******************************************************************************** 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/415/415.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10626 1.0000 500 12570 1.0000 500 1732 1.0000 500 20630 1.0000 500 20925 1.0000 500 21284 1.0000 500 21364 1.0000 500 21839 1.0000 500 21852 1.0000 500 21997 1.0000 500 22023 1.0000 500 22333 1.0000 500 22426 1.0000 500 22620 1.0000 500 22922 1.0000 500 23494 1.0000 500 23587 1.0000 500 23602 1.0000 500 24231 1.0000 500 24618 1.0000 500 24633 1.0000 500 24753 1.0000 500 24783 1.0000 500 24877 1.0000 500 24997 1.0000 500 25323 1.0000 500 25397 1.0000 500 25451 1.0000 500 25600 1.0000 500 25603 1.0000 500 25617 1.0000 500 25640 1.0000 500 25911 1.0000 500 260818 1.0000 500 262120 1.0000 500 263755 1.0000 500 269724 1.0000 500 269896 1.0000 500 4347 1.0000 500 5829 1.0000 500 6922 1.0000 500 7121 1.0000 500 8733 1.0000 500 9790 1.0000 500 bd705 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/415/415.seqs.fa -oc motifs/415 -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= 45 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= 22500 N= 45 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.232 G 0.243 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.232 G 0.243 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 26 llr = 314 E-value = 4.1e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::1:2111:3:23:22:22:: pos.-specific C 12:43:32:3::152:1:122 probability G 1:82:93:a:17:253:53:8 matrix T 88:45:47:39252159348: bits 2.1 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * * * * * ** Entropy 1.1 * * * * * * ** (17.4 bits) 0.8 *** * ** * * ** 0.6 *** * ** ** * *** ** 0.4 ****** ** **** *** ** 0.2 ********************* 0.0 --------------------- Multilevel TTGTTGTTGATGTCGTTGTTG consensus CC CC C AGAG TGC sequence G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 21284 244 1.92e-10 AAGAATGTTA TTGTTGCTGTTGTTGTTGTTG GCCATTCTCA 25323 9 2.44e-10 TATTGCTG TTGCTGCTGCTGTCAGTGGTG GATGCGGAGG 12570 29 6.17e-08 GAAGAGGCTG TTGCCGTTGCTGACGATACTG GAGACGATCA 24877 3 1.77e-07 AG TTACTGCTGCTTTGATTGTTG CAGGTGCTGC 25397 192 1.97e-07 TTCATGCGTA TTGGTGGCGCTGTCCATATTG TTTCTGGTGT 22426 52 1.97e-07 GTCGACGGCG TCGTTGTCGCTGAGCTTGATG ACGGACATGC 23602 172 2.20e-07 GCTGCGGTGA TTGGAGTTGTTGTCAGTTGTC AGGAGGAGGG 22620 58 3.03e-07 TGCATGTGCA TCGCCGCTGTTGTTGGTAGCG AGGACGACGG 6922 134 3.36e-07 TGTAGTTTGA CTGCTGGTGTTGTGGGTTGCG AGACGGCCAA 23587 71 3.36e-07 ATCTTGACCG TCGTCGTCGTCGTCGTTGTTG TAGCCGTTTG 21839 103 3.36e-07 GTGGTGGTGG TTGCTGCAGATGATGATGATG ATGATACATG 21997 151 5.04e-07 TCGGTTGACC TTGTCGGAGAGGACATTGTTG