vertebrates/MA1574.1.pwm | 30 +-- profiles/vertebrates/MA1575.1.pwm | 38 ++-- profiles/vertebrates/MA1576.1.pwm | 19 ++ profiles/vertebrates/MA1577.1.pwm | 16 +- profiles/vertebrates/MA1578.1.pwm | 20 +- profiles/vertebrates/MA1579.1.pwm | 15 ++ profiles/vertebrates/MA1580.1.pwm | 10 + profiles/vertebrates/MA1581.1.pwm | 26 +-- profiles/vertebrates/MA1583.1.pwm | 13 ++ profiles/vertebrates/MA1584.1.pwm | 16 ++ profiles/vertebrates/MA1585.1.pwm | 20 +- profiles/vertebrates/MA1587.1.pwm | 28 +-- profiles/vertebrates/MA1588.1.pwm | 15 ++ profiles/vertebrates/MA1589.1.pwm | 21 ++ profiles/vertebrates/MA1592.1.pwm | 32 +-- profiles/vertebrates/MA1593.1.pwm | 24 +-- profiles/vertebrates/MA1594.1.pwm | 24 +++ profiles/vertebrates/MA1596.1.pwm | 16 ++ profiles/vertebrates/MA1597.1.pwm | 17 ++ profiles/vertebrates/MA1599.1.pwm | 32 +-- profiles/vertebrates/MA1600.1.pwm | 18 ++ profiles/vertebrates/MA1601.1.pwm | 10 + profiles/vertebrates/MA1601.2.pwm | 24 +-- profiles/vertebrates/MA1602.1.pwm | 12 ++ profiles/vertebrates/MA1603.1.pwm | 26 +-- profiles/vertebrates/MA1604.1.pwm | 13 ++ profiles/vertebrates/MA1606.1.pwm | 22 +- profiles/vertebrates/MA1607.1.pwm | 28 +-- profiles/vertebrates/MA1608.1.pwm | 22 +- profiles/vertebrates/MA1615.1.pwm | 13 ++ profiles/vertebrates/MA1616.1.pwm | 15 ++ profiles/vertebrates/MA1618.1.pwm | 26 +-- profiles/vertebrates/MA1619.1.pwm | 24 +-- profiles/vertebrates/MA1620.1.pwm | 24 +-- profiles/vertebrates/MA1621.1.pwm | 28 +-- profiles/vertebrates/MA1622.1.pwm | 14 ++ profiles/vertebrates/MA1623.1.pwm | 26 +-- profiles/vertebrates/MA1624.1.pwm | 24 +-- profiles/vertebrates/MA1625.1.pwm | 30 +-- profiles/vertebrates/MA1627.1.pwm | 28 +-- profiles/vertebrates/MA1628.1.pwm | 11 + profiles/vertebrates/MA1629.1.pwm | 14 ++ profiles/vertebrates/MA1630.1.pwm | 11 + profiles/vertebrates/MA1630.2.pwm | 24 +-- profiles/vertebrates/MA1631.1.pwm | 13 ++ profiles/vertebrates/MA1632.1.pwm | 13 ++ profiles/vertebrates/MA1633.1.pwm | 26 +-- profiles/vertebrates/MA1633.2.pwm | 18 +- profiles/vertebrates/MA1634.1.pwm | 22 +- profiles/vertebrates/MA1635.1.pwm | 20 +- profiles/vertebrates/MA1636.1.pwm | 15 ++ profiles/vertebrates/MA1637.1.pwm | 26 +-- profiles/vertebrates/MA1638.1.pwm | 10 + profiles/vertebrates/MA1639.1.pwm | 26 +-- profiles/vertebrates/MA1640.1.pwm | 15 ++ profiles/vertebrates/MA1641.1.pwm | 12 ++ profiles/vertebrates/MA1642.1.pwm | 13 ++ profiles/vertebrates/MA1643.1.pwm | 42 ++-- profiles/vertebrates/MA1644.1.pwm | 22 +- profiles/vertebrates/MA1645.1.pwm | 28 +-- profiles/vertebrates/MA1646.1.pwm | 24 +-- profiles/vertebrates/MA1647.1.pwm | 11 + profiles/vertebrates/MA1647.2.pwm | 17 ++ profiles/vertebrates/MA1648.1.pwm | 22 +- profiles/vertebrates/MA1649.1.pwm | 11 + profiles/vertebrates/MA1650.1.pwm | 24 +-- profiles/vertebrates/MA1651.1.pwm | 21 ++ profiles/vertebrates/MA1652.1.pwm | 28 +-- profiles/vertebrates/MA1653.1.pwm | 12 ++ profiles/vertebrates/MA1654.1.pwm | 23 +++ profiles/vertebrates/MA1655.1.pwm | 24 +-- profiles/vertebrates/MA1656.1.pwm | 28 +-- profiles/vertebrates/MA1657.1.pwm | 12 ++ profiles/vertebrates/MA1683.1.pwm | 22 +- profiles/vertebrates/MA1684.1.pwm | 12 +- profiles/vertebrates/MA1707.1.pwm | 24 +-- profiles/vertebrates/MA1708.1.pwm | 11 + profiles/vertebrates/MA1709.1.pwm | 30 +-- profiles/vertebrates/MA1710.1.pwm | 24 +-- profiles/vertebrates/MA1711.1.pwm | 34 +-- profiles/vertebrates/MA1712.1.pwm | 36 ++-- profiles/vertebrates/MA1713.1.pwm | 14 ++ profiles/vertebrates/MA1714.1.pwm | 21 ++ profiles/vertebrates/MA1715.1.pwm | 30 +-- profiles/vertebrates/MA1716.1.pwm | 42 ++-- profiles/vertebrates/MA1717.1.pwm | 11 + profiles/vertebrates/MA1718.1.pwm | 40 ++-- profiles/vertebrates/MA1719.1.pwm | 36 ++-- profiles/vertebrates/MA1720.1.pwm | 32 +-- profiles/vertebrates/MA1721.1.pwm | 32 +-- profiles/vertebrates/MA1722.1.pwm | 19 ++ profiles/vertebrates/MA1723.1.pwm | 24 +++ profiles/vertebrates/MA1724.1.pwm | 13 ++ profiles/vertebrates/MA1725.1.pwm | 26 +-- profiles/vertebrates/MA1726.1.pwm | 28 +-- profiles/vertebrates/MA1727.1.pwm | 15 ++ profiles/vertebrates/MA1728.1.pwm | 12 ++ profiles/vertebrates/MA1729.1.pwm | 15 ++ profiles/vertebrates/MA1730.1.pwm | 15 ++ profiles/vertebrates/MA1731.1.pwm | 36 ++-- profiles/vertebrates/MA1928.1.pwm | 12 ++ profiles/vertebrates/MA1929.1.pwm | 68 +++--- profiles/vertebrates/MA1930.1.pwm | 35 ++++ profiles/vertebrates/MA1931.1.pwm | 28 +-- profiles/vertebrates/MA1932.1.pwm | 16 ++ profiles/vertebrates/MA1933.1.pwm | 16 ++ profiles/vertebrates/MA1934.1.pwm | 16 ++ profiles/vertebrates/MA1935.1.pwm | 28 +-- profiles/vertebrates/MA1936.1.pwm | 14 ++ profiles/vertebrates/MA1937.1.pwm | 32 +-- profiles/vertebrates/MA1938.1.pwm | 34 +-- profiles/vertebrates/MA1939.1.pwm | 34 +-- profiles/vertebrates/MA1940.1.pwm | 14 ++ profiles/vertebrates/MA1941.1.pwm | 16 ++ profiles/vertebrates/MA1942.1.pwm | 15 ++ profiles/vertebrates/MA1943.1.pwm | 15 ++ profiles/vertebrates/MA1944.1.pwm | 14 ++ profiles/vertebrates/MA1945.1.pwm | 30 +-- profiles/vertebrates/MA1946.1.pwm | 13 ++ profiles/vertebrates/MA1947.1.pwm | 13 ++ profiles/vertebrates/MA1948.1.pwm | 14 ++ profiles/vertebrates/MA1949.1.pwm | 15 ++ profiles/vertebrates/MA1950.1.pwm | 28 +-- profiles/vertebrates/MA1951.1.pwm | 28 +-- profiles/vertebrates/MA1952.1.pwm | 14 ++ profiles/vertebrates/MA1953.1.pwm | 28 +-- profiles/vertebrates/MA1954.1.pwm | 28 +-- profiles/vertebrates/MA1955.1.pwm | 14 ++ profiles/vertebrates/MA1956.1.pwm | 14 ++ profiles/vertebrates/MA1957.1.pwm | 28 +-- profiles/vertebrates/MA1958.1.pwm | 34 +-- profiles/vertebrates/MA1959.1.pwm | 9 + profiles/vertebrates/MA1960.1.pwm | 12 ++ profiles/vertebrates/MA1961.1.pwm | 24 +-- profiles/vertebrates/MA1962.1.pwm | 34 +-- profiles/vertebrates/MA1963.1.pwm | 26 +-- profiles/vertebrates/MA1964.1.pwm | 10 + profiles/vertebrates/MA1965.1.pwm | 20 +- profiles/vertebrates/MA1966.1.pwm | 32 +-- profiles/vertebrates/MA1967.1.pwm | 16 ++ profiles/vertebrates/MA1968.1.pwm | 20 +- profiles/vertebrates/MA1969.1.pwm | 24 +++ profiles/vertebrates/MA1970.1.pwm | 12 ++ profiles/vertebrates/MA1971.1.pwm | 14 ++ profiles/vertebrates/MA1972.1.pwm | 15 ++ profiles/vertebrates/MA1973.1.pwm | 20 ++ profiles/vertebrates/MA1974.1.pwm | 30 +-- profiles/vertebrates/MA1975.1.pwm | 30 +-- profiles/vertebrates/MA1976.1.pwm | 54 ++--- profiles/vertebrates/MA1977.1.pwm | 42 ++-- profiles/vertebrates/MA1978.1.pwm | 42 ++-- profiles/vertebrates/MA1979.1.pwm | 11 + profiles/vertebrates/MA1980.1.pwm | 30 +-- profiles/vertebrates/MA1981.1.pwm | 36 ++-- profiles/vertebrates/MA1982.1.pwm | 30 +-- profiles/vertebrates/MA1983.1.pwm | 42 ++-- profiles/vertebrates/MA1984.1.pwm | 12 ++ profiles/vertebrates/MA1985.1.pwm | 30 +-- profiles/vertebrates/MA1986.1.pwm | 20 +- profiles/vertebrates/MA1987.1.pwm | 21 ++ profiles/vertebrates/MA1988.1.pwm | 11 + profiles/vertebrates/MA1989.1.pwm | 14 ++ profiles/vertebrates/MA1990.1.pwm | 28 +-- profiles/vertebrates/MA1991.1.pwm | 14 ++ profiles/vertebrates/MA1992.1.pwm | 15 ++ profiles/vertebrates/MA1993.1.pwm | 10 + profiles/vertebrates/MA1994.1.pwm | 13 ++ profiles/vertebrates/MA1995.1.pwm | 22 +- profiles/vertebrates/MA1996.1.pwm | 11 + profiles/vertebrates/MA1997.1.pwm | 20 +- profiles/vertebrates/MA1998.1.pwm | 24 +-- profiles/vertebrates/MA1999.1.pwm | 15 ++ profiles/vertebrates/MA2000.1.pwm | 34 +-- profiles/vertebrates/MA2001.1.pwm | 11 + profiles/vertebrates/MA2002.1.pwm | 11 + profiles/vertebrates/MA2003.1.pwm | 20 +- scan-sequence.py | 250 +++++++++++++++++++++++ scan-sequences.sh | 25 +++ scans2bigBed | 4 +- scans2bigBed.sh | 5 + 2352 files changed, 29152 insertions(+), 14381 deletions(-) rename environment.yml => conda/environment.yml (95%) mode change 100644 => 100755 create mode 100755 scan-sequence.py create mode 100755 scan-sequences.sh create mode 100755 scans2bigBed.sh diff --git a/README.md b/README.md index 7b67e61..a7c0567 100755 --- a/README.md +++ b/README.md @@ -6,10 +6,10 @@ This repository contains the data and code used to generate the JASPAR UCSC Geno ## Content * The `genomes` folder contains scripts to download and process different genome assemblies -* The `profiles` folder contains the output from the script [`get_profiles.py`](https://github.com/wassermanlab/JASPAR-UCSC-tracks/blob/master/profiles/get_profiles.py), which downloads the JASPAR CORE profiles for different taxons -* The file [`environment.yml`](https://github.com/wassermanlab/JASPAR-UCSC-tracks/blob/master/environment.yml) contains the conda environment used to generate the genomic tracks for JASPAR 2020 (see installation) +* The `profiles` folder contains the output from the script [`get-profiles.py`](https://github.com/wassermanlab/JASPAR-UCSC-tracks/blob/master/profiles/get_profiles.py), which downloads the JASPAR CORE profiles for different taxons +* The file [`environment.yml`](https://github.com/wassermanlab/JASPAR-UCSC-tracks/blob/master/environment.yml), within the `conda` folder, contains the conda environment used to generate the genomic tracks for JASPAR 2022 (see installation) * The script [`install-pwmscan.sh`](https://github.com/wassermanlab/JASPAR-UCSC-tracks/blob/master/install-pwmscan.sh) downloads and installs PWMscan and places its binaries in the in the `bin` folder. -* The script [`scan_sequence.py`](https://github.com/wassermanlab/JASPAR-UCSC-tracks/blob/master/scan_sequence.py) takes as its input the `profiles` folder and a nucleotide sequence in [FASTA format](https://en.wikipedia.org/wiki/FASTA_format)
(*e.g.* a genome), and outputs TFBS predictions +* The script [`scan-sequence.py`](https://github.com/wassermanlab/JASPAR-UCSC-tracks/blob/master/scan_sequence.py) takes as its input the `profiles` folder and a nucleotide sequence in [FASTA format](https://en.wikipedia.org/wiki/FASTA_format)
(*e.g.* a genome), and outputs TFBS predictions * The script [`scans2bigBed`](https://github.com/wassermanlab/JASPAR-UCSC-tracks/blob/master/scans2bigBed) creates a [bigBed track file](https://genome.ucsc.edu/goldenPath/help/bigBed.html) from TFBS predictions The original scripts used for the publication of [JASPAR 2018](https://doi.org/10.1093/nar/gkx1126) have been placed in the folder [`version-1.0`](https://github.com/wassermanlab/JASPAR-UCSC-tracks/tree/master/version-1.0). @@ -26,26 +26,26 @@ To install PWMScan, execute the script [`install-pwmscan.sh`](https://github.com The remaining dependencies can be installed through the [conda](https://docs.conda.io/en/latest/) package manager: ``` -conda env create -f ./environment.yml +conda env create -f ./conda/environment.yml ``` ## Availability -Genomic tracks and TFBS predictions for human and six other model organisms are available online: -* [http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2020/](http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2020/) +Genomic tracks and TFBS predictions for human and **seven** other model organisms, covering **11** genome assemblies, are available online: +* [http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/](http://expdata.cmmt.ubc.ca/JASPAR/downloads/UCSC_tracks/2022/) ## Usage To illustrate how the genomic tracks are generated, we provide an example for the [baker's yeast genome](https://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2/): * Download the genome sequence and chromosome sizes (automated in this [script](https://github.com/wassermanlab/JASPAR-UCSC-tracks/blob/master/genomes/sacCer3/sacCer3.sh)) * Scan the genome sequence using [**all** fungi profiles from the JASPAR CORE](http://jaspar.genereg.net/search?q=&collection=CORE&tax_group=fungi) ``` -./scan_sequence.py --fasta-file ./genomes/sacCer3/sacCer3.fa --profiles-dir ./profiles/ \ +./scan-sequence.py --fasta-file ./genomes/sacCer3/sacCer3.fa --profiles-dir ./profiles/ \ --output-dir ./tracks/sacCer3/ --threads 4 --latest --taxon fungi ``` For this example, the scanning step should take no longer than a minute. For human and other similar genomes, this step is usually finished within a few hours (the final amount of time will depend on the number of `--threads` specified). * Create the genomic track ``` -./scans2bigBed -c ./genomes/sacCer3/sacCer3.chrom.sizes -i ./tracks/sacCer3/ -o ./tracks/sacCer3.bb -t 4 +./scans2bigBed -c ./genomes/sacCer3/sacCer3.fa.sizes -i ./tracks/sacCer3/ -o ./tracks/sacCer3.bb -t 4 ``` TFBS predictions from the previous step are merged into a [bigBed track file](https://genome.ucsc.edu/goldenPath/help/bigBed.html). In column five, we use as scores the p-values from PWMScan (scaled between 0-1000, where 0 corresponds to p-value = 1 and 1000 to p-value ≤ 10-10). This allows for comparison of prediction confidence across TFBSs. Again, for this example, this step should be completed within a few minutes, while for larger genomes it can take a few hours. -**Important note:** both disk space and memory requirements for large genomes (*i.e.* danRer11, hg19, hg38 and mm10) are substantial. In these cases, we highly recommend allocating at least 1Tb of disk space and 512Gb of ram. \ No newline at end of file +**Important note:** disk space requirements for large genomes (*i.e.