******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/428/428.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10178 1.0000 500 10239 1.0000 500 10772 1.0000 500 11305 1.0000 500 12013 1.0000 500 19081 1.0000 500 20330 1.0000 500 2037 1.0000 500 20431 1.0000 500 20579 1.0000 500 2100 1.0000 500 21130 1.0000 500 22026 1.0000 500 22862 1.0000 500 24721 1.0000 500 261001 1.0000 500 263000 1.0000 500 263297 1.0000 500 263816 1.0000 500 2755 1.0000 500 32795 1.0000 500 33676 1.0000 500 34838 1.0000 500 37137 1.0000 500 38886 1.0000 500 4048 1.0000 500 4691 1.0000 500 5503 1.0000 500 5664 1.0000 500 5927 1.0000 500 7330 1.0000 500 7343 1.0000 500 8924 1.0000 500 9404 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/428/428.seqs.fa -oc motifs/428 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 34 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 17000 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.232 G 0.239 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.232 G 0.239 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 20 llr = 254 E-value = 7.6e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 51352561835235791:683 pos.-specific C 367593:92538644248337 probability G :3:1:2:::12:1:::21::: matrix T 31:::251:21::1::412:: bits 2.1 1.9 1.7 1.5 * * Relative 1.3 * * ** * * * ** Entropy 1.1 * * ** * ** * ** (18.3 bits) 0.8 *** *** ** ** * ** 0.6 **** *** ***** **** 0.4 ***** *** ********** 0.2 ********************* 0.0 --------------------- Multilevel ACCCCAACACACCAAACCAAC consensus CGAA CT CACAACC T CCA sequence T TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 21130 472 2.68e-12 ACGTCATCGC ACCCCCACACACCAAACCAAC ACACAATC 261001 407 1.65e-08 ACCGTTCATC ACAACAACACACGCAACCAAA CCAACTCACC 33676 360 3.23e-08 CACCAGACCG ACCGCCACACGCCAAACCACC ATCGCTAGTT 10239 471 7.65e-08 CCACGACGAA AGCACCTCCCCCCAAACCCAA ACTCTCGAC 12013 474 1.86e-07 TCTCGCATTC AGCACATCAAACACAACTCAC GTCACG 10178 464 3.43e-07 TCAGCACACA TCAACATCAGGCACAATCACC CTCCGCCACA 20431 271 4.16e-07 CTACTACTCA ACAACAACACCAGCCAGCAAC AACAACAATT 32795 439 4.57e-07 ACTTCGTCAT TCACCAACCTACCAACTCACC ACCAATCCGA 5927 45 6.60e-07 TTGACACTGT TACCCAACACTCCAAACGAAC CAAGCCGAAC 5503 476 6.60e-07 CCCAACATCA ACCACTTCAATCACCCTCAAC CACC 37137 245 8.60e-07 CACTCTCACA TCAACAACATGCCAAATGTAC AGCAACCAAC 263297 331 9.37e-07 GATCCCGGCT CGCCAGTCACGCCACACCCAA CTGATCATCC 9404 184 1.11e-06 CGTTTTGTAG CCCCAAACAACCAACAGCCAA ATATTGTACA 22026 431 1.31e-06 ACCGGACGAC CGCCACACAGCCACAATCACC ACTCTTCCTC 11305 9 1.42e-06 