CCGGCGACGG 25600 89 8.17e-07 TTTCAAGACG TTGTTGTTGCTACCCTTTTCC CTTCCTTTCC 23494 84 8.17e-07 GGAGGGTGGA TTGATGATGATATTGGTGTTG ATAAAGTTGG bd705 56 1.42e-06 GTCGTGTTCA TTGTCGTCGTGTTCATTGTCG TCGTCTTTCC 21364 184 1.42e-06 GTGGATGATG TTGCCGATGATGTGTTCAGTG AAGACGACAC 20630 411 1.69e-06 TTTAACACCT TTGTAATTGATATTCTTTGTG CTCTTGTTTA 24753 58 1.84e-06 GGATGGTTTG TTTGTGTCGCTGACTTTTTTG ACGCTGCCGA 5829 28 3.30e-06 GAACGACTAG GTGCTGGCATTGACGTTTGTG CTCTTACCAC 24997 336 3.30e-06 AGTACATCAT CCGTTGCTGCTGAGCATGATG CATGATATCT 22333 438 3.87e-06 TGTTGAGCGG TAGCAGCTGATTACAGTGTCG GCAAGTCCAT 22922 45 4.89e-06 TGGTGCAACG TGGTGGGTGATGGCGGTGGTG GAGGAGGACG 25451 403 7.11e-06 GAGTCCATCG TTGTCGGTGATAAGTGTGCCC CATTTCTTAT 24783 359 1.17e-05 CCTTGAGATC GTACAGTTGATGCCGTTTATC GAGGAATCGT 263755 223 1.53e-05 TCGACAATCT TTGGAAGTGGTATCGTCGTTG TTCTCTCCCA 260818 3 2.40e-05 CA TTATCGTTGCTTCTGTCAGTC TAAGATTGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21284 1.9e-10 243_[+1]_236 25323 2.4e-10 8_[+1]_471 12570 6.2e-08 28_[+1]_451 24877 1.8e-07 2_[+1]_477 25397 2e-07 191_[+1]_288 22426 2e-07 51_[+1]_428 23602 2.2e-07 171_[+1]_308 22620 3e-07 57_[+1]_422 6922 3.4e-07 133_[+1]_346 23587 3.4e-07 70_[+1]_409 21839 3.4e-07 102_[+1]_377 21997 5e-07 150_[+1]_329 25600 8.2e-07 88_[+1]_391 23494 8.2e-07 83_[+1]_396 bd705 1.4e-06 55_[+1]_424 21364 1.4e-06 183_[+1]_296 20630 1.7e-06 410_[+1]_69 24753 1.8e-06 57_[+1]_422 5829 3.3e-06 27_[+1]_452 24997 3.3e-06 335_[+1]_144 22333 3.9e-06 437_[+1]_42 22922 4.9e-06 44_[+1]_435 25451 7.1e-06 402_[+1]_77 24783 1.2e-05 358_[+1]_121 263755 1.5e-05 222_[+1]_257 260818 2.4e-05 2_[+1]_477 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=26 21284 ( 244) TTGTTGCTGTTGTTGTTGTTG 1 25323 ( 9) TTGCTGCTGCTGTCAGTGGTG 1 12570 ( 29) TTGCCGTTGCTGACGATACTG 1 24877 ( 3) TTACTGCTGCTTTGATTGTTG 1 25397 ( 192) TTGGTGGCGCTGTCCATATTG 1 22426 ( 52) TCGTTGTCGCTGAGCTTGATG 1 23602 ( 172) TTGGAGTTGTTGTCAGTTGTC 1 22620 ( 58) TCGCCGCTGTTGTTGGTAGCG 1 6922 ( 134) CTGCTGGTGTTGTGGGTTGCG 1 23587 ( 71) TCGTCGTCGTCGTCGTTGTTG 1 21839 ( 103) TTGCTGCAGATGATGATGATG 1 21997 ( 151) TTGTCGGAGAGGACATTGTTG 1 25600 ( 89) TTGTTGTTGCTACCCTTTTCC 1 23494 ( 84) TTGATGATGATATTGGTGTTG 1 bd705 ( 56) TTGTCGTCGTGTTCATTGTCG 1 21364 ( 184) TTGCCGATGATGTGTTCAGTG 1 20630 ( 411) TTGTAATTGATATTCTTTGTG 1 24753 ( 58) TTTGTGTCGCTGACTTTTTTG 1 5829 ( 28) GTGCTGGCATTGACGTTTGTG 1 24997 ( 336) CCGTTGCTGCTGAGCATGATG 1 22333 ( 438) TAGCAGCTGATTACAGTGTCG 1 22922 ( 45) TGGTGGGTGATGGCGGTGGTG 1 25451 ( 403) TTGTCGGTGATAAGTGTGCCC 1 24783 ( 359) GTACAGTTGATGCCGTTTATC 1 263755 ( 223) TTGGAAGTGGTATCGTCGTTG 1 260818 ( 3) TTATCGTTGCTTCTGTCAGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 