* danRer11, hg19, hg38, mm10, and mm39) are substantial. In these cases, we highly recommend allocating at least 1Tb of disk space. \ No newline at end of file diff --git a/environment.yml b/conda/environment.yml old mode 100644 new mode 100755 similarity index 95% rename from environment.yml rename to conda/environment.yml index 428f515..b5dca43 --- a/environment.yml +++ b/conda/environment.yml @@ -14,6 +14,7 @@ dependencies: - pip=19.2.2 - pyfaidx=0.5.5.2 - python=3.7.3 + - seaborn=0.11.2 - setuptools=41.0.1 - tqdm=4.35.0 - ucsc-bedtobigbed diff --git a/genomes/get-genomes.sh b/genomes/get-genomes.sh index 037ea12..69ada76 100755 --- a/genomes/get-genomes.sh +++ b/genomes/get-genomes.sh @@ -6,7 +6,7 @@ if ! [ -f araTha1/araTha1.fa.sizes ]; then wget https://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/araTha1/araTha1.2bit twoBitToFa araTha1.2bit araTha1.fa faidx -x araTha1.fa - faidx araTha1.fa -i chromsizes > araTha1.chrom.sizes + faidx araTha1.fa -i chromsizes > araTha1.fa.sizes rm araTha1.2bit chr*.fa cd .. fi diff --git a/profiles/fungi/MA0265.1.pwm b/profiles/fungi/MA0265.1.pwm index e69de29..51dd454 100644 --- a/profiles/fungi/MA0265.1.pwm +++ b/profiles/fungi/MA0265.1.pwm @@ -0,0 +1,16 @@ + -103 66 -208 76 + -346 188 -346 -297 + -345 -345 190 -345 + -345 -345 -345 190 + 66 -50 -17 -29 + -17 -5 5 15 + 59 -57 15 -50 + 41 -42 -29 15 + 63 -23 -5 -65 + 69 -343 114 -343 + -94 -1 -127 105 + -346 -346 160 -36 + 178 -139 -346 -346 + -346 79 -126 82 + 52 -17 -42 -11 + 41 -42 -74 41 diff --git a/profiles/fungi/MA0265.2.pwm b/profiles/fungi/MA0265.2.pwm index e69de29..5d77443 100644 --- a/profiles/fungi/MA0265.2.pwm +++ b/profiles/fungi/MA0265.2.pwm @@ -0,0 +1,20 @@ + 20 -56 -45 53 + -4 -30 -57 62 + -8 -65 -78 87 + -59 -54 -288 133 + -346 193 -418 -444 + -361 -444 192 -346 + -346 -444 -378 192 + 79 -65 -16 -43 + -28 -22 -67 76 + 106 -137 -54 -25 + 52 -107 -69 56 + 140 -107 -92 -151 + 23 -418 143 -378 + -361 -128 -333 177 + -418 -397 193 -361 + 192 -378 -418 -361 + -378 64 -247 113 + 107 -97 -63 -41 + -1 -20 -43 48 + 39 -85 -26 39 diff --git a/profiles/fungi/MA0266.1.pwm b/profiles/fungi/MA0266.1.pwm index e69de29..a3a00fb 100644 --- a/profiles/fungi/MA0266.1.pwm +++ b/profiles/fungi/MA0266.1.pwm @@ -0,0 +1,7 @@ + -42 59 0 -42 + -126 -126 -261 158 + -346 190 -346 -346 + -346 -346 -346 190 + 190 -346 -346 -346 + -346 -346 190 -346 + 181 -262 -262 -262 diff --git a/profiles/fungi/MA0267.1.pwm b/profiles/fungi/MA0267.1.pwm index 9897d6f..bdb5eb9 100644 --- a/profiles/fungi/MA0267.1.pwm +++ b/profiles/fungi/MA0267.1.pwm @@ -1,7 +1,7 @@ - 86 18 -24 -231 - -464 188 -206 -464 - -10000 200 -10000 -10000 - 185 -132 -10000 -10000 - -10000 -10000 200 -10000 - -10000 200 -10000 -10000 - 97 -32 -56 -84 + 80 16 -21 -186 + -297 178 -169 -297 + -346 190 -346 -346 + 175 -114 -346 -346 + -346 -346 190 -346 + -346 190 -346 -346 + 91 -29 -50 -74 diff --git a/profiles/fungi/MA0268.1.pwm b/profiles/fungi/MA0268.1.pwm index d96b472..50a03c6 100644 --- a/profiles/fungi/MA0268.1.pwm +++ b/profiles/fungi/MA0268.1.pwm @@ -1,7 +1,7 @@ - 71 -6 -94 -18 - -10000 200 -10000 -10000 - -10000 177 -10000 -74 - -10000 200 -10000 -10000 - -10000 200 -10000 -10000 - 136 -206 -32 -132 - 44 103 -206 -147 + 66 -5 -83 -17 + -346 190 -346 -346 + -346 167 -346 -65 + -346 190 -346 -346 + -346 190 -346 -346 + 127 -169 -29 -114 + 41 96 -169 -126 diff --git a/profiles/fungi/MA0269.1.pwm b/profiles/fungi/MA0269.1.pwm index e69de29..82cd189 100644 --- a/profiles/fungi/MA0269.1.pwm +++ b/profiles/fungi/MA0269.1.pwm @@ -0,0 +1,21 @@ + -118 -27 -11 85 + -66 0 -18 57 + 52 -33 -17 -19 + -46 65 -16 -31 + 75 -11 -67 -40 + -84 -158 -78 134 + 149 -297 -273 -14 + -75 -273 20 108 + -262 -223 -246 178 + -62 -385 167 -343 + -384 192 -377 -384 + 191 -393 -349 -356 + -402 193 -393 -385 + -297 190 -470 -343 + -326 154 -362 -14 + -44 4 96 -182 + 8 1 -5 -5 + 20 -66 -43 57 + 14 -45 -176 90 + -97 -14 50 22 + -67 -8 86 -71 diff --git a/profiles/fungi/MA0270.1.pwm b/profiles/fungi/MA0270.1.pwm index e69de29..2794b3d 100644 --- a/profiles/fungi/MA0270.1.pwm +++ b/profiles/fungi/MA0270.1.pwm @@ -0,0 +1,8 @@ + -139 79 10 -29 + 140 -346 24 -346 + -346 190 -346 -346 + 190 -346 -346 -346 + -346 190 -346 -346 + -346 190 -346 -346 + -346 190 -346 -346 + -124 71 11 -21 diff --git a/profiles/fungi/MA0271.1.pwm b/profiles/fungi/MA0271.1.pwm index e69de29..180410e 100644 --- a/profiles/fungi/MA0271.1.pwm +++ b/profiles/fungi/MA0271.1.pwm @@ -0,0 +1,6 @@ + 110 -351 -351 75 + -438 -438 195 -438 + 190 -353 -353 -353 + -438 195 -438 -438 + -12 -377 68 49 + -426 184 -426 -161 diff --git a/profiles/fungi/MA0272.1.pwm b/profiles/fungi/MA0272.1.pwm index da7665b..b7f2452 100644 --- a/profiles/fungi/MA0272.1.pwm +++ b/profiles/fungi/MA0272.1.pwm @@ -1,8 +1,8 @@ - 25 -204 75 -17 - -277 -10000 -336 191 - -169 -10000 188 -10000 - 200 -10000 -10000 -10000 - -10000 199 -10000 -609 - -537 -10000 -10000 199 - -10000 200 -10000 -10000 - 34 34 -354 46 + 24 -176 71 -16 + -221 -362 -255 182 + -153 -423 183 -423 + 191 -366 -366 -366 + -430 194 -430 -395 + -328 -363 -363 190 + -434 195 -434 -434 + 32 32 -271 43 diff --git a/profiles/fungi/MA0273.1.pwm b/profiles/fungi/MA0273.1.pwm index f04bf6a..258e6f3 100644 --- a/profiles/fungi/MA0273.1.pwm +++ b/profiles/fungi/MA0273.1.pwm @@ -1,21 +1,21 @@ - -129 -69 109 -25 - 40 -37 27 -52 - -99 -10 35 37 - 70 2 -30 -88 - 64 -37 -12 -42 - 31 -33 -89 51 - -159 -70 43 77 - -264 157 -306 -43 - -564 -11 -496 160 - -564 198 -796 -564 - -796 -350 196 -796 - -796 -564 199 -696 - -406 52 24 40 - 143 -596 -538 35 - 147 -188 -206 -46 - -125 -17 58 26 - 11 -107 -37 74 - 50 -25 -28 -12 - 4 -20 -49 47 - -8 -128 48 31 - 16 1 -55 26 + -123 -66 107 -24 + 39 -36 26 -50 + -94 -10 34 36 + 69 2 -29 -84 + 63 -36 -12 -41 + 30 -32 -85 50 + -150 -67 42 75 + -243 155 -277 -42 + -432 -11 -402 157 + -432 195 -485 -432 + -486 -311 193 -486 + -485 -432 195 -470 + -349 51 23 39 + 140 -444 -421 34 + 144 -176 -192 -45 + -119 -16 56 25 + 10 -102 -36 73 + 49 -24 -27 -11 + 4 -20 -47 46 + -8 -121 47 30 + 15 1 -53 25 diff --git a/profiles/fungi/MA0274.1.pwm b/profiles/fungi/MA0274.1.pwm index e69de29..e981237 100644 --- a/profiles/fungi/MA0274.1.pwm +++ b/profiles/fungi/MA0274.1.pwm @@ -0,0 +1,8 @@ + 191 -368 -368 -368 + -97 55 -73 51 + -59 55 -389 85 + -369 -369 -369 191 + 30 -420 141 -420 + 144 -14 -167 -386 + 162 -376 -49 -284 + -163 -372 -70 158 diff --git a/profiles/fungi/MA0275.1.pwm b/profiles/fungi/MA0275.1.pwm index e69de29..aa8b4d6 100644 --- a/profiles/fungi/MA0275.1.pwm +++ b/profiles/fungi/MA0275.1.pwm @@ -0,0 +1,6 @@ + -346 151 -346 -5 + -346 190 -346 -346 + -346 -346 190 -346 + -346 -346 190 -346 + 145 -101 -56 -345 + 101 -346 -346 85 diff --git 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+ 49 24 -50 -50 diff --git a/profiles/fungi/MA0435.1.pwm b/profiles/fungi/MA0435.1.pwm index e69de29..b34f740 100644 --- a/profiles/fungi/MA0435.1.pwm +++ b/profiles/fungi/MA0435.1.pwm @@ -0,0 +1,20 @@ + -163 -4 -76 108 + -63 -28 44 23 + 60 -53 -51 13 + 58 -5 -83 -3 + 13 -215 87 -23 + 112 -54 -5 -252 + -343 155 -337 -19 + -444 -444 195 -470 + -470 -343 -456 194 + 194 -411 -456 -432 + 179 -485 -114 -444 + 195 -470 -444 -421 + -432 -470 -470 195 + -443 195 -485 -393 + 37 118 -203 -234 + -145 -17 -160 127 + 5 -38 -34 49 + 83 -113 -51 9 + 17 65 -188 6 + 41 39 -176 9 diff --git a/profiles/fungi/MA0436.1.pwm b/profiles/fungi/MA0436.1.pwm index 78ed5ad..0130835 100644 --- a/profiles/fungi/MA0436.1.pwm +++ b/profiles/fungi/MA0436.1.pwm @@ -1,7 +1,7 @@ - -75 139 -10000 -34 - -10000 200 -10000 -10000 - -10000 200 -10000 -10000 - -10000 200 -10000 -10000 - 200 -10000 -10000 -10000 - -10000 200 -10000 -10000 - -13 4 43 -49 + -67 130 -347 -30 + -346 190 -346 -346 + -346 190 -346 -346 + -346 190 -346 -346 + 190 -346 -346 -346 + -346 190 -346 -346 + -12 4 40 -44 diff --git a/profiles/fungi/MA0437.1.pwm b/profiles/fungi/MA0437.1.pwm index e69de29..4be5b3c 100644 --- a/profiles/fungi/MA0437.1.pwm +++ b/profiles/fungi/MA0437.1.pwm @@ -0,0 +1,9 @@ + 121 -346 5 -83 + 33 -346 -346 136 + -50 -346 -346 164 + -4 -207 -260 139 + -50 76 -103 15 + -92 33 -153 91 + -346 180 -153 -346 + -346 190 -346 -346 + -233 -347 178 -189 diff --git a/profiles/fungi/MA0438.1.pwm b/profiles/fungi/MA0438.1.pwm index e69de29..57da1bd 100644 --- a/profiles/fungi/MA0438.1.pwm +++ b/profiles/fungi/MA0438.1.pwm @@ -0,0 +1,8 @@ + 96 -65 -11 -103 + -261 181 -261 -261 + -346 -346 190 -346 + -346 -346 190 -346 + 190 -346 -346 -346 + 118 -92 -57 -92 + 180 -297 -297 -187 + -92 -139 -208 151 diff --git a/profiles/fungi/MA0439.1.pwm b/profiles/fungi/MA0439.1.pwm index e69de29..2012753 100644 --- a/profiles/fungi/MA0439.1.pwm +++ b/profiles/fungi/MA0439.1.pwm @@ -0,0 +1,11 @@ + -23 69 -17 -65 + -56 -56 -112 113 + -17 -139 -208 132 + 173 -297 -261 -139 + -36 -126 -208 136 + 14 36 -140 31 + -209 -18 -155 135 + -346 190 -346 -346 + -346 190 -346 -346 + -232 -346 183 -261 + -169 66 -74 59 diff --git a/profiles/fungi/MA0440.1.pwm b/profiles/fungi/MA0440.1.pwm index e69de29..608471e 100644 --- a/profiles/fungi/MA0440.1.pwm +++ b/profiles/fungi/MA0440.1.pwm @@ -0,0 +1,15 @@ + 191 -365 -365 -365 + -433 195 -433 -433 + -433 195 -433 -433 + -390 88 -390 102 + -365 -365 -365 191 + 104 58 -138 -388 + 191 -365 -365 -365 + 124 -133 22 -383 + -433 -433 195 -433 + -433 -433 195 -433 + -365 -365 -365 191 + -121 82 -49 12 + 130 -377 28 -198 + -187 -117 -367 168 + -38 -415 164 -415 diff --git a/profiles/fungi/MA0441.1.pwm b/profiles/fungi/MA0441.1.pwm index de209af..3ea25c7 100644 --- a/profiles/fungi/MA0441.1.pwm +++ b/profiles/fungi/MA0441.1.pwm @@ -1,9 +1,9 @@ - -74 -74 -74 114 - 32 -117 -117 89 - -10000 200 -10000 -10000 - -10000 200 -10000 -10000 - -10000 200 -10000 -10000 - -10000 200 -10000 -10000 - -41 -266 110 -7 - -232 177 -232 -232 - 100 -132 -132 26 + -65 -65 -65 106 + 30 -101 -101 83 + -346 190 -346 -346 + -346 190 -346 -346 + -346 190 -346 -346 + -346 190 -346 -346 + -37 -209 103 -7 + -187 167 -187 -187 + 93 -114 -114 24 diff --git a/profiles/fungi/MA0929.1.pwm b/profiles/fungi/MA0929.1.pwm index e69de29..a393606 100644 --- a/profiles/fungi/MA0929.1.pwm +++ b/profiles/fungi/MA0929.1.pwm @@ -0,0 +1,12 @@ + 37 -15 -15 -15 + -15 -15 -15 37 + 35 -93 -12 36 + -71 -204 154 -204 + -112 -503 -503 180 + 165 -124 -503 -131 + 197 -503 -503 -503 + 181 -503 -503 -124 + -293 103 -293 76 + 185 -293 -293 -293 + 79 -18 -97 -18 + 71 -34 -34 -34 diff --git a/profiles/fungi/MA1431.1.pwm b/profiles/fungi/MA1431.1.pwm index e69de29..2d6aa02 100644 --- a/profiles/fungi/MA1431.1.pwm +++ b/profiles/fungi/MA1431.1.pwm @@ -0,0 +1,10 @@ + 4 -59 -36 61 + 63 -39 -28 -21 + -311 188 -362 -292 + -411 178 -444 -115 + -503 196 -470 -486 + -421 195 -503 -470 + -25 -243 106 -17 + -201 181 -470 -231 + 60 -20 -89 11 + -57 59 -79 32 diff --git a/profiles/fungi/MA1432.1.pwm b/profiles/fungi/MA1432.1.pwm index e69de29..651cf50 100644 --- a/profiles/fungi/MA1432.1.pwm +++ b/profiles/fungi/MA1432.1.pwm @@ -0,0 +1,8 @@ + -402 195 -503 -432 + -503 157 -503 -5 + -182 177 -246 -306 + -503 197 -503 -503 + 98 -503 95 -377 + -81 58 2 -11 + 18 -11 -3 -5 + 16 25 6 -63 diff --git a/profiles/fungi/MA1433.1.pwm b/profiles/fungi/MA1433.1.pwm index 2acb42e..119206c 100644 --- a/profiles/fungi/MA1433.1.pwm +++ b/profiles/fungi/MA1433.1.pwm @@ -1,8 +1,8 @@ - -7 82 -11 -150 - -564 196 -564 -388 - -10000 190 -10000 -194 - -10000 198 -10000 -450 - -564 183 -10000 -119 - -350 -396 -450 193 - -2 -10000 84 29 - 113 -257 -76 7 + -7 80 -11 -143 + -432 193 -432 -337 + -503 187 -503 -182 + -503 195 -503 -377 + -432 179 -503 -114 + -311 -343 -377 189 + -2 -503 82 28 + 111 -237 -73 7 diff --git a/profiles/fungi/MA1434.1.pwm b/profiles/fungi/MA1434.1.pwm index 4374309..6a10376 100644 --- a/profiles/fungi/MA1434.1.pwm +++ b/profiles/fungi/MA1434.1.pwm @@ -1,7 +1,7 @@ - 91 -10000 -10000 109 - 200 -10000 -10000 -10000 - -321 196 -10000 -10000 - -10000 200 -10000 -10000 - -10000 200 -10000 -10000 - 196 -321 -10000 -10000 - -438 57 11 47 + 89 -503 -503 106 + 197 -503 -503 -503 + -288 193 -503 -503 + -503 197 -503 -503 + -503 197 -503 -503 + 193 -288 -503 -503 + -369 56 11 46 diff --git a/profiles/fungi/MA1435.1.pwm b/profiles/fungi/MA1435.1.pwm index e69de29..bbf7455 100644 --- a/profiles/fungi/MA1435.1.pwm +++ b/profiles/fungi/MA1435.1.pwm @@ -0,0 +1,10 @@ + -24 30 -28 13 + -377 -172 -377 183 + -503 197 -503 -503 + -503 179 -503 -107 + -503 -107 179 -503 + -503 197 -503 -503 + -503 -503 197 -503 + -503 -503 197 -503 + 62 -45 35 -113 + -7 -7 18 -7 diff --git a/profiles/fungi/MA1436.1.pwm b/profiles/fungi/MA1436.1.pwm index a0dbcff..ef5a514 100644 --- a/profiles/fungi/MA1436.1.pwm +++ b/profiles/fungi/MA1436.1.pwm @@ -1,8 +1,8 @@ - 0 114 -232 -74 - -10000 200 -10000 -10000 - 190 -196 -10000 -10000 - -10000 200 -10000 -10000 - -10000 -10000 200 -10000 - -10000 -10000 -10000 200 - -10000 -10000 200 -10000 - 12 86 -247 -14 + 0 111 -215 -71 + -503 197 -503 -503 + 187 -184 -503 -503 + -503 197 -503 -503 + -503 -503 197 -503 + -503 -503 -503 197 + -503 -503 197 -503 + 12 84 -228 -13 diff --git a/profiles/fungi/MA1437.1.pwm b/profiles/fungi/MA1437.1.pwm index 5c5ab0b..756d954 100644 --- a/profiles/fungi/MA1437.1.pwm +++ b/profiles/fungi/MA1437.1.pwm @@ -1,8 +1,8 @@ - 48 85 -132 -132 - -32 168 -10000 -10000 - -10000 -10000 200 -10000 - 200 -10000 -10000 -10000 - -10000 -10000 -10000 200 - -10000 200 -10000 -10000 - -10000 -10000 169 -37 - 132 -26 -159 -159 + 47 83 -125 -125 + -31 165 -503 -503 + -503 -503 197 -503 + 197 -503 -503 -503 + -503 -503 -503 197 + -503 197 -503 -503 + -503 -503 166 -36 + 130 -25 -150 -150 diff --git a/profiles/get-profiles.py b/profiles/get-profiles.py index fcb4d00..c8d4dda 100755 --- a/profiles/get-profiles.py +++ b/profiles/get-profiles.py @@ -39,12 +39,12 @@ def main(): # Get profiles get_profiles(args.o) - # Get profile names - get_profile_names(args.o) - - # To PWM + # Convert profiles to PWMs jaspar_to_pwm(args.o) + # Get profile names + get_names(args.o) + def get_profiles(output_dir="./"): """ For each taxon, this function downloads all profiles from the JASPAR CORE @@ -88,7 +88,42 @@ def get_profiles(output_dir="./"): # Return to original directory os.chdir(cwd) -def get_profile_names(output_dir="./"): +def jaspar_to_pwm(output_dir="./"): + """ + For each taxon, this function reformats all profiles from JASPAR to + PWMScan format. + """ + + # Initialize + # perl_script = os.path.join(os.path.dirname(os.path.realpath(__file__)), + # "jasparconvert.pl") + + # For each taxon... + for taxon in taxons: + + # Initialize + taxon_dir = os.path.join(os.path.abspath(output_dir), taxon) + + # For each profile... + for f in os.listdir(taxon_dir): + + # Skip non-JASPAR profiles + if not f.endswith(".jaspar"): + continue + + # JASPAR to PWMScan + with open(os.path.join(taxon_dir, f)) as handle: + m = motifs.read(handle, "jaspar") + m.pseudocounts = motifs.jaspar.calculate_pseudocounts(m) + pwm = list(map(list, zip(*[m.pssm[nt] for nt in "ACGT"]))) + pwm_file = os.path.join(taxon_dir, f"{f[:8]}.pwm") + if not os.path.exists(pwm_file): + with open(pwm_file, "w") as handle: + for i in pwm: + s = " ".join(["{:7d}".format(round(j*100)) for j in i]) + handle.write("%s\n" % s) + +def get_names(output_dir="./"): """ This function extracts the name of each JASPAR profile and saves them in a JSON file. @@ -127,65 +162,6 @@ def get_profile_names(output_dir="./"): with open(json_file, "w") as handle: json.dump(names, handle, sort_keys=True, indent=4) -def jaspar_to_pwm(output_dir="./"): - """ - For each taxon, this function reformats all profiles from JASPAR to - PWMScan format. - """ - - # Initialize - perl_script = os.path.join(os.path.dirname(os.path.realpath(__file__)), - "jasparconvert.pl") - - # For each taxon... - for taxon in taxons: - - # Initialize - taxon_dir = os.path.join(os.path.abspath(output_dir), taxon) - - # For each profile... - for f in os.listdir(taxon_dir): - - # Skip non-JASPAR profiles - if not f.endswith(".jaspar"): - continue - - # JASPAR to PWMScan - matrix_file = os.path.join(taxon_dir, f) - pwm_file = os.path.join(taxon_dir, f"{f[:8]}.pwm") - options = f"-noheader -o {pwm_file} -w l" - cmd = f"{perl_script} {options} {matrix_file}" - _ = sp.run([cmd], stdout=sp.DEVNULL, stderr=sp.DEVNULL, shell=True) - -def jaspar_to_pwm(output_dir="./"): - """ - For each taxon, this function reformats all profiles from JASPAR to - PWMScan format. - """ - - # Initialize - perl_script = os.path.join(os.path.dirname(os.path.realpath(__file__)), - "jasparconvert.pl") - taxons = ["fungi", "insects", "nematodes", "plants", "urochordates", - "vertebrates"] - - # For each taxon... - for taxon in taxons: - - # Initialize - taxon_dir = os.path.join(os.path.abspath(output_dir), taxon) - - # For each profile... - for f in os.listdir(taxon_dir): - - # JASPAR to PWMScan - matrix_file = os.path.join(taxon_dir, f) - pwm_file = os.path.join(taxon_dir, f"{f[:8]}.pwm") - if not os.path.exists(pwm_file): - options = f"-noheader -o {pwm_file} -w l" - cmd = f"{perl_script} {options} {matrix_file}" - sp.run([cmd], stdout=sp.DEVNULL, stderr=sp.DEVNULL, shell=True) - #-------------# # Main # #-------------# diff --git a/profiles/insects/MA0010.1.pwm b/profiles/insects/MA0010.1.pwm index e69de29..b6313e6 100644 --- a/profiles/insects/MA0010.1.pwm +++ b/profiles/insects/MA0010.1.pwm @@ -0,0 +1,14 @@ + 32 -78 66 -78 + -78 -78 -78 117 + 94 -13 -78 -78 + 137 -200 -78 -78 + 32 -200 -200 117 + 117 -200 -200 32 + 66 -78 66 -200 + 137 -200 -78 -78 + -78 154 -200 -200 + 170 -200 -200 -200 + 154 -200 -78 -200 + 94 -200 32 -78 + 66 -200 -200 94 + -13 32 -13 -13 diff --git a/profiles/insects/MA0011.1.pwm b/profiles/insects/MA0011.1.pwm index eeaf929..4362572 100644 --- a/profiles/insects/MA0011.1.pwm +++ b/profiles/insects/MA0011.1.pwm @@ -1,8 +1,8 @@ - 0 -158 -158 122 - 74 -58 -158 42 - -10000 174 -10000 -58 - -10000 -158 -10000 187 - 200 -10000 -10000 -10000 - -158 -158 -58 142 - -58 -10000 -158 158 - -158 -58 -158 142 + 0 -105 -105 102 + 60 -43 -105 33 + -216 149 -216 -43 + -216 -105 -216 162 + 173 -216 -216 -216 + -105 -105 -43 120 + -43 -216 -105 135 + -105 -43 -105 120 diff --git a/profiles/insects/MA0012.1.pwm b/profiles/insects/MA0012.1.pwm index c04e442..825e665 100644 --- a/profiles/insects/MA0012.1.pwm +++ b/profiles/insects/MA0012.1.pwm @@ -1,11 +1,11 @@ - 0 -158 -158 122 - 158 -58 -158 -10000 - 174 -10000 -10000 -58 - 200 -10000 -10000 -10000 - -10000 174 -158 -158 - 42 -10000 -10000 142 - 174 -10000 -10000 -58 - 100 -10000 42 -58 - 100 -158 -58 0 - 42 0 -58 0 - -58 0 74 -58 + 0 -105 -105 102 + 135 -43 -105 -216 + 149 -216 -216 -43 + 173 -216 -216 -216 + -216 149 -105 -105 + 33 -216 -216 120 + 149 -216 -216 -43 + 83 -216 33 -43 + 83 -105 -43 0 + 33 0 -43 0 + -43 0 60 -43 diff --git a/profiles/insects/MA0013.1.pwm b/profiles/insects/MA0013.1.pwm index ac0cbbd..3919e5a 100644 --- a/profiles/insects/MA0013.1.pwm +++ b/profiles/insects/MA0013.1.pwm @@ -1,11 +1,11 @@ - -58 -58 -10000 142 - 142 -10000 -10000 42 - 42 -10000 142 -10000 - -58 -10000 -10000 174 - 174 -10000 -58 -10000 - 200 -10000 -10000 -10000 - 174 -10000 -58 -10000 - -58 100 -58 -58 - 100 -10000 -58 42 - 174 -10000 -10000 -58 - 100 -58 -10000 42 + -39 -39 -179 113 + 113 -179 -179 31 + 31 -179 113 -179 + -39 -179 -179 141 + 141 -179 -39 -179 + 165 -179 -179 -179 + 141 -179 -39 -179 + -39 77 -39 -39 + 77 -179 -39 31 + 141 -179 -179 -39 + 77 -39 -179 31 diff --git a/profiles/insects/MA0015.1.pwm b/profiles/insects/MA0015.1.pwm index e69de29..9f14de5 100644 --- a/profiles/insects/MA0015.1.pwm +++ b/profiles/insects/MA0015.1.pwm @@ -0,0 +1,10 @@ + 29 -55 93 -239 + -278 -239 -278 181 + 178 -239 -183 -331 + -331 -98 -183 164 + 185 -239 -331 -331 + -278 -183 -278 178 + 96 -239 78 -278 + -239 -98 -278 166 + 131 -209 0 -183 + -64 49 -37 24 diff --git a/profiles/insects/MA0016.1.pwm b/profiles/insects/MA0016.1.pwm index 0a5a6c4..4e9e6d6 100644 --- a/profiles/insects/MA0016.1.pwm +++ b/profiles/insects/MA0016.1.pwm @@ -1,10 +1,10 @@ - -10000 -325 196 -10000 - -325 -10000 192 -325 - -10000 -10000 200 -10000 - -10000 -10000 200 -10000 - -10000 -10000 -10000 200 - -10000 192 -325 -325 - 188 -10000 -166 -10000 - -93 140 -166 -93 - -93 -25 121 -166 - -66 7 75 -66 + -284 -212 180 -284 + -212 -284 177 -212 + -284 -284 184 -284 + -284 -284 184 -284 + -284 -284 -284 184 + -284 177 -212 -212 + 173 -284 -128 -284 + -76 127 -128 -76 + -76 -21 109 -128 + -55 6 67 -55 diff --git a/profiles/insects/MA0022.1.pwm b/profiles/insects/MA0022.1.pwm index 25d2b63..2986d42 100644 --- a/profiles/insects/MA0022.1.pwm +++ b/profiles/insects/MA0022.1.pwm @@ -1,12 +1,12 @@ - -10000 62 88 -70 - -10000 -10000 188 -170 - -10000 -170 176 -170 - -10000 -10000 162 -12 - -170 -170 -12 130 - -170 -10000 -70 162 - -170 -10000 -10000 188 - -10000 -10000 -10000 200 - -10000 -12 -10000 162 - -170 147 -10000 -12 - -170 147 -170 -70 - -12 62 62 -10000 + -220 51 73 -52 + -220 -220 164 -113 + -220 -113 152 -113 + -220 -220 139 -9 + -113 -113 -9 110 + -113 -220 -52 139 + -113 -220 -220 164 + -220 -220 -220 174 + -220 -9 -220 139 + -113 125 -220 -9 + -113 125 -113 -52 + -9 51 51 -220 diff --git a/profiles/insects/MA0023.1.pwm b/profiles/insects/MA0023.1.pwm index 9e62850..c22c543 100644 --- a/profiles/insects/MA0023.1.pwm +++ b/profiles/insects/MA0023.1.pwm @@ -1,10 +1,10 @@ - -10000 -117 164 -117 - -10000 -10000 164 -17 - -10000 -10000 200 -10000 - -10000 -10000 183 -117 - 83 -117 -10000 83 - -17 -117 -10000 142 - -10000 -10000 -10000 200 - -10000 -117 -10000 183 - -10000 200 -10000 -10000 - -117 183 -10000 -10000 + -200 -78 137 -78 + -200 -200 137 -13 + -200 -200 170 -200 + -200 -200 154 -78 + 66 -78 -200 66 + -13 -78 -200 117 + -200 -200 -200 170 + -200 -78 -200 154 + -200 170 -200 -200 + -78 154 -200 -200 diff --git a/profiles/insects/MA0026.1.pwm b/profiles/insects/MA0026.1.pwm index f092fdc..a457831 100644 --- a/profiles/insects/MA0026.1.pwm +++ b/profiles/insects/MA0026.1.pwm @@ -1,7 +1,7 @@ - -109 150 -109 -209 - 23 150 -10000 -10000 - -10000 -10000 200 -10000 - -10000 -10000 200 -10000 - 200 -10000 -10000 -10000 - 200 -10000 -10000 -10000 - 23 -209 123 -209 + -80 130 -80 -138 + 19 130 -236 -236 + -236 -236 177 -236 + -236 -236 177 -236 + 177 -236 -236 -236 + 177 -236 -236 -236 + 19 -138 106 -138 diff --git a/profiles/insects/MA0049.1.pwm b/profiles/insects/MA0049.1.pwm index e69de29..ff96727 100644 --- a/profiles/insects/MA0049.1.pwm +++ b/profiles/insects/MA0049.1.pwm @@ -0,0 +1,10 @@ + -132 26 85 -74 + 49 85 -74 -232 + 100 -32 0 -232 + 0 -32 -132 85 + 149 -132 -232 -74 + 177 -232 -232 -232 + 177 -232 -232 -232 + 158 -232 -74 -232 + 168 -132 -232 -232 + 100 -74 -74 -32 diff --git a/profiles/insects/MA0085.1.pwm b/profiles/insects/MA0085.1.pwm index e69de29..bc09c51 100644 --- 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-94 -102 138 + -136 120 -145 -8 + -118 -106 -180 148 + -114 -34 109 -68 + -291 -234 -323 183 + -323 -323 -278 186 + 170 -81 -388 -323 + -244 182 -388 -225 + -278 -217 -278 180 + -363 -388 -388 192 + -323 -388 188 -291 + -341 190 -388 -323 + 178 -208 -306 -225 + -266 -244 180 -244 + -306 189 -363 -341 + -291 149 -388 0 + 76 -25 -29 -62 + 168 -225 -151 -208 + 161 -201 -122 -193 + 87 -49 -136 10 + -34 -180 133 -131 diff --git a/profiles/vertebrates/MA1984.1.pwm b/profiles/vertebrates/MA1984.1.pwm index e69de29..561ce25 100644 --- a/profiles/vertebrates/MA1984.1.pwm +++ b/profiles/vertebrates/MA1984.1.pwm @@ -0,0 +1,12 @@ + -362 -180 14 134 + -362 -180 -103 165 + 174 -362 -180 -180 + 108 -15 -180 -53 + 14 -362 145 -362 + 165 -362 -53 -362 + -362 -362 183 -180 + -362 191 -362 -362 + -53 -103 -362 145 + -362 191 -362 -362 + 174 -103 -362 -362 + 14 -15 78 -180 diff --git a/profiles/vertebrates/MA1985.1.pwm b/profiles/vertebrates/MA1985.1.pwm index cb59f19..d6cd1ad 100644 --- a/profiles/vertebrates/MA1985.1.pwm +++ b/profiles/vertebrates/MA1985.1.pwm @@ -1,15 +1,15 @@ - -79 -100 123 -79 - -332 -564 195 -564 - -332 -564 195 -564 - -100 -43 123 -125 - -247 132 -564 38 - -564 -564 198 -564 - 189 -194 -564 -564 - -564 96 -564 101 - -564 -564 198 -564 - 150 -29 -332 -194 - -564 182 -564 -125 - -332 169 -156 -156 - 96 -194 62 -194 - -125 96 -15 -43 - -194 -125 -125 154 + -75 -96 120 -75 + -297 -432 192 -432 + -297 -432 192 -432 + -96 -42 120 -119 + -229 130 -432 37 + -432 -432 194 -432 + 185 -182 -432 -432 + -432 93 -432 99 + -432 -432 194 -432 + 147 -28 -297 -182 + -432 179 -432 -119 + -297 166 -147 -147 + 93 -182 61 -182 + -119 93 -15 -42 + -182 -119 -119 151 diff --git a/profiles/vertebrates/MA1986.1.pwm b/profiles/vertebrates/MA1986.1.pwm index 3f7a249..e3d54e8 100644 --- a/profiles/vertebrates/MA1986.1.pwm +++ b/profiles/vertebrates/MA1986.1.pwm @@ -1,10 +1,10 @@ - -75 -25 64 1 - -94 -103 135 -117 - -10000 -490 199 -769 - -644 -939 199 -669 - -664 199 -858 -693 - -603 196 -348 -730 - -981 197 -393 -700 - 197 -10000 -368 -10000 - -166 90 46 -117 - -13 40 13 -57 + -74 -24 63 1 + -92 -102 134 -115 + -671 -455 198 -612 + -557 -650 198 -571 + -568 198 -636 -582 + -534 195 -334 -598 + -655 196 -375 -585 + 196 -671 -352 -671 + -163 89 46 -116 + -13 39 13 -56 diff --git a/profiles/vertebrates/MA1987.1.pwm b/profiles/vertebrates/MA1987.1.pwm index e69de29..022213e 100644 --- a/profiles/vertebrates/MA1987.1.pwm +++ b/profiles/vertebrates/MA1987.1.pwm @@ -0,0 +1,21 @@ + -289 -349 190 -456 + 188 -456 -213 -456 + -289 -289 188 -456 + 26 126 -146 -456 + 171 -349 -86 -349 + -213 102 2 -44 + -146 99 -74 8 + 81 -64 -36 -28 + 81 -99 -20 -20 + 77 -128 60 -146 + -165 -456 181 -289 + -349 -456 194 -456 + -349 -213 185 -349 + -44 -456 156 -188 + -113 -456 177 -349 + 77 -146 84 -289 + 144 -213 -74 -113 + 46 -64 14 -20 + 14 -74 31 8 + -5 -128 56 20 + -28 -36 65 -28 diff --git a/profiles/vertebrates/MA1988.1.pwm b/profiles/vertebrates/MA1988.1.pwm index e69de29..564a553 100644 --- a/profiles/vertebrates/MA1988.1.pwm +++ b/profiles/vertebrates/MA1988.1.pwm @@ -0,0 +1,11 @@ + 5 -54 21 17 + 69 -33 24 -130 + -442 -424 -505 195 + -308 -478 183 -179 + 196 -505 -470 -450 + -256 174 -159 -256 + -252 -461 -327 188 + -133 176 -444 -268 + 192 -423 -358 -386 + -73 -7 -6 57 + 22 6 -41 6 diff --git a/profiles/vertebrates/MA1989.1.pwm b/profiles/vertebrates/MA1989.1.pwm index e69de29..cae9094 100644 --- a/profiles/vertebrates/MA1989.1.pwm +++ b/profiles/vertebrates/MA1989.1.pwm @@ -0,0 +1,14 @@ + 33 -19 -11 -8 + 32 -12 -2 -25 + 131 -96 -141 -67 + 165 -207 -169 -171 + 186 -279 -255 -394 + -279 188 -362 -349 + -317 191 -442 -349 + 188 -334 -356 -287 + -250 185 -298 -344 + 185 -279 -295 -313 + 125 -148 -48 -87 + 7 -41 71 -83 + 29 0 -9 -26 + 28 2 -27 -8 diff --git a/profiles/vertebrates/MA1990.1.pwm b/profiles/vertebrates/MA1990.1.pwm index 8eaf1c7..baa1742 100644 --- a/profiles/vertebrates/MA1990.1.pwm +++ b/profiles/vertebrates/MA1990.1.pwm @@ -1,14 +1,14 @@ - 3 23 -9 -20 - 8 13 16 -44 - 109 -174 14 -107 - -315 -237 182 -263 - 164 -160 -101 -421 - -332 190 -351 -382 - -382 193 -376 -435 - 187 -378 -352 -240 - -472 194 -374 -399 - -84 169 -279 -388 - -271 183 -319 -252 - 173 -241 -200 -199 - -77 52 62 -118 - 12 -16 49 -70 + 3 22 -8 -20 + 8 13 15 -43 + 107 -169 14 -105 + -298 -228 180 -252 + 163 -155 -98 -386 + -313 189 -329 -355 + -355 191 -350 -397 + 185 -352 -331 -230 + -424 192 -348 -369 + -82 168 -266 -360 + -259 182 -301 -242 + 171 -232 -193 -192 + -75 52 61 -115 + 12 -16 48 -69 diff --git a/profiles/vertebrates/MA1991.1.pwm b/profiles/vertebrates/MA1991.1.pwm index e69de29..89bcee1 100644 --- a/profiles/vertebrates/MA1991.1.pwm +++ b/profiles/vertebrates/MA1991.1.pwm @@ -0,0 +1,14 @@ + -40 2 3 27 + -79 15 30 11 + -152 123 -59 -63 + -358 183 -275 -218 + -353 -305 -434 190 + -369 -242 -222 182 + -369 -402 -395 192 + -305 -134 170 -206 + 182 -287 -369 -197 + -150 -343 -301 178 + -177 112 27 -159 + -96 -55 -157 130 + -77 18 16 22 + -31 -3 16 13 diff --git a/profiles/vertebrates/MA1992.1.pwm b/profiles/vertebrates/MA1992.1.pwm index e69de29..8e1bc9f 100644 --- a/profiles/vertebrates/MA1992.1.pwm +++ b/profiles/vertebrates/MA1992.1.pwm @@ -0,0 +1,15 @@ + 33 -20 22 -50 + -6 21 29 -60 + 91 -75 9 -113 + -235 173 -145 -294 + 180 -211 -243 -346 + -459 -429 195 -438 + -352 -363 192 -420 + 190 -318 -331 -438 + 181 -389 -341 -158 + -146 -251 174 -318 + -130 -97 -135 143 + -119 -102 142 -137 + -32 -25 78 -65 + -24 0 54 -50 + -14 -21 35 -7 diff --git a/profiles/vertebrates/MA1993.1.pwm b/profiles/vertebrates/MA1993.1.pwm index e69de29..fa6d70e 100644 --- a/profiles/vertebrates/MA1993.1.pwm +++ b/profiles/vertebrates/MA1993.1.pwm @@ -0,0 +1,10 @@ + 29 -12 36 -82 + 29 38 26 -184 + -756 199 -687 -713 + 198 -520 -478 -787 + -768 -754 199 -750 + -750 199 -754 -768 + -787 -478 -520 198 + -713 -687 199 -756 + -184 26 38 29 + -82 36 -12 29 diff --git a/profiles/vertebrates/MA1994.1.pwm b/profiles/vertebrates/MA1994.1.pwm index e69de29..f3c8503 100644 --- a/profiles/vertebrates/MA1994.1.pwm +++ b/profiles/vertebrates/MA1994.1.pwm @@ -0,0 +1,13 @@ + 36 -39 4 -11 + 12 40 11 -97 + -367 187 -426 -216 + 192 -374 -452 -345 + -436 194 -477 -356 + -335 -440 -268 189 + -385 -290 -356 189 + -214 -257 180 -290 + 190 -390 -406 -284 + 102 -64 3 -171 + 36 45 -74 -40 + 11 -20 -39 36 + 1 5 -33 22 diff --git a/profiles/vertebrates/MA1995.1.pwm b/profiles/vertebrates/MA1995.1.pwm index 443d53e..e2884b8 100644 --- a/profiles/vertebrates/MA1995.1.pwm +++ b/profiles/vertebrates/MA1995.1.pwm @@ -1,11 +1,11 @@ - 19 2 0 -24 - 7 -3 7 -13 - -205 -219 -167 169 - -275 178 -195 -275 - -212 -268 183 -415 - -418 -440 -316 192 - -532 -361 194 -425 - 174 -185 -261 -213 - -247 170 -179 -186 - 12 -41 -53 55 - -19 17 15 -16 + 18 2 0 -24 + 7 -3 7 -13 + -201 -213 -164 168 + -266 177 -191 -267 + -207 -260 182 -392 + -394 -413 -304 191 + -483 -345 193 -400 + 173 -181 -253 -208 + -240 169 -175 -182 + 12 -40 -52 54 + -19 17 15 -16 diff --git a/profiles/vertebrates/MA1996.1.pwm b/profiles/vertebrates/MA1996.1.pwm index e69de29..d3dcfa6 100644 --- a/profiles/vertebrates/MA1996.1.pwm +++ b/profiles/vertebrates/MA1996.1.pwm @@ -0,0 +1,11 @@ + -25 28 -15 6 + 21 -10 -27 11 + 84 -73 32 -145 + 192 -340 -386 -421 + -434 -354 191 -340 + -430 -525 195 -415 + -474 -527 -513 197 + -373 191 -457 -295 + 193 -492 -310 -522 + -44 30 -1 6 + 14 -12 1 -5 diff --git a/profiles/vertebrates/MA1997.1.pwm b/profiles/vertebrates/MA1997.1.pwm index 7b7a8bb..a47418b 100644 --- a/profiles/vertebrates/MA1997.1.pwm +++ b/profiles/vertebrates/MA1997.1.pwm @@ -1,10 +1,10 @@ - 31 -3 11 -51 - 15 26 37 -133 - -1058 200 -707 -826 - 197 -452 -437 -10000 - -1009 -973 200 -854 - -854 200 -973 -1009 - -10000 -437 -452 197 - -826 -707 200 -1058 - -133 37 26 15 - -51 11 -3 31 + 31 -3 11 -51 + 15 26 36 -132 + -774 199 -645 -710 + 196 -439 -426 -796 + -766 -759 199 -722 + -722 199 -759 -766 + -796 -426 -439 196 + -710 -645 199 -774 + -132 36 26 15 + -51 11 -3 31 diff --git a/profiles/vertebrates/MA1998.1.pwm b/profiles/vertebrates/MA1998.1.pwm index e99ca98..f4c1626 100644 --- a/profiles/vertebrates/MA1998.1.pwm +++ b/profiles/vertebrates/MA1998.1.pwm @@ -1,12 +1,12 @@ - 11 10 -28 5 - 47 -126 49 -33 - -224 -168 169 -207 - -356 -260 185 -271 - -267 -318 -149 176 - -370 185 -262 -278 - -306 -144 -424 179 - -471 180 -196 -213 - -409 -364 -476 194 - 186 -278 -314 -317 - 89 -64 -81 -9 - -73 73 -10 -31 + 11 9 -28 5 + 47 -124 48 -33 + -219 -165 169 -203 + -344 -254 184 -264 + -261 -309 -147 175 + -356 185 -256 -271 + -297 -142 -404 178 + -443 179 -192 -209 + -391 -350 -447 193 + 185 -271 -305 -308 + 88 -63 -80 -9 + -72 72 -10 -31 diff --git a/profiles/vertebrates/MA1999.1.pwm b/profiles/vertebrates/MA1999.1.pwm index e69de29..6aed5bf 100644 --- a/profiles/vertebrates/MA1999.1.pwm +++ b/profiles/vertebrates/MA1999.1.pwm @@ -0,0 +1,15 @@ + -47 94 -91 -28 + -78 -18 -6 66 + -216 -152 161 -144 + -154 -105 -176 152 + -295 -195 -213 176 + -284 183 -328 -238 + -207 -234 -284 178 + -307 183 -238 -301 + -274 185 -295 -314 + 160 -113 -204 -192 + -295 -154 -51 150 + -195 145 -105 -94 + -102 -34 -138 122 + -23 16 14 -12 + -35 30 18 -25 diff --git a/profiles/vertebrates/MA2000.1.pwm b/profiles/vertebrates/MA2000.1.pwm index 86e51d9..bbb1fe3 100644 --- a/profiles/vertebrates/MA2000.1.pwm +++ b/profiles/vertebrates/MA2000.1.pwm @@ -1,17 +1,17 @@ - 35 -22 8 -30 - -6 -18 2 19 - 15 -73 68 -54 - 133 -156 -89 -70 - -73 -107 127 -95 - -164 -65 -69 128 - -288 -106 -318 171 - -403 188 -264 -329 - 187 -261 -323 -367 - 189 -377 -288 -340 - -347 -471 193 -379 - -375 -447 192 -333 - -159 -28 -278 143 - -413 186 -339 -225 - 184 -303 -293 -257 - -41 -5 44 -12 - -26 58 -26 -27 + 34 -21 8 -30 + -5 -18 2 19 + 15 -72 67 -53 + 131 -152 -87 -69 + -72 -105 125 -94 + -160 -64 -68 126 + -275 -104 -302 170 + -374 186 -253 -312 + 185 -250 -307 -345 + 187 -353 -275 -322 + -327 -426 191 -354 + -352 -409 190 -315 + -155 -28 -266 142 + -382 185 -321 -217 + 182 -289 -280 -247 + -40 -4 43 -12 + -25 57 -26 -26 diff --git a/profiles/vertebrates/MA2001.1.pwm b/profiles/vertebrates/MA2001.1.pwm index e69de29..b9994d3 100644 --- a/profiles/vertebrates/MA2001.1.pwm +++ b/profiles/vertebrates/MA2001.1.pwm @@ -0,0 +1,11 @@ + -60 -116 123 -88 + 47 -75 -45 37 + 191 -324 -389 -362 + 187 -308 -380 -274 + -227 169 -305 -119 + -113 163 -306 -159 + -232 -194 -227 174 + -296 -275 185 -305 + 193 -380 -399 -397 + -36 5 20 4 + 32 38 -63 -32 diff --git a/profiles/vertebrates/MA2002.1.pwm b/profiles/vertebrates/MA2002.1.pwm index e69de29..f323447 100644 --- a/profiles/vertebrates/MA2002.1.pwm +++ b/profiles/vertebrates/MA2002.1.pwm @@ -0,0 +1,11 @@ + 23 -13 43 -81 + 23 -13 6 -20 + -70 -168 -43 122 + -244 186 -335 -335 + 179 -214 -335 -214 + -335 -244 184 -282 + -335 -335 186 -244 + -244 184 -282 -335 + 167 -282 -92 -282 + -43 38 33 -52 + -35 17 -61 52 diff --git a/profiles/vertebrates/MA2003.1.pwm b/profiles/vertebrates/MA2003.1.pwm index 6dfd965..43b437e 100644 --- a/profiles/vertebrates/MA2003.1.pwm +++ b/profiles/vertebrates/MA2003.1.pwm @@ -1,10 +1,10 @@ - -46 116 -13 -312 - -458 183 -558 -137 - 163 -160 -450 -89 - -10000 200 -10000 -10000 - -10000 -360 -824 197 - -300 -2 -500 151 - -61 55 78 -268 - 171 -270 -267 -125 - 49 26 10 -164 - 27 56 -40 -84 + -45 115 -12 -292 + -382 180 -431 -130 + 160 -152 -385 -86 + -489 196 -489 -489 + -492 -315 -479 193 + -277 -2 -419 149 + -59 54 77 -248 + 168 -249 -247 -119 + 49 26 10 -160 + 27 55 -39 -81 diff --git a/scan-sequence.py b/scan-sequence.py new file mode 100755 index 0000000..377df6a --- /dev/null +++ b/scan-sequence.py @@ -0,0 +1,250 @@ +#!/usr/bin/env python + +import click +from click_option_group import optgroup +from functools import partial +from itertools import chain +import json +from multiprocessing import Pool +from numpy import log10 as log +import os +import re +import shutil +import subprocess +from tqdm import tqdm + +# Authorship +__author__ = "Oriol Fornes" +__organization__ = "The JASPAR Consortium" +__version__ = "2021.9.1" +__maintainer__ = "Oriol Fornes" +__email__ = "oriol@cmmt.ubc.ca" +__status__ = "Production" + +# Globals +pid = os.getpid() +taxons = ["fungi", "insects", "nematodes", "plants", "urochordates", + "vertebrates"] + +CONTEXT_SETTINGS = { + "help_option_names": ["-h", "--help"], +} + +@click.command(no_args_is_help=True, context_settings=CONTEXT_SETTINGS) +@click.argument( + "fasta_file", + type=click.Path(exists=True, resolve_path=True), +) +@click.argument( + "profiles_dir", + type=click.Path(exists=True, resolve_path=True), +) +@click.option( + "-d", "--dummy-dir", + help="Dummy directory.", + type=click.Path(exists=True, resolve_path=True), + default="/tmp/", + show_default=True, +) +@click.option( + "-o", "--output-dir", + help="Output directory.", + type=click.Path(resolve_path=True), + default="./", + show_default=True, +) +@click.option( + "-t", "--threads", + help="Number of CPU threads to use.", + type=int, + default=1, + show_default=True, +) +@optgroup.group("Search arguments") +@optgroup.option( + "-b", "--background", + help="A, C, G, T background probabilities.", + type=float, + nargs=4, + default=[.25, .25, .25, .25], + show_default=True, +) +@optgroup.option( + "-l", "--latest", + help="Use the latest version of each profile.", + is_flag=True, +) +@optgroup.option( + "--profile", + help="Profile ID(s) to use. [default: all]", + multiple=True, +) +@optgroup.option( + "--pthresh", + help="P-value threshold.", + type=float, + default=.05, + show_default=True, +) +@optgroup.option( + "--rthresh", + help="Relative score threshold.", + type=float, + default=.8, + show_default=True, +) +@optgroup.option( + "--taxon", + help="Taxon(s) to use. [default: all]", + multiple=True, + default=taxons, +) + +def main(**params): + + # Scan sequence + scan_sequence(params["fasta_file"], params["profiles_dir"], + params["dummy_dir"], params["output_dir"], params["threads"], + params["background"], params["latest"], set(params["profile"]), + params["pthresh"], params["rthresh"], params["taxon"]) + +def scan_sequence(fasta_file, profiles_dir, dummy_dir="/tmp/", output_dir="./", + threads=1, background=(.25, .25, .25, .25), latest=False, profile=set(), + pthresh=.05, rthresh=.8, taxon=taxons): + + # Initialize + A, C, G, T = background + + # Create output directory + if not os.path.exists(output_dir): + os.makedirs(output_dir) + + # Get profiles with which to scan sequence + profiles = _get_profiles(profiles_dir, latest, profile, taxon) + + # Get profile names + with open(os.path.join(profiles_dir, "names.json")) as handle: + names = json.load(handle) + + # Scan profiles against sequence + _scan_profiles(profiles, fasta_file, names, dummy_dir, output_dir, threads, + A, C, G, T, pthresh, rthresh) + +def _get_profiles(profiles_dir, latest=False, profile=set(), taxon=taxons): + + # Initialize + profiles = [] + profiles_dict = {} + + # For each taxon... + for t in taxon: + + # Initialize + taxon_dir = os.path.join(os.path.abspath(profiles_dir), t) + + # For each profile... + for profile_file in sorted(os.listdir(taxon_dir), reverse=True): + + # Ignore profiles + if len(profile) > 0: + if profile_file[:8] not in profile: + continue + + # Initialize key + key = profile_file[:6] + profiles_dict.setdefault(key, []) + + # Skip profile if only using the latest version of each profile + if latest: + if len(profiles_dict[key]) == 1: + continue + + # Add profile + profiles_dict[key].append(os.path.join(taxon_dir, profile_file)) + + # Create list of profiles + for value_list in profiles_dict.values(): + for p in value_list: + profiles.append(p) + + return(profiles) + +def _scan_profiles(profiles, fasta_file, names, dummy_dir="/tmp/", + output_dir="./", threads=1, A=.25, C=.25, G=.25, T=.25, pthresh=.05, + rthresh=.8): + + # Parallelize scanning + kwargs = {"total": len(profiles), "ncols": 100} + pool = Pool(threads) + p = partial(_scan_profile, fasta_file=fasta_file, names=names, + dummy_dir=dummy_dir, output_dir=output_dir, threads=threads, + A=A, C=C, G=G, T=T, pthresh=pthresh, rthresh=rthresh) + for _ in tqdm(pool.imap(p, profiles), **kwargs): + pass + pool.close() + pool.join() + +def _scan_profile(profile_file, fasta_file, names, dummy_dir="/tmp/", + output_dir="./", threads=1, A=.25, C=.25, G=.25, T=.25, pthresh=.05, + rthresh=.8): + + # Initialize + cutoff = None + matrix_id = os.path.basename(profile_file)[:8] + bin_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "bin") + tsv_file = os.path.join(dummy_dir, "%s.%s.%s" % \ + (os.path.basename(__file__), pid, matrix_id)) + gzipped_file = "%s.gz" % tsv_file + output_file = os.path.join(output_dir, "%s.tsv.gz" % matrix_id) + + # Skip if profile already scanned (i.e. for speed) + output_file = os.path.join(output_dir, "%s.tsv.gz" % matrix_id) + if not os.path.exists(output_file): + + # Calculate distribution of PWM scores + cmd = "%s %s" % (os.path.join(bin_dir, "matrix_prob"), profile_file) + process = subprocess.run([cmd], shell=True, stdout=subprocess.PIPE, + stderr=subprocess.PIPE) + + with open(tsv_file, "w") as f: + + for line in process.stdout.decode("utf-8").split("\n"): + + matches = re.findall("(\S+)", line) + + if len(matches) == 3: + + score = matches[0] + p_value = float(matches[1]) + perc = float(matches[2][:-1]) + + f.write(f"{score}\t{int(perc * 10)}\t" +\ + f"{int(log(p_value) * 1000 / -10)}\n") + + # Get PWM score cutoff + if cutoff is None: + cutoff = score + elif p_value < pthresh and perc >= rthresh * 100: + cutoff = score + + # Scan FASTA file (ugly code but very efficient) + cmd_1 = "%s -m %s -c %s %s" % (os.path.join(bin_dir, "matrix_scan"), + profile_file, cutoff, fasta_file) + cmd_2 = "gzip > %s" % gzipped_file + cmd = '''%s | awk -v score_tab="%s" -v name="%s" 'BEGIN { while((getline line < score_tab) > 0 ) {split(line,f," "); scores[f[1]]=f[2]; pvalues[f[1]]=f[3]} close(score_tab) } {print $1"\t"$2"\t"$3"\t"name"\t"scores[$5]"\t"pvalues[$5]"\t"$6}' | %s''' % \ + (cmd_1, tsv_file, names[matrix_id], cmd_2) + subprocess.call(cmd, shell=True, stderr=subprocess.STDOUT) + + # Write output + shutil.copy(gzipped_file, output_file) + + # Remove dummy files + os.remove(tsv_file) + os.remove(gzipped_file) + +#-------------# +# Main # +#-------------# + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/scan-sequences.sh b/scan-sequences.sh new file mode 100755 index 0000000..450f2eb --- /dev/null +++ b/scan-sequences.sh @@ -0,0 +1,25 @@ +#!/usr/bin/env bash + +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/sacCer3/ --taxon fungi ./genomes/sacCer3/sacCer3.fa ./profiles/ +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/dm6/ --taxon insects ./genomes/dm6/dm6.fa ./profiles/ +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/ce10/ --taxon nematodes ./genomes/ce10/ce10.fa ./profiles/ +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/ce11/ --taxon nematodes ./genomes/ce11/ce11.fa ./profiles/ +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/araTha1/ --taxon plants ./genomes/araTha1/araTha1.fa ./profiles/ +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/ci3/ --taxon urochordates ./genomes/ci3/ci3.fa ./profiles/ +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/danRer11/ --taxon vertebrates ./genomes/danRer11/danRer11.fa \ + ./profiles/ +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/hg19/ --taxon vertebrates ./genomes/hg19/hg19.fa ./profiles/ +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/hg38/ --taxon vertebrates ./genomes/hg38/hg38.fa ./profiles/ +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/mm10/ --taxon vertebrates ./genomes/mm10/mm10.fa ./profiles/ +./scan-sequence.py --threads 4 --latest \ + -o ./tracks/mm39/ --taxon vertebrates ./genomes/mm39/mm39.fa ./profiles/ \ No newline at end of file diff --git a/scans2bigBed b/scans2bigBed index a48bcfd..bcac353 100755 --- a/scans2bigBed +++ b/scans2bigBed @@ -104,7 +104,7 @@ LC_ALL=C sort --parallel=$THREADS --buffer-size=${MEM}G -T $DUMMY_DIR -k1,1 -k2, ## ## Remove BED file ## -rm $BED_FILE +#rm $BED_FILE ## ## Create bigBed @@ -114,4 +114,4 @@ bedToBigBed -type=bed6 -tab $SORTED_BED_FILE $CHROM_SIZES $OUT_FILE ## ## Remove sorted BED file ## -rm $SORTED_BED_FILE +#rm $SORTED_BED_FILE diff --git a/scans2bigBed.sh b/scans2bigBed.sh new file mode 100755 index 0000000..a883742 --- /dev/null +++ b/scans2bigBed.sh @@ -0,0 +1,5 @@ +#!/usr/bin/env bash + +./scans2bigBed -c ./genomes/hg38/hg38.fa.sizes -i ./tracks/hg38/ -d ./ -o ./tracks/hg38.bb -t 4 +./scans2bigBed -c ./genomes/mm10/mm10.fa.sizes -i ./tracks/mm10/ -d ./ -o ./tracks/mm10.bb -t 4 +./scans2bigBed -c ./genomes/mm39/mm39.fa.sizes -i ./tracks/mm39/ -d ./ -o ./tracks/mm39.bb -t 4 \ No newline at end of file