GCAAATCT CTCCCTTCATCACAAATCACC AACGCCTTCT 5664 417 1.66e-06 GCAGCAACCT TCCCCTTTCCACCCCACCAAA GCGAAGCTGC 2037 479 2.44e-06 GTTGATCGAT AGCACGTCATAACTCATCTAC A 7343 281 2.62e-06 AATGCTACTA ATCCCAAAAAACACAAGCAAA GTGGGGTGTG 34838 473 2.62e-06 TTCTCTTCGT CCAACGACACACCTCAACTAC CTTCATC 38886 440 3.49e-06 TCAAACCAAC ACCCCCTCCAAACAACTTCAC TGAGCACTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21130 2.7e-12 471_[+1]_8 261001 1.6e-08 406_[+1]_73 33676 3.2e-08 359_[+1]_120 10239 7.6e-08 470_[+1]_9 12013 1.9e-07 473_[+1]_6 10178 3.4e-07 463_[+1]_16 20431 4.2e-07 270_[+1]_209 32795 4.6e-07 438_[+1]_41 5927 6.6e-07 44_[+1]_435 5503 6.6e-07 475_[+1]_4 37137 8.6e-07 244_[+1]_235 263297 9.4e-07 330_[+1]_149 9404 1.1e-06 183_[+1]_296 22026 1.3e-06 430_[+1]_49 11305 1.4e-06 8_[+1]_471 5664 1.7e-06 416_[+1]_63 2037 2.4e-06 478_[+1]_1 7343 2.6e-06 280_[+1]_199 34838 2.6e-06 472_[+1]_7 38886 3.5e-06 439_[+1]_40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=20 21130 ( 472) ACCCCCACACACCAAACCAAC 1 261001 ( 407) ACAACAACACACGCAACCAAA 1 33676 ( 360) ACCGCCACACGCCAAACCACC 1 10239 ( 471) AGCACCTCCCCCCAAACCCAA 1 12013 ( 474) AGCACATCAAACACAACTCAC 1 10178 ( 464) TCAACATCAGGCACAATCACC 1 20431 ( 271) ACAACAACACCAGCCAGCAAC 1 32795 ( 439) TCACCAACCTACCAACTCACC 1 5927 ( 45) TACCCAACACTCCAAACGAAC 1 5503 ( 476) ACCACTTCAATCACCCTCAAC 1 37137 ( 245) TCAACAACATGCCAAATGTAC 1 263297 ( 331) CGCCAGTCACGCCACACCCAA 1 9404 ( 184) CCCCAAACAACCAACAGCCAA 1 22026 ( 431) CGCCACACAGCCACAATCACC 1 11305 ( 9) CTCCCTTCATCACAAATCACC 1 5664 ( 417) TCCCCTTTCCACCCCACCAAA 1 2037 ( 479) AGCACGTCATAACTCATCTAC 1 7343 ( 281) ATCCCAAAAAACACAAGCAAA 1 34838 ( 473) CCAACGACACACCTCAACTAC 1 38886 ( 440) ACCCCCTCCAAACAACTTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 11.1457 E= 7.6e-008 93 11 -1097 -10 -239 137 7 -142 20 160 -1097 -1097 78 111 -225 -1097 -80 188 -1097 -1097 78 11 -67 -84 107 -1097 -1097 75 -239 196 -1097 -242 161 -21 -1097 -1097 -7 96 -125 -42 78 11 -25 -142 -39 179 -1097 -1097 20 137 -125 -1097 93 79 -1097 -142 131 60 -1097 -1097 170 -63 -1097 -1097 -239 79 -67 58 -1097 179 -125 -142 120 11 -1097 -84 152 11 -1097 -1097 20 160 -1097 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 20 E= 7.6e-008 0.500000 0.250000 0.000000 0.250000 0.050000 0.600000 0.250000 0.100000 0.300000 0.700000 0.000000 0.000000 0.450000 0.500000 0.050000 0.000000 0.150000 0.850000 0.000000 0.000000 0.450000 0.250000 0.150000 0.150000 0.550000 0.000000 0.000000 0.450000 0.050000 0.900000 0.000000 0.050000 0.800000 0.200000 0.000000 0.000000 0.250000 0.450000 0.100000 0.200000 0.450000 0.250000 0.200000 0.100000 0.200000 0.800000 0.000000 0.000000 0.300000 0.600000 0.100000 0.000000 0.500000 0.400000 0.000000 0.100000 0.650000 0.350000 0.000000 0.000000 0.850000 0.150000 0.000000 0.000000 0.050000 0.400000 0.150000 0.400000 0.000000 0.800000 0.100000 0.100000 0.600000 0.250000 0.000000 0.150000 0.750000 0.250000 0.000000 0.000000 0.300000 0.700000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ACT][CG][CA][CA]C[AC][AT]C[AC][CAT][ACG][CA][CA][AC][AC]A[CT]C[AC][AC][CA] -------------------------------------------------------------------------------- Time 10.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 20 llr = 242 E-value = 1.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 122:1142:3::13:13:411 pos.-specific C 315:543292182:7:5a:2a probability G 25344:4:12:25:283:2:: matrix T 531716:714913821::58: bits 2.1 * 1.9 * * 1.7 * * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 * * ** * * * * (17.5 bits) 0.8 * * ** ** *** * ** 0.6 * * ** ** *** * ** 0.4 ******* *********** 0.2 ********* *********** 0.0 --------------------- Multilevel TGCTCTATCTTCGTCGCCTTC consensus CTGGGCG A TAT A A sequence G A C C C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10239 139 3.19e-10 TGGATTCATC TGCTGTGTCTTCGTGGCCTTC AAAGTGGAGA 261001 79 2.41e-08 CCTCCTGTAC TGCTGCGTCCTGTTCGCCATC GGTTTCGACA 7330 332 4.14e-08 TCTCGTATGA TTCTGTGTCTTCGTTGCCTAC AATTGGACGG 8924 8 1.42e-07 ACCACTC TGCTCTCTCTCCCTCTCCTTC TCCTCTAACC 7343 9 1.79e-07 TGTTGTTG TTGGCTCTCATCGTTGGCGTC GTGTTCATTG 21130 439 2.78e-07 TGGAGTGAAG CGAGGTATCACCGTCGACGTC GTACGTCATC 33676 471 3.82e-07 GCGCCATAGC GTCTTCATCTTCGTCACCATC TAATGTACC 20579 474 9.30e-07 CTATGCAACA CGATCAGCCATCTTCGACATC GATCCA 10178 26 1.02e-06 CTTCTACACC GGATACACCGTCGTCGACTTC GTGATCGGCG 10772 140 1.12e-06 TCTTATCCAA CGCGTTAACATTCTCGCCTTC ATCATCGATA 32795 41 1.34e-06 TGAGGGCTGT TGGGCTGTTTTCTTTGGCGTC GCCATTGACG 12013 45 1.47e-06 TTTGGTGCCA GGATCTATCATGTAGGGCTTC CATTCAACTA 5927 405 1.75e-06 TTCGTCAACA ACCGCCGCCCTCGACGCCTTC GTCCCACTCA 37137 185 2.08e-06 CTCCTCCCTC TTCTCTCATTTTTTCGCCTTC GATTTCGCCG 2037 398 2.08e-06 CTGTTCTCTC TACTCCATCATCATTGACACC TTCCTCCCGA 4048 476 2.90e-06 GCTCCAGCCT GAGGCTCTCTTCGTCTGCACC ACCG 2755 367 3.99e-06 CTGCAATCTT TCGGCCATCGTCGACGACTTA CGACGTCCGT 5503 271 4.31e-06 GACATATCGT CGGTGTAACCTCCAGGACTCC CCGGCAACCA 38886 155 8.35e-06 CAGTTTGCCG CTTTGTGTGGTGGTCGCCATC GCGCTCATCA 9404 303 1.52e-05 CATGAACACG CACTGCCTCCTCCACAGCAAC AACCGCTATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10239 3.2e-10 138_[+2]_341 261001 2.4e-08 78_[+2]_401 7330 4.1e-08 331_[+2]_148 8924 1.4e-07 7_[+2]_472 7343 1.8e-07 8_[+2]_471 21130 2.8e-07 438_[+2]_41 33676 3.8e-07 470_[+2]_9 20579 9.3e-07 473_[+2]_6 10178 1e-06 25_[+2]_454 10772 1.1e-06 139_[+2]_340 32795 1.3e-06 40_[+2]_439 12013 1.5e-06 44_[+2]_435 5927 1.8e-06 404_[+2]_75 37137 2.1e-06 184_[+2]_295 2037 2.1e-06 397_[+2]_82 4048 2.9e-06 475_[+2]_4 2755 4e-06 366_[+2]_113 5503 4.3e-06 270_[+2]_209 38886 8.3e-06 154_[+2]_325 9404 1.5e-05 302_[+2]_177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=20 10239 ( 139) TGCTGTGTCTTCGTGGCCTTC 1 261001 ( 79) TGCTGCGTCCTGTTCGCCATC 1 7330 ( 332) TTCTGTGTCTTCGTTGCCTAC 1 8924 ( 8) TGCTCTCTCTCCCTCTCCTTC 1 7343 ( 9) TTGGCTCTCATCGTTGGCGTC 1 21130 ( 439) CGAGGTATCACCGTCGACGTC 1 33676 ( 471) GTCTTCATCTTCGTCACCATC 1 20579 ( 474) CGATCAGCCATCTTCGACATC 1 10178 ( 26) GGATACACCGTCGTCGACTTC 1 10772 ( 140) CGCGTTAACATTCTCGCCTTC 1 32795 ( 41) TGGGCTGTTTTCTTTGGCGTC 1 12013 ( 45) GGATCTATCATGTAGGGCTTC 1 5927 ( 405) ACCGCCGCCCTCGACGCCTTC 1 37137 ( 185) TTCTCTCATTTTTTCGCCTTC 1 2037 ( 398) TACTCCATCATCATTGACACC 1 4048 ( 476) GAGGCTCTCTTCGTCTGCACC 1 2755 ( 367) TCGGCCATCGTCGACGACTTA 1 5503 ( 271) CGGTGTAACCTCCAGGACTCC 1 38886 ( 155) CTTTGTGTGGTGGTCGCCATC 1 9404 ( 303) CACTGCCTCCTCCACAGCAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 10.6149 E= 1.5e-002 -239 37 -25 75 -80 -121 107 -10 -39 111 7 -242 -1097 -1097 55 128 -239 111 55 -142 -239 60 -1097 116 61 11 55 -1097 -80 -63 -1097 139 -1097 188 -225 -142 20 -21 -67 39 -1097 -121 -1097 175 -1097 169 -67 -142 -239 -21 107 -10 -7 -1097 -1097 148 -1097 149 -67 -42 -139 -1097 175 -142 20 96 7 -1097 -1097 211 -1097 -1097 42 -1097 -67 90 -139 -63 -1097 148 -239 204 -1097 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 20 E= 1.5e-002 0.050000 0.300000 0.200000 0.450000 0.150000 0.100000 0.500000 0.250000 0.200000 0.500000 0.250000 0.050000 0.000000 0.000000 0.350000 0.650000 0.050000 0.500000 0.350000 0.100000 0.050000 0.350000 0.000000 0.600000 0.400000 0.250000 0.350000 0.000000 0.150000 0.150000 0.000000 0.700000 0.000000 0.850000 0.050000 0.100000 0.300000 0.200000 0.150000 0.350000 0.000000 0.100000 0.000000 0.900000 0.000000 0.750000 0.150000 0.100000 0.050000 0.200000 0.500000 0.250000 0.250000 0.000000 0.000000 0.750000 0.000000 0.650000 0.150000 0.200000 0.100000 0.000000 0.800000 0.100000 0.300000 0.450000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.350000 0.000000 0.150000 0.500000 0.100000 0.150000 0.000000 0.750000 0.050000 0.950000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TCG][GT][CGA][TG][CG][TC][AGC]TC[TAC]TC[GTC][TA][CT]G[CAG]C[TA]TC -------------------------------------------------------------------------------- Time 20.52 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 34 llr = 272 E-value = 1.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :5331181265: pos.-specific C 1:::::22:::: probability G 814:99:68438 matrix T 1347:::1:122 bits 2.1 1.9 1.7 * 1.5 ** Relative 1.3 *** * * Entropy 1.1 * **** * * (11.5 bits) 0.8 * **** ** * 0.6 * **** ** * 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GATTGGAGGAAG consensus TGA GG sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 5664 217 4.56e-07 TTGTTGATGC GTGTGGAGGAAG AGAGCCATCT 8924 218 1.13e-06 GAAGTGTTGG GTGTGGAGGAGG CGTTGTTGTG 261001 179 2.21e-06 ACTCAAGTTT GATTGGACGAAG GATTCATCGA 19081 52 3.49e-06 AATTTCAAAA GTAAGGAGGAAG GTGAGAGACT 2755 30 3.84e-06 AGAAAGCGTG GATTGGACGAGG GTGACACATC 263297 176 6.20e-06 AACCGTGTCC GAGTGGAGAGAG CTCAGAATGC 263000 278 8.29e-06 ACGATGGTAG GAGTGGCGGGGG GAGAAGGTAC 10178 97 9.65e-06 TTCATTGTTG GAAAGGAGGGTG AGATAGCAAA 7343 50 1.87e-05 TCGTCGTCTT TAGTGGAGGAAG AGGATCTCCT 33676 218 2.34e-05 GTGTTCGTGG GAAAGGAAGAGG GAGAGAAAGG 4691 60 2.63e-05 AGAGGGAGGT GATTAGAGGAAG CTGAAGGATT 2100 272 2.63e-05 TAAAGGTGTT GGTTGGCGGAAG CTTCCTTTTT 22026 144 2.88e-05 AATATCTCCT GTTTGAAGGAGG TGCAGCGACG 4048 199 4.36e-05 TTGATGGGTG GTATGGATGATG AGGTACGAGG 20330 82 4.85e-05 ACTGATTTAT TTATGGAGGAAG AGGAAGATTG 11305 432 4.85e-05 TTTCATGTGA GATAGGAGAGTG TCCATCAATT 7330 448 6.54e-05 AATACTGCAG GAGAGGACGGAT CACAAAAATA 24721 41 6.54e-05 TTGAGTGATA GAGTGGATGAGT GAACCGATTG 9404 50 7.21e-05 ATGGAGTATG CTTTGGCGGAAG ACATAGTTGC 22862 164 1.05e-04 AGATGTCATT GTGTGGACGTGG TCGTTTGACG 2037 117 1.05e-04 GGGTAGATCG GTTTGAAGAAAG AAGTGAAGTG 5503 300 1.15e-04 CCCCGGCAAC CAGAGGAAGAGG AACCCCAGAA 38886 375 1.15e-04 AAGGGTCTTA GAAAGGAGAAAT TTCGATGGAA 32795 103 1.15e-04 TTTTTGGGAG GGTTGGAGGGTT CTTCGGTTGA 12013 321 1.15e-04 GTCGACATGG CAATGGATGAGG ATATAGTTAG 34838 290 1.36e-04 ATCGACTGTT GTTTGGCAGGTG GTTAACCTTC 21130 12 1.75e-04 TTGAGCAGCA GCGAGGACGGAG GCACCAAAGA 5927 294 2.56e-04 AGGAGCTTGA CGGTGGAGGGAT GCTGTGTCAT 37137 31 2.56e-04 GACATTCACC GAATGACAGAAG GCTCCTGCTG 10239 48 4.22e-04 CCTCCTTTTT GGATGGCGAGTG AGCGTAGGTG 20579 78 4.82e-04 ATGAATATTC AATAGGAAGGGG TGAATAAAAT 10772 167 5.14e-04 CTTCATCATC GATAGGAGCTAG CTTACTATCT 263816 85 6.59e-04 TGTCAAAGCA GTTTGAACGGTT GTACCATGCG 20431 372 8.81e-04 TGACAGCTAT GAGAAGATAGAG GAGTCTTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5664 4.6e-07 216_[+3]_272 8924 1.1e-06 217_[+3]_271 261001 2.2e-06 178_[+3]_310 19081 3.5e-06 51_[+3]_437 2755 3.8e-06 29_[+3]_459 263297 6.2e-06 175_[+3]_313 263000 8.3e-06 277_[+3]_211 10178 9.7e-06 96_[+3]_392 7343 1.9e-05 49_[+3]_439 33676 2.3e-05 217_[+3]_271 4691 2.6e-05 59_[+3]_429 2100 2.6e-05 271_[+3]_217 22026 2.9e-05 143_[+3]_345 4048 4.4e-05 198_[+3]_290 20330 4.9e-05 81_[+3]_407 11305 4.9e-05 431_[+3]_57 7330 6.5e-05 447_[+3]_41 24721 6.5e-05 40_[+3]_448 9404 7.2e-05 49_[+3]_439 22862 0.0001 163_[+3]_325 2037 0.0001 116_[+3]_372 5503 0.00011 299_[+3]_189 38886 0.00011 374_[+3]_114 32795 0.00011 102_[+3]_386 12013 0.00011 320_[+3]_168 34838 0.00014 289_[+3]_199 21130 0.00017 11_[+3]_477 5927 0.00026 293_[+3]_195 37137 0.00026 30_[+3]_458 10239 0.00042 47_[+3]_441 20579 0.00048 77_[+3]_411 10772 0.00051 166_[+3]_322 263816 0.00066 84_[+3]_404 20431 0.00088 371_[+3]_117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=34 5664 ( 217) GTGTGGAGGAAG 1 8924 ( 218) GTGTGGAGGAGG 1 261001 ( 179) GATTGGACGAAG 1 19081 ( 52) GTAAGGAGGAAG 1 2755 ( 30) GATTGGACGAGG 1 263297 ( 176) GAGTGGAGAGAG 1 263000 ( 278) GAGTGGCGGGGG 1 10178 ( 97) GAAAGGAGGGTG 1 7343 ( 50) TAGTGGAGGAAG 1 33676 ( 218) GAAAGGAAGAGG 1 4691 ( 60) GATTAGAGGAAG 1 2100 ( 272) GGTTGGCGGAAG 1 22026 ( 144) GTTTGAAGGAGG 1 4048 ( 199) GTATGGATGATG 1 20330 ( 82) TTATGGAGGAAG 1 11305 ( 432) GATAGGAGAGTG 1 7330 ( 448) GAGAGGACGGAT 1 24721 ( 41) GAGTGGATGAGT 1 9404 ( 50) CTTTGGCGGAAG 1 22862 ( 164) GTGTGGACGTGG 1 2037 ( 117) GTTTGAAGAAAG 1 5503 ( 300) CAGAGGAAGAGG 1 38886 ( 375) GAAAGGAGAAAT 1 32795 ( 103) GGTTGGAGGGTT 1 12013 ( 321) CAATGGATGAGG 1 34838 ( 290) GTTTGGCAGGTG 1 21130 ( 12) GCGAGGACGGAG 1 5927 ( 294) CGGTGGAGGGAT 1 37137 ( 31) GAATGACAGAAG 1 10239 ( 48) GGATGGCGAGTG 1 20579 ( 78) AATAGGAAGGGG 1 10772 ( 167) GATAGGAGCTAG 1 263816 ( 85) GTTTGAACGGTT 1 20431 ( 372) GAGAAGATAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 16626 bayes= 9.72667 E= 1.9e+000 -315 -98 173 -219 101 -297 -102 27 2 -1173 57 51 30 -1173 -1173 134 -215 -1173 198 -1173 -115 -1173 189 -1173 165 -39 -1173 -1173 -83 -39 123 -119 -57 -297 173 -1173 109 -1173 68 -219 93 -1173 30 -38 -1173 -1173 179 -60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 34 E= 1.9e+000 0.029412 0.117647 0.794118 0.058824 0.529412 0.029412 0.117647 0.323529 0.264706 0.000000 0.352941 0.382353 0.323529 0.000000 0.000000 0.676471 0.058824 0.000000 0.941176 0.000000 0.117647 0.000000 0.882353 0.000000 0.823529 0.176471 0.000000 0.000000 0.147059 0.176471 0.558824 0.117647 0.176471 0.029412 0.794118 0.000000 0.558824 0.000000 0.382353 0.058824 0.500000 0.000000 0.294118 0.205882 0.000000 0.000000 0.823529 0.176471 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AT][TGA][TA]GGAGG[AG][AGT]G -------------------------------------------------------------------------------- Time 30.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10178 9.80e-08 25_[+2(1.02e-06)]_50_[+3(9.65e-06)]_\ 355_[+1(3.43e-07)]_16 10239 4.29e-10 138_[+2(3.19e-10)]_311_\ [+1(7.65e-08)]_9 10772 4.69e-03 139_[+2(1.12e-06)]_340 11305 6.33e-04 8_[+1(1.42e-06)]_402_[+3(4.85e-05)]_\ 57 12013 7.23e-07 44_[+2(1.47e-06)]_408_\ [+1(1.86e-07)]_6 19081 2.07e-02 51_[+3(3.49e-06)]_437 20330 2.26e-01 81_[+3(4.85e-05)]_407 2037 9.11e-06 397_[+2(2.08e-06)]_60_\ [+1(2.44e-06)]_1 20431 3.77e-03 270_[+1(4.16e-07)]_209 20579 1.07e-03 473_[+2(9.30e-07)]_6 2100 7.80e-02 271_[+3(2.63e-05)]_217 21130 7.61e-12 438_[+2(2.78e-07)]_12_\ [+1(2.68e-12)]_8 22026 3.18e-04 143_[+3(2.88e-05)]_275_\ [+1(1.31e-06)]_49 22862 1.68e-01 500 24721 3.28e-02 40_[+3(6.54e-05)]_92_[+2(7.02e-05)]_\ 335 261001 4.73e-11 78_[+2(2.41e-08)]_79_[+3(2.21e-06)]_\ 216_[+1(1.65e-08)]_4_[+1(1.67e-05)]_48 263000 5.42e-02 247_[+3(6.54e-05)]_18_\ [+3(8.29e-06)]_21_[+3(4.85e-05)]_178 263297 9.16e-05 175_[+3(6.20e-06)]_143_\ [+1(9.37e-07)]_149 263816 3.91e-01 500 2755 2.96e-04 [+3(9.56e-05)]_17_[+3(3.84e-06)]_49_\ [+2(2.07e-05)]_72_[+3(3.60e-05)]_171_[+2(3.99e-06)]_113 32795 1.50e-06 40_[+2(1.34e-06)]_377_\ [+1(4.57e-07)]_11_[+1(3.99e-05)]_9 33676 1.03e-08 217_[+3(2.34e-05)]_130_\ [+1(3.23e-08)]_90_[+2(3.82e-07)]_9 34838 8.31e-04 472_[+1(2.62e-06)]_7 37137 7.75e-06 184_[+2(2.08e-06)]_39_\ [+1(8.60e-07)]_235 38886 4.59e-05 154_[+2(8.35e-06)]_264_\ [+1(3.49e-06)]_40 4048 1.31e-03 198_[+3(4.36e-05)]_265_\ [+2(2.90e-06)]_4 4691 9.86e-02 45_[+3(3.60e-05)]_2_[+3(2.63e-05)]_\ 429 5503 5.90e-06 270_[+2(4.31e-06)]_184_\ [+1(6.60e-07)]_4 5664 6.79e-06 216_[+3(4.56e-07)]_188_\ [+1(1.66e-06)]_63 5927 5.26e-06 44_[+1(6.60e-07)]_339_\ [+2(1.75e-06)]_75 7330 1.72e-05 331_[+2(4.14e-08)]_95_\ [+3(6.54e-05)]_41 7343 2.33e-07 8_[+2(1.79e-07)]_20_[+3(1.87e-05)]_\ 219_[+1(2.62e-06)]_51_[+1(2.96e-05)]_127 8924 6.20e-06 7_[+2(1.42e-07)]_16_[+2(2.20e-05)]_\ 152_[+3(1.13e-06)]_271 9404 1.91e-05 49_[+3(7.21e-05)]_40_[+1(2.71e-05)]_\ 61_[+1(1.11e-06)]_98_[+2(1.52e-05)]_177 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************