21600 bayes= 10.2276 E= 4.1e-012 -1134 -159 -166 171 -280 -59 -265 158 -121 -1134 180 -274 -280 73 -66 71 -48 41 -265 84 -180 -1134 193 -1134 -180 22 15 58 -180 -1 -1134 142 -280 -1134 199 -1134 37 58 -265 6 -1134 -259 -166 178 -48 -1134 143 -75 37 -101 -265 95 -1134 122 -7 -16 -21 -27 93 -116 -80 -1134 34 106 -1134 -101 -1134 178 -48 -1134 115 6 -80 -159 51 71 -1134 -1 -1134 158 -1134 -27 173 -1134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 26 E= 4.1e-012 0.000000 0.076923 0.076923 0.846154 0.038462 0.153846 0.038462 0.769231 0.115385 0.000000 0.846154 0.038462 0.038462 0.384615 0.153846 0.423077 0.192308 0.307692 0.038462 0.461538 0.076923 0.000000 0.923077 0.000000 0.076923 0.269231 0.269231 0.384615 0.076923 0.230769 0.000000 0.692308 0.038462 0.000000 0.961538 0.000000 0.346154 0.346154 0.038462 0.269231 0.000000 0.038462 0.076923 0.884615 0.192308 0.000000 0.653846 0.153846 0.346154 0.115385 0.038462 0.500000 0.000000 0.538462 0.230769 0.230769 0.230769 0.192308 0.461538 0.115385 0.153846 0.000000 0.307692 0.538462 0.000000 0.115385 0.000000 0.884615 0.192308 0.000000 0.538462 0.269231 0.153846 0.076923 0.346154 0.423077 0.000000 0.230769 0.000000 0.769231 0.000000 0.192308 0.807692 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTG[TC][TC]G[TCG][TC]G[ACT]TG[TA][CGT][GA][TG]T[GT][TG][TC]G -------------------------------------------------------------------------------- Time 16.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 31 llr = 291 E-value = 4.6e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 5262:a4:92:9 pos.-specific C 5511a:2a:1a: probability G :1:1::3:13:1 matrix T :236::2::5:: bits 2.1 * * * 1.9 * * * 1.7 ** * * 1.5 ** ** * Relative 1.3 ** ** ** Entropy 1.1 * ** ** ** (13.6 bits) 0.8 * ** ** ** 0.6 * * ** ** ** 0.4 ****** ** ** 0.2 ****** ***** 0.0 ------------ Multilevel CCATCAACATCA consensus A T G G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 22333 291 3.01e-07 CGCCTCTCCC CCATCAACAGCA AGCAGACGCT 22620 293 4.26e-07 ACCAACAACG CCTTCAACATCA TGAATTCTTG bd705 213 5.47e-07 GCAGTGCCAT CCATCATCATCA ACGCTCATAA 21997 10 6.00e-07 ATTAGGGCT CCATCAGCAGCA GTAGTAGTCG 23587 478 1.09e-06 CCGACCGGGC ACATCATCATCA AGATCAAGAT 25603 264 2.26e-06 GATGTTGTAG CCATCAACACCA AGCATCAAAA 10626 110 3.63e-06 CTTCCCCGAG CCATCAACATCG CACAACTAAA 269896 443 4.25e-06 AGCAGCATGA ACTTCAGCAGCA GTCACAGTGG 25640 477 4.25e-06 GCCCAAACAT CCATCACCACCA TCAATATCCA 1732 318 5.64e-06 CCAGACACAT CAATCAGCAGCA CATTTTGGAG 24783 121 6.69e-06 GCGGCCTCCA ATTTCAACATCA ACTCTTCGGC 25617 486 8.27e-06 TCCACACAAA ACAACAACAGCA AAT 21852 336 8.27e-06 CCTCCTCTCG