******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= *.seq ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ . . .35094-2335693c.seq 1.0000 600 . . .07124-2807482d.seq 1.0000 359 . . .27135-3428063d.seq 1.0000 929 . . .701219-701460c.seq 1.0000 242 . . .704034-704678d.seq 1.0000 645 . . .77940-4478869d.seq 1.0000 930 ******************************************************************************** meme *.seq ******************************************************************************** MOTIF 1 width = 21 sites = 6.0 ******************************************************************************** Simplified A :::2:2::::33:6:65:22: motif letter- C 9333735:::::3::::::3: probability G :23:22:::7265393:5356 matrix T :535:359925:2:::555:3 bits 2.2 2.0 1.7 1.5 Information 1.3 * * content 1.1 * ** * (14.5 bits) 0.9 * * *** * 0.7 * * **** * * * 0.4 * * **** * ***** * 0.2 ***** *************** 0.0 --------------------- Multilevel CTTTCTTTTGTGGAGAATTGG consensus CGC CC AACG GTGGCT sequence C -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=6 /home/mic653/71c_2335094-2335693c.seq ( 102) CCGCGACTTGAGCAGGAGGAT 0.999973 /home/mic653/71c_2807124-2807482d.seq ( 161) CTCCCTTTTGTGCAGATGTCG 0.999999 /home/mic653/71c_3427135-3428063d.seq ( 353) CTCTCTCTTGGGTGGGATTCT 0.999962 /home/mic653/71c_701219-701460c.seq ( 100) CTTACCTTTTAAGAGATTAGG 0.999626 /home/mic653/71c_704034-704678d.seq ( 431) CCTTCCCTTGTAGGGAAGTGG 0.999973 /home/mic653/nc_4477940-4478869d.seq ( 1) CGGTCGTTTGTGGAGATTGGG 0.999982 // -------------------------------------------------------------------------------- Possible examples of motif 1 in the training set -------------------------------------------------------------------------------- Sequence name strand Start Score Site ------------- ------ ----- ----- --------------------- . . .35094-2335693c.seq + 102 16.31 GTAGTTTTTC CCGCGACTTGAGCAGGAGGAT A . . .07124-2807482d.seq + 161 23.31 GATTAACTTT CTCCCTTTTGTGCAGATGTCG A . . .27135-3428063d.seq + 353 18.90 GCTTTAGTAT CTCTCTCTTGGGTGGGATTCT G . . .701219-701460c.seq + 100 17.48 CACCCTAACT CTTACCTTTTAAGAGATTAGG C . . .704034-704678d.seq + 431 22.65 CCCCCAGCCC CCTTCCCTTGTAGGGAAGTGG G . . .77940-4478869d.seq + 1 22.17 CGGTCGTTTGTGGAGATTGGG T -------------------------------------------------------------------------------- --------- --------- CCATTGATC AAGAAAGGT CCTGCAATT AGGGGAAAA AGCCAAACT GTAGTGGTG --------- letter-probability matrix: alength= 4 w= 21 n= 3585 0.040307 0.888805 0.032697 0.038191 0.040257 0.317430 0.175551 0.466761 0.040254 0.317442 0.318452 0.323852 0.183071 0.317479 0.032697 0.466754 0.040266 0.745946 0.175594 0.038194 0.183159 0.317389 0.175552 0.323899 0.040256 0.460289 0.032740 0.466715 0.040256 0.031717 0.032697 0.895330 0.040257 0.031717 0.032702 0.895324 0.040254 0.031724 0.747019 0.181003 0.325915 0.031760 0.175549 0.466776 0.325926 0.031717 0.604166 0.038190 0.040256 0.317434 0.461221 0.181090 0.611682 0.031717 0.318408 0.038193 0.040258 0.031717 0.889827 0.038198 0.611687 0.031717 0.318403 0.038193 0.468861 0.031720 0.032701 0.466719 0.040254 0.031724 0.461267 0.466755 0.183060 0.031718 0.318462 0.466760 0.183156 0.317438 0.461213 0.038193 0.040253 0.031721 0.604077 0.323948 ******************************************************************************** MOTIF 2 width = 14 sites = 6.0 ******************************************************************************** Simplified A 8:55526:::::82 motif letter- C :33::7::3::7:: probability G :6::3:::299227 matrix T 2:252:395::::: bits 2.2 2.0 1.7 1.5 Information 1.3 ** content 1.1 * ** (11.6 bits) 0.9 * * *** * 0.7 ** * * ***** 0.4 ** * *** ***** 0.2 ************** 0.0 -------------- Multilevel AGAAACATTGGCAG consensus CCTG T C sequence -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=6 /home/mic653/71c_2335094-2335693c.seq ( 221) AGCAGCATTGGCAG 0.999863 /home/mic653/71c_2807124-2807482d.seq ( 304) AGATGCTTTGGCAG 0.999678 /home/mic653/71c_3427135-3428063d.seq ( 817) AGATACATTGGCAG 0.999935 /home/mic653/71c_701219-701460c.seq ( 176) ACCAAATTGGGGAG 0.988819 /home/mic653/71c_704034-704678d.seq ( 286) TGAAACATCGGCGG 0.999063 /home/mic653/nc_4477940-4478869d.seq ( 892) ACTTTCATCGGCAA 0.984927 // -------------------------------------------------------------------------------- Possible examples of motif 2 in the training set -------------------------------------------------------------------------------- Sequence name strand Start Score Site ------------- ------ ----- ----- -------------- . . .35094-2335693c.seq + 221 18.76 TAGCCGAACA AGCAGCATTGGCAG AATACGGT . . .07124-2807482d.seq + 304 18.21 AGTAGGGCTT AGATGCTTTGGCAG ATTCTGGT . . .27135-3428063d.seq + 817 19.30 ATTTTTTAAA AGATACATTGGCAG TACATTAA . . .701219-701460c.seq + 176 11.57 AACAAAATCT ACCAAATTGGGGAG CAAAATCA . . .704034-704678d.seq + 286 15.17 TTACCTTCAG TGAAACATCGGCGG CGTGTCAG . . .77940-4478869d.seq + 892 13.16 AATTGGTATT ACTTTCATCGGCAA AATTCAGA -------------------------------------------------------------------------------- -- -- TA TT AA GC TC TA -- letter-probability matrix: alength= 4 w= 14 n= 3627 0.752604 0.032015 0.032830 0.182552 0.040484 0.315432 0.605402 0.038682 0.469772 0.317074 0.032759 0.180395 0.468819 0.031797 0.033951 0.465433 0.468950 0.031777 0.319936 0.179337 0.183922 0.744883 0.032950 0.038245 0.611151 0.031797 0.032936 0.324117 0.040349 0.032054 0.032739 0.894858 0.040437 0.316279 0.174625 0.468659 0.041346 0.031813 0.888387 0.038454 0.040575 0.031810 0.889275 0.038339 0.040416 0.746709 0.174521 0.038355 0.753314 0.031756 0.175849 0.039081 0.183163 0.031928 0.746600 0.038308 ******************************************************************************** MOTIF 3 width = 21 sites = 6.0 ******************************************************************************** Simplified A 8985362322:22:3:66323 motif letter- C ::23:2323:755969::636 probability G 2:::::3:::233::::3::: matrix T :::2622558::::::3::5: bits 2.2 2.0 1.7 1.5 Information 1.3 * * content 1.1 * * * (14.3 bits) 0.9 * * * * 0.7 *** ** *** * * 0.4 *** * ** ****** * 0.2 ****** ************** 0.0 --------------------- Multilevel AAAATAGTTTCCCCCCAACTC consensus CA CAC GG A TGACA sequence -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=6 /home/mic653/71c_2335094-2335693c.seq ( 332) AAAATTGTCTCGCCCCAACCC 0.999999 /home/mic653/71c_2807124-2807482d.seq ( 82) AAAATAGATTCGGCACAAAAA 0.999902 /home/mic653/71c_3427135-3428063d.seq ( 784) GAATAAATTTCCACCCAAATA 0.999745 /home/mic653/71c_701219-701460c.seq ( 49) AACCTATCATCAGCACTGCTC 0.998206 /home/mic653/71c_704034-704678d.seq ( 410) AAAAACCTTACCCCCCAGCCC 0.999904 /home/mic653/nc_4477940-4478869d.seq ( 95) AAACTACACTGCCCCCTACTC 0.999964 // -------------------------------------------------------------------------------- Possible examples of motif 3 in the training set -------------------------------------------------------------------------------- Sequence name strand Start Score Site ------------- ------ ----- ----- --------------------- . . .35094-2335693c.seq + 332 23.52 AACTTGTAAC AAAATTGTCTCGCCCCAACCC T . . .07124-2807482d.seq + 82 19.49 TGTGCTATTA AAAATAGATTCGGCACAAAAA C . . .27135-3428063d.seq + 784 17.04 GGAAATACCG GAATAAATTTCCACCCAAATA T . . .701219-701460c.seq + 49 15.77 GCTTACTTTA AACCTATCATCAGCACTGCTC A . . .704034-704678d.seq + 410 20.91 TTCATTAATC AAAAACCTTACCCCCCAGCCC C . . .77940-4478869d.seq + 95 22.32 GCTTGGTAAA AAACTACACTGCCCCCTACTC C -------------------------------------------------------------------------------- --------- --------- AAATCTACG AATCTATCT GATTTTTTA TACTACTGT CTTCCCTTG CTTTCCCCC --------- letter-probability matrix: alength= 4 w= 21 n= 3585 0.754477 0.031746 0.175573 0.038204 0.897355 0.031730 0.032713 0.038202 0.754713 0.174372 0.032709 0.038206 0.468948 0.317261 0.032718 0.181073 0.326036 0.031727 0.032709 0.609528 0.611572 0.174611 0.032714 0.181103 0.183128 0.317524 0.318494 0.180853 0.326046 0.174384 0.032706 0.466864 0.182912 0.317521 0.032711 0.466856 0.183164 0.031730 0.032712 0.752394 0.040279 0.745914 0.175602 0.038206 0.182913 0.460387 0.318497 0.038202 0.183144 0.460422 0.318232 0.038202 0.040280 0.888799 0.032711 0.038210 0.325803 0.603277 0.032706 0.038214 0.040269 0.888822 0.032706 0.038202 0.611807 0.031740 0.032706 0.323747 0.611827 0.031731 0.318240 0.038202 0.326035 0.603042 0.032721 0.038202 0.183158 0.317528 0.032707 0.466607 0.326023 0.603061 0.032711 0.038205 Search completed after finding the 3 motifs requested.