******************************************************************************** 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/93/93.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11231 1.0000 500 11489 1.0000 500 11933 1.0000 500 13448 1.0000 500 1755 1.0000 500 1941 1.0000 500 1942 1.0000 500 21393 1.0000 500 21825 1.0000 500 22642 1.0000 500 23773 1.0000 500 24077 1.0000 500 25324 1.0000 500 25807 1.0000 500 2594 1.0000 500 25977 1.0000 500 260997 1.0000 500 261844 1.0000 500 38187 1.0000 500 4796 1.0000 500 5425 1.0000 500 7247 1.0000 500 7974 1.0000 500 8371 1.0000 500 8382 1.0000 500 8669 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/93/93.seqs.fa -oc motifs/93 -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= 26 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= 13000 N= 26 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.233 G 0.237 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.233 G 0.237 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 26 llr = 248 E-value = 8.2e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 222128:3::5:2:32 pos.-specific C 8:726:62:72339:8 probability G ::1221:32::2:1:: matrix T :8:61:4283355:7: bits 2.1 1.9 1.7 * 1.5 * * Relative 1.3 ** * * * Entropy 1.1 ** ** ** * * (13.8 bits) 0.8 ** ** ** * * 0.6 *** ** ** * *** 0.4 ******* ******** 0.2 ******* ******** 0.0 ---------------- Multilevel CTCTCACATCATTCTC consensus TG TTCC A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 1942 388 1.91e-09 TTCAAATGTA CTCTCACGTCACTCTC GTTCTCTCCC 8669 409 4.34e-09 TTTGTTGTTT CTCTCACTTCTTTCTC CACTTGCAGC 25977 404 1.36e-07 CACCAACAAC CTCCCACATCCTCCTC CACCCTCCGT 1941 435 1.06e-06 TCGTGCCGGC CTCCCACTTCAGCCAC TTTGTACTTG 21393 180 1.36e-06 AAGAGAATGT CTGTCACTGCTTTCTC TTCCCTTCGT 4796 423 1.55e-06 ATGATACATG CTACCATGTCTCTCTC ATAAAATTCA 38187 474 1.75e-06 AAATGCTCAC CTCTCACACTACTCTC ACATTCACCG 23773 349 2.82e-06 CATACACCTC CTCTGATATCATTGTC TCTTTGAGCA 13448 219 3.53e-06 CTGCTCTAGA CTCTCGTTTCTCTCAC CTCCTACCTT 22642 467 4.40e-06 CCCTTTGTTT ATCTGATGTCCTCCTC TCGCGGCGAA 25324 244 7.44e-06 TCGATCGGGG ATGTGACCTCACTCTC TACGAGAATG 8382 415 8.24e-06 CCCTCGCTTG CAATCATATCACACTC GTCCGTATCA 11231 309 1.00e-05 AGCTGGACAC AACTCACATTTTTCAC GTGAATGATT 5425 338 1.76e-05 GAACGTTAGC CTCGCTCGTCACACTC GTCACCTCAA 260997 213 2.10e-05 TTATCATCCA ATCTAATGGTACTCTC TCCGACCTGA 11933 400 2.50e-05 CCTCCTTTTA CTCACACCTTTTTCGC TTTAAAATTT 25807 68 3.22e-05 ATCTGGGAGT CTCTCATAGTTGGCTC AACCGACGAA 8371 274 3.49e-05 TCCAACACAT CTACAACATTATACAC ATCCATCAGA 21825 346 4.80e-05 AAACTCAACG CTCGTACCTCTTCCCC TCTTTGCTCT 1755 293 4.80e-05 CCGTCTAGTA CTAAAATTTCCTCCTC AACGCATCCA 2594 217 5.18e-05 GAAGGACCGT CTGTGGCGGTATCCTC GACACCATCG 7974 263 6.97e-05 TCGATTGTTG CTCTTGCCTTACCCTA CCCTAGCCAC 7247 223 9.24e-05 TACTCTGATA CACTGATGTCTGTCAA TATATGTCAA 24077 474 1.13e-04 TGGAACTTGA ATAGCACATCATACAA TACACAGTAA 261844 185 2.80e-04 GATGCCCCCG CTTGCATCGCATCCAA ACAAGATTCC 11489 46 3.83e-04 GATCGTTCAT CACCAACTTTCGCGTC AGTATGAGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1942 1.9e-09 387_[+1]_97 8669 4.3e-09 408_[+1]_76 25977 1.4e-07 403_[+1]_81 1941 1.1e-06 434_[+1]_50 21393 1.4e-06 179_[+1]_305 4796 1.5e-06 422_[+1]_62 38187 1.7e-06 473_[+1]_11 23773 2.8e-06 348_[+1]_136 13448 3.5e-06 218_[+1]_266 22642 4.4e-06 466_[+1]_18 25324 7.4e-06 243_[+1]_241 8382 8.2e-06 414_[+1]_70 11231 1e-05 308_[+1]_176 5425 1.8e-05 337_[+1]_147 260997 2.1e-05 212_[+1]_272 11933 2.5e-05 399_[+1]_85 25807 3.2e-05 67_[+1]_417 8371 3.5e-05 273_[+1]_211 21825 4.8e-05 345_[+1]_139 1755 4.8e-05 292_[+1]_192 2594 5.2e-05 216_[+1]_268 7974 7e-05 262_[+1]_222 7247 9.2e-05 222_[+1]_262 24077 0.00011 473_[+1]_11 261844 0.00028 184_[+1]_300 11489 0.00038 45_[+1]_439 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=26 1942 ( 388) CTCTCACGTCACTCTC 1 8669 ( 409) CTCTCACTTCTTTCTC 1 25977 ( 404) CTCCCACATCCTCCTC 1 1941 ( 435) CTCCCACTTCAGCCAC 1 21393 ( 180) CTGTCACTGCTTTCTC 1 4796 ( 423) CTACCATGTCTCTCTC 1 38187 ( 474) CTCTCACACTACTCTC 1 23773 ( 349) CTCTGATATCATTGTC 1 13448 ( 219) CTCTCGTTTCTCTCAC 1 22642 ( 467) ATCTGATGTCCTCCTC 1 25324 ( 244) ATGTGACCTCACTCTC 1 8382 ( 415) CAATCATATCACACTC 1 11231 ( 309) AACTCACATTTTTCAC 1 5425 ( 338) CTCGCTCGTCACACTC 1 260997 ( 213) ATCTAATGGTACTCTC 1 11933 ( 400) CTCACACCTTTTTCGC 1 25807 ( 68) CTCTCATAGTTGGCTC 1 8371 ( 274) CTACAACATTATACAC 1 21825 ( 346) CTCGTACCTCTTCCCC 1 1755 ( 293) CTAAAATTTCCTCCTC 1 2594 ( 217) CTGTGGCGGTATCCTC 1 7974 ( 263) CTCTTGCCTTACCCTA 1 7247 ( 223) CACTGATGTCTGTCAA 1 24077 ( 474) ATAGCACATCATACAA 1 261844 ( 185) CTTGCATCGCATCCAA 1 11489 ( 46) CACCAACTTTCGCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 12610 bayes= 9.45029 E= 8.2e-006 -48 179 -1134 -1134 -80 -1134 -1134 169 -48 149 -104 -277 -180 -28 -62 114 -80 131 -30 -177 166 -1134 -104 -277 -1134 140 -1134 55 20 -28 19 -19 -1134 -260 -30 155 -1134 149 -1134 40 90 -60 -1134 40 -1134 57 -62 93 -80 57 -262 81 -1134 199 -162 -1134 1 -260 -262 132 -80 186 -1134 -1134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 26 E= 8.2e-006 0.192308 0.807692 0.000000 0.000000 0.153846 0.000000 0.000000 0.846154 0.192308 0.653846 0.115385 0.038462 0.076923 0.192308 0.153846 0.576923 0.153846 0.576923 0.192308 0.076923 0.846154 0.000000 0.115385 0.038462 0.000000 0.615385 0.000000 0.384615 0.307692 0.192308 0.269231 0.230769 0.000000 0.038462 0.192308 0.769231 0.000000 0.653846 0.000000 0.346154 0.500000 0.153846 0.000000 0.346154 0.000000 0.346154 0.153846 0.500000 0.153846 0.346154 0.038462 0.461538 0.000000 0.923077 0.076923 0.000000 0.269231 0.038462 0.038462 0.653846 0.153846 0.846154 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CTCTCA[CT][AGT]T[CT][AT][TC][TC]C[TA]C -------------------------------------------------------------------------------- Time 5.84 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 21 llr = 238 E-value = 2.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :76:851733524:7445392 pos.-specific C a11a:38146:7372343613 probability G :1::211:2:1:21::11::: matrix T :13::1:2::3::2:2:11:5 bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * Relative 1.3 * ** * Entropy 1.1 * ** * * * (16.3 bits) 0.8 * ** * * * * * 0.6 * ** ** * * ** ** 0.4 ******** *** ** ***** 0.2 ********************* 0.0 --------------------- Multilevel CAACAACACCACACAACACAT consensus T C AATAC CCACA C sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25807 174 3.14e-11 TCCGCCCACC CAACACCACCACACAACCCAT CACCAGGGAG 25977 303 8.94e-08 TCCTCAACAG CAACAACAACTACCCAATCAT GCCACGAAAC 8669 477 1.90e-07 AAGATAGTAT CAACAAGACATCACAACATAC ACC 23773 21 1.90e-07 GTGCACCTAC CGACACCTACTCACCAAACAT GTCTGTAGCC 21825 381 2.71e-07 TTGCGACAAG CAACAACTCATAACACACAAC TAGCAACCGA 1755 371 5.34e-07 ATAATCGTGG CAACAACCCCACATCCAACCC CTCAACACTC 11933 32 5.34e-07 CTCCATCACC CATCAACATCAACCATCTCAT ATCCAACAGA 13448 479 8.18e-07 GCATCCTCAA CAGCAACAACAACTACCCAAT C 24077 300 9.07e-07 GAAGGCAACG CAACAGCAAAGCACCACCAAC AATCATGTGA 1942 154 1.11e-06 TCCCCACAAA CATCAAACACACGTACACCAT GACGAGGCCA 38187 72 3.16e-06 AGGAGAATTC CAACAAAAGCTTACACAATAC AACTTGGTAC 7974 451 4.11e-06 CAAAACACTG CTCCGACACATCGTATCACAT CACAAACCGC 11231 432 5.77e-06 GAATAACTCA CATCACATCAACGCAAAGCAA AGGAGCACAA 8371 459 6.26e-06 GCACATCGCC CAACACGAGCACCCTACACCA AAGTCTCTGT 5425 431 6.26e-06 TTCATGCTGG CTACAACAATGCACACGACCT GAACCGATCA 1941 379 6.26e-06 TCTCAACGCT CCACATCAAAGCAGAACAAAT AAACAAGTCA 8382 453 7.36e-06 CACCTCTCCT CAACGCCAGCACTAACACAAT TTACACTGTA 7247 132 1.26e-05 TCAGAGTGTT CATCGTCACCACCGATGATAC TTTTTGTTTG 2594 322 1.26e-05 ATTCAAAAAG CTCCACCAGCACCCATTGAAT GCATAGACCA 260997 143 2.55e-05 GATCCAAGAG CGTCGACCGCTACCAGCACAA TGGCCAAGAC 22642 362 2.72e-05 GACAACCAAC CCTCAGCTCAACGCCTGACAA CTCAACGCTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25807 3.1e-11 173_[+2]_306 25977 8.9e-08 302_[+2]_177 8669 1.9e-07 476_[+2]_3 23773 1.9e-07 20_[+2]_459 21825 2.7e-07 380_[+2]_99 1755 5.3e-07 370_[+2]_109 11933 5.3e-07 31_[+2]_448 13448 8.2e-07 478_[+2]_1 24077 9.1e-07 299_[+2]_180 1942 1.1e-06 153_[+2]_326 38187 3.2e-06 71_[+2]_408 7974 4.1e-06 450_[+2]_29 11231 5.8e-06 431_[+2]_48 8371 6.3e-06 458_[+2]_21 5425 6.3e-06 430_[+2]_49 1941 6.3e-06 378_[+2]_101 8382 7.4e-06 452_[+2]_27 7247 1.3e-05 131_[+2]_348 2594 1.3e-05 321_[+2]_158 260997 2.5e-05 142_[+2]_337 22642 2.7e-05 361_[+2]_118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=21 25807 ( 174) CAACACCACCACACAACCCAT 1 25977 ( 303) CAACAACAACTACCCAATCAT 1 8669 ( 477) CAACAAGACATCACAACATAC 1 23773 ( 21) CGACACCTACTCACCAAACAT 1 21825 ( 381) CAACAACTCATAACACACAAC 1 1755 ( 371) CAACAACCCCACATCCAACCC 1 11933 ( 32) CATCAACATCAACCATCTCAT 1 13448 ( 479) CAGCAACAACAACTACCCAAT 1 24077 ( 300) CAACAGCAAAGCACCACCAAC 1 1942 ( 154) CATCAAACACACGTACACCAT 1 38187 ( 72) CAACAAAAGCTTACACAATAC 1 7974 ( 451) CTCCGACACATCGTATCACAT 1 11231 ( 432) CATCACATCAACGCAAAGCAA 1 8371 ( 459) CAACACGAGCACCCTACACCA 1 5425 ( 431) CTACAACAATGCACACGACCT 1 1941 ( 379) CCACATCAAAGCAGAACAAAT 1 8382 ( 453) CAACGCCAGCACTAACACAAT 1 7247 ( 132) CATCGTCACCACCGATGATAC 1 2594 ( 322) CTCCACCAGCACCCATTGAAT 1 260997 ( 143) CGTCGACCGCTACCAGCACAA 1 22642 ( 362) CCTCAGCTCAACGCCTGACAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12480 bayes= 9.5179 E= 2.2e-002 -1104 210 -1104 -1104 132 -129 -131 -88 109 -129 -231 12 -1104 210 -1104 -1104 160 -1104 -31 -1104 97 29 -131 -146 -90 171 -131 -1104 132 -71 -1104 -46 32 71 1 -246 32 141 -1104 -246 97 -1104 -73 34 -17 162 -1104 -246 68 52 -31 -246 -249 152 -131 -46 142 3 -1104 -246 51 52 -231 -14 51 88 -73 -246 97 29 -131 -146 9 129 -1104 -88 168 -71 -1104 -1104 -49 29 -1104 100 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 21 E= 2.2e-002 0.000000 1.000000 0.000000 0.000000 0.666667 0.095238 0.095238 0.142857 0.571429 0.095238 0.047619 0.285714 0.000000 1.000000 0.000000 0.000000 0.809524 0.000000 0.190476 0.000000 0.523810 0.285714 0.095238 0.095238 0.142857 0.761905 0.095238 0.000000 0.666667 0.142857 0.000000 0.190476 0.333333 0.380952 0.238095 0.047619 0.333333 0.619048 0.000000 0.047619 0.523810 0.000000 0.142857 0.333333 0.238095 0.714286 0.000000 0.047619 0.428571 0.333333 0.190476 0.047619 0.047619 0.666667 0.095238 0.190476 0.714286 0.238095 0.000000 0.047619 0.380952 0.333333 0.047619 0.238095 0.380952 0.428571 0.142857 0.047619 0.523810 0.285714 0.095238 0.095238 0.285714 0.571429 0.000000 0.142857 0.857143 0.142857 0.000000 0.000000 0.190476 0.285714 0.000000 0.523810 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CA[AT]CA[AC]CA[CAG][CA][AT][CA][AC]C[AC][ACT][CA][AC][CA]A[TC] -------------------------------------------------------------------------------- Time 11.15 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 26 llr = 262 E-value = 1.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:33:82186323295:36: pos.-specific C :1:11::322::53:21:12 probability G 53528:45:17725118737 matrix T 4714:132:2:2:::32:1: bits 2.1 1.9 1.7 1.5 * Relative 1.3 ** * * Entropy 1.1 ** * * * ** (14.6 bits) 0.8 * ** * ** * ** * 0.6 ** ** * ** ** ** * 0.4 *** ** ******* **** 0.2 ******************** 0.0 -------------------- Multilevel GTGTGAGGAAGGCGAAGGAG consensus TGAA TC A AC T AG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 25324 381 3.98e-09 TTGCGAGAGT GTGAGAGCAAGGAGAAGGAC CCCAAATCTC 2594 86 1.18e-08 ATGATCCATC TCGAGAGCAAGGCGATGGAG ATAACGCAGC 11489 177 7.82e-08 CATGTGATGT GTGTGATGCAGACGATGGGG GTGTTTCGAA 5425 152 9.04e-08 TGTAGGCTGT GTAGGAGCAAAGCCAAGGAC GGTGGCTGCC 7247 384 8.03e-07 GCACCGTCGT GTGAGATGAAATCAAATGAG AGCGTTGGGC 24077 344 8.03e-07 TGAATGCGTT GTGTGAGCAAGGGCATGGGT ATGATGCTGC 1755 184 2.17e-06 GAATGATATT TTTTGTTGCAAGCGAAGGAG TGGGGGAAGG 4796 189 2.41e-06 GCCATTGTTT TTGTGATGAAAGGAAGGAGG TGCTGTGGTG 25977 193 2.41e-06 ATTCAGCCAA TTAAGAGTACAGACACGAAG AGATACATCG 13448 372 2.41e-06 ATTCAGCCAA TTAAGAGTACAGACACGAAG AGATACATCG 21825 68 2.67e-06 TGAATTACAG GTGAGCGTACGGCGACGAAG TAAATGAGAG 38187 201 4.87e-06 CAAACGTATC GTACGTGCAAGTCAATGGAG TTAGGGAGTA 21393 17 4.87e-06 TAGTTGCCAC GGTGGATTCAGACGATGGAG TACGTCCCAG 261844 294 5.90e-06 CCAACGATTT GGATGATGAGGAGGATGAGG ATGTGCCGTT 8382 338 7.12e-06 TTACTTTCTC TTGTGAAAAGGGACAATGAG TAAACCACAT 23773 125 9.37e-06 GAGTTAATGG AGATGAGGACGGCAAATAGG ACAGTGGGCG 22642 82 1.12e-05 CATTTGCAAA TCGGGAGGATGAGGAAGGTG CACGTGACAC 11231 76 1.73e-05 GATGGCTTGG ATGATATGATGGCCGAGGAG AAGGCGGAGC 11933 89 4.15e-05 GGCAGCTACC AGAGCAATCAGGCGATGGGG TGGAAGGATA 260997 164 4.82e-05 ACCAGCACAA TGGCCAAGACGGCGAGGGTG AGGAAGCAAA 25807 35 4.82e-05 CCATGCCGTG GGCAGAACAAGGAGATGAAA ACTATCTGGG 8371 140 6.45e-05 CAAAGGTATC TTTTGAGCGTGGGGACGGGC CTCATCACGA 1942 217 6.45e-05 TGAAAGCCAA GTGTCAAGAAGGAAGACGAC CAAGTGGGTT 7974 217 7.43e-05 TCCTCTTTAG GGGGGACAAAGTCCAAGACG GCGGGAACTC 1941 185 9.14e-05 GAGTGTTGTC TTATGTTGATGTTGAACGAG AGTTTACCTG 8669 36 1.54e-04 GTCAGATGCG TTAAGATGAAAAACGATGCC TTGACATCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25324 4e-09 380_[+3]_100 2594 1.2e-08 85_[+3]_395 11489 7.8e-08 176_[+3]_304 5425 9e-08 151_[+3]_329 7247 8e-07 383_[+3]_97 24077 8e-07 343_[+3]_137 1755 2.2e-06 183_[+3]_297 4796 2.4e-06 188_[+3]_292 25977 2.4e-06 192_[+3]_288 13448 2.4e-06 371_[+3]_109 21825 2.7e-06 67_[+3]_413 38187 4.9e-06 200_[+3]_280 21393 4.9e-06 16_[+3]_464 261844 5.9e-06 293_[+3]_187 8382 7.1e-06 337_[+3]_143 23773 9.4e-06 124_[+3]_356 22642 1.1e-05 81_[+3]_399 11231 1.7e-05 75_[+3]_405 11933 4.2e-05 88_[+3]_392 260997 4.8e-05 163_[+3]_317 25807 4.8e-05 34_[+3]_446 8371 6.5e-05 139_[+3]_341 1942 6.5e-05 216_[+3]_264 7974 7.4e-05 216_[+3]_264 1941 9.1e-05 184_[+3]_296 8669 0.00015 35_[+3]_445 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=26 25324 ( 381) GTGAGAGCAAGGAGAAGGAC 1 2594 ( 86) TCGAGAGCAAGGCGATGGAG 1 11489 ( 177) GTGTGATGCAGACGATGGGG 1 5425 ( 152) GTAGGAGCAAAGCCAAGGAC 1 7247 ( 384) GTGAGATGAAATCAAATGAG 1 24077 ( 344) GTGTGAGCAAGGGCATGGGT 1 1755 ( 184) TTTTGTTGCAAGCGAAGGAG 1 4796 ( 189) TTGTGATGAAAGGAAGGAGG 1 25977 ( 193) TTAAGAGTACAGACACGAAG 1 13448 ( 372) TTAAGAGTACAGACACGAAG 1 21825 ( 68) GTGAGCGTACGGCGACGAAG 1 38187 ( 201) GTACGTGCAAGTCAATGGAG 1 21393 ( 17) GGTGGATTCAGACGATGGAG 1 261844 ( 294) GGATGATGAGGAGGATGAGG 1 8382 ( 338) TTGTGAAAAGGGACAATGAG 1 23773 ( 125) AGATGAGGACGGCAAATAGG 1 22642 ( 82) TCGGGAGGATGAGGAAGGTG 1 11231 ( 76) ATGATATGATGGCCGAGGAG 1 11933 ( 89) AGAGCAATCAGGCGATGGGG 1 260997 ( 164) TGGCCAAGACGGCGAGGGTG 1 25807 ( 35) GGCAGAACAAGGAGATGAAA 1 8371 ( 140) TTTTGAGCGTGGGGACGGGC 1 1942 ( 217) GTGTCAAGAAGGAAGACGAC 1 7974 ( 217) GGGGGACAAAGTCCAAGACG 1 1941 ( 185) TTATGTTGATGTTGAACGAG 1 8669 ( 36) TTAAGATGAAAAACGATGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 12506 bayes= 8.90689 E= 1.2e-003 -121 -1134 96 69 -1134 -160 19 132 37 -260 108 -119 37 -160 -30 55 -1134 -101 184 -277 166 -260 -1134 -119 -48 -260 84 40 -180 21 96 -45 159 -60 -262 -1134 111 -28 -162 -77 1 -1134 163 -1134 -48 -1134 147 -77 1 110 -30 -277 -48 40 108 -1134 172 -1134 -104 -1134 79 -60 -162 23 -1134 -160 170 -77 20 -1134 155 -1134 111 -160 19 -177 -280 -28 163 -277 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 26 E= 1.2e-003 0.115385 0.000000 0.461538 0.423077 0.000000 0.076923 0.269231 0.653846 0.346154 0.038462 0.500000 0.115385 0.346154 0.076923 0.192308 0.384615 0.000000 0.115385 0.846154 0.038462 0.846154 0.038462 0.000000 0.115385 0.192308 0.038462 0.423077 0.346154 0.076923 0.269231 0.461538 0.192308 0.807692 0.153846 0.038462 0.000000 0.576923 0.192308 0.076923 0.153846 0.269231 0.000000 0.730769 0.000000 0.192308 0.000000 0.653846 0.153846 0.269231 0.500000 0.192308 0.038462 0.192308 0.307692 0.500000 0.000000 0.884615 0.000000 0.115385 0.000000 0.461538 0.153846 0.076923 0.307692 0.000000 0.076923 0.769231 0.153846 0.307692 0.000000 0.692308 0.000000 0.576923 0.076923 0.269231 0.076923 0.038462 0.192308 0.730769 0.038462 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT][TG][GA][TA]GA[GT][GC]AA[GA]G[CA][GC]A[AT]G[GA][AG]G -------------------------------------------------------------------------------- Time 16.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11231 1.61e-05 75_[+3(1.73e-05)]_213_\ [+1(1.00e-05)]_107_[+2(5.77e-06)]_48 11489 7.76e-05 176_[+3(7.82e-08)]_304 11933 9.51e-06 31_[+2(5.34e-07)]_36_[+3(4.15e-05)]_\ 291_[+1(2.50e-05)]_85 13448 1.88e-07 218_[+1(3.53e-06)]_137_\ [+3(2.41e-06)]_87_[+2(8.18e-07)]_1 1755 1.22e-06 124_[+2(5.67e-05)]_38_\ [+3(2.17e-06)]_89_[+1(4.80e-05)]_62_[+2(5.34e-07)]_109 1941 1.02e-05 184_[+3(9.14e-05)]_174_\ [+2(6.26e-06)]_35_[+1(1.06e-06)]_50 1942 5.09e-09 153_[+2(1.11e-06)]_42_\ [+3(6.45e-05)]_151_[+1(1.91e-09)]_97 21393 1.43e-04 16_[+3(4.87e-06)]_143_\ [+1(1.36e-06)]_305 21825 8.00e-07 67_[+3(2.67e-06)]_258_\ [+1(4.80e-05)]_19_[+2(2.71e-07)]_99 22642 2.09e-05 81_[+3(1.12e-05)]_260_\ [+2(2.72e-05)]_84_[+1(4.40e-06)]_18 23773 1.40e-07 20_[+2(1.90e-07)]_83_[+3(9.37e-06)]_\ 204_[+1(2.82e-06)]_136 24077 1.72e-06 299_[+2(9.07e-07)]_23_\ [+3(8.03e-07)]_137 25324 1.70e-07 222_[+3(1.46e-05)]_1_[+1(7.44e-06)]_\ 121_[+3(3.98e-09)]_100 25807 1.95e-09 34_[+3(4.82e-05)]_13_[+1(3.22e-05)]_\ 90_[+2(3.14e-11)]_306 2594 2.04e-07 85_[+3(1.18e-08)]_88_[+3(7.97e-05)]_\ 3_[+1(5.18e-05)]_89_[+2(1.26e-05)]_158 25977 1.24e-09 39_[+1(3.53e-06)]_137_\ [+3(2.41e-06)]_90_[+2(8.94e-08)]_59_[+2(2.41e-06)]_[+1(1.36e-07)]_81 260997 2.70e-04 142_[+2(2.55e-05)]_[+3(4.82e-05)]_\ 29_[+1(2.10e-05)]_272 261844 7.34e-03 293_[+3(5.90e-06)]_187 38187 6.41e-07 71_[+2(3.16e-06)]_108_\ [+3(4.87e-06)]_253_[+1(1.75e-06)]_11 4796 8.19e-05 188_[+3(2.41e-06)]_76_\ [+3(4.82e-05)]_49_[+1(5.58e-05)]_53_[+1(1.55e-06)]_62 5425 2.60e-07 151_[+3(9.04e-08)]_166_\ [+1(1.76e-05)]_77_[+2(6.26e-06)]_49 7247 1.50e-05 131_[+2(1.26e-05)]_70_\ [+1(9.24e-05)]_145_[+3(8.03e-07)]_97 7974 2.26e-04 216_[+3(7.43e-05)]_26_\ [+1(6.97e-05)]_30_[+2(7.49e-05)]_121_[+2(4.11e-06)]_29 8371 1.60e-04 139_[+3(6.45e-05)]_114_\ [+1(3.49e-05)]_169_[+2(6.26e-06)]_21 8382 7.69e-06 337_[+3(7.12e-06)]_57_\ [+1(8.24e-06)]_22_[+2(7.36e-06)]_27 8669 4.64e-09 408_[+1(4.34e-09)]_52_\ [+2(1.90e-07)]_3 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************