CCAACAACAACA TACATGCTTC 260818 479 1.10e-05 CCAGGAGGAA CGATCACCATCA TTCTCTGAAG 24997 8 1.52e-05 CACCTAC ATATCACCAACA CCGCTGAGGT 22922 78 1.52e-05 GGAGGACGAG ACATCACCGTCA CGGAGAAGAG 9790 408 2.09e-05 GGGCAGGGAG ACAGCAGCAACA CTGACAGTCG 25451 85 2.27e-05 GTGTGGTGCA ACAGCATCAGCA GTGAGAGAGA 25911 468 3.03e-05 GATAGACACA CCCGCAGCATCA TCACAGCACC 22023 434 3.62e-05 ACGTATTAGC CACTCATCATCA CTCGCTCCAC 6922 483 5.02e-05 ACCCTCCACC AATCCAACATCA TACACC 269724 15 6.68e-05 AAGACTCGCC AATTCACCATCG TCTTCTTCCA 21364 446 6.68e-05 ACGAGGTGCA CTTCCAGCAGCA CAACTCTTGC 24618 430 7.19e-05 TCCCCCACAC CTCACAGCATCA GTGCTAACAC 24633 486 7.72e-05 GCCTCTCGGC ACATCACCGTCG CTT 25600 396 8.17e-05 TGAACCTTCC AGTTCAACACCA ATTTCATCGT 23602 446 8.70e-05 GCGCACCTTC CTATCGCCATCA TCAAAGCAGG 263755 150 9.28e-05 AACAAGAATC AATACAGCAACA GTCACTGCAA 25323 245 9.28e-05 GGCCGACTGG ACAGCAACGACA TCAACGGCCG 24231 480 9.82e-05 ACCAACCAAA CATCCATCAGCA ATCATCATC 5829 171 1.16e-04 CCCTCGTCTT CTAACAACAACG ATGTGAGGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22333 3e-07 290_[+2]_198 22620 4.3e-07 292_[+2]_196 bd705 5.5e-07 212_[+2]_276 21997 6e-07 9_[+2]_479 23587 1.1e-06 477_[+2]_11 25603 2.3e-06 263_[+2]_225 10626 3.6e-06 109_[+2]_379 269896 4.3e-06 442_[+2]_46 25640 4.3e-06 476_[+2]_12 1732 5.6e-06 317_[+2]_171 24783 6.7e-06 120_[+2]_368 25617 8.3e-06 485_[+2]_3 21852 8.3e-06 335_[+2]_153 260818 1.1e-05 478_[+2]_10 24997 1.5e-05 7_[+2]_481 22922 1.5e-05 77_[+2]_411 9790 2.1e-05 407_[+2]_81 25451 2.3e-05 84_[+2]_404 25911 3e-05 467_[+2]_21 22023 3.6e-05 433_[+2]_55 6922 5e-05 482_[+2]_6 269724 6.7e-05 14_[+2]_474 21364 6.7e-05 445_[+2]_43 24618 7.2e-05 429_[+2]_59 24633 7.7e-05 485_[+2]_3 25600 8.2e-05 395_[+2]_93 23602 8.7e-05 445_[+2]_43 263755 9.3e-05 149_[+2]_339 25323 9.3e-05 244_[+2]_244 24231 9.8e-05 479_[+2]_9 5829 0.00012 170_[+2]_318 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=31 22333 ( 291) CCATCAACAGCA 1 22620 ( 293) CCTTCAACATCA 1 bd705 ( 213) CCATCATCATCA 1 21997 ( 10) CCATCAGCAGCA 1 23587 ( 478) ACATCATCATCA 1 25603 ( 264) CCATCAACACCA 1 10626 ( 110) CCATCAACATCG 1 269896 ( 443) ACTTCAGCAGCA 1 25640 ( 477) CCATCACCACCA 1 1732 ( 318) CAATCAGCAGCA 1 24783 ( 121) ATTTCAACATCA 1 25617 ( 486) ACAACAACAGCA 1 21852 ( 336) CCAACAACAACA 1 260818 ( 479) CGATCACCATCA 1 24997 ( 8) ATATCACCAACA 1 22922 ( 78) ACATCACCGTCA 1 9790 ( 408) ACAGCAGCAACA 1 25451 ( 85) ACAGCATCAGCA 1 25911 ( 468) CCCGCAGCATCA 1 22023 ( 434) CACTCATCATCA 1 6922 ( 483) AATCCAACATCA 1 269724 ( 15) AATTCACCATCG 1 21364 ( 446) CTTCCAGCAGCA 1 24618 ( 430) CTCACAGCATCA 1 24633 ( 486) ACATCACCGTCG 1 25600 ( 396) AGTTCAACACCA 1 23602 ( 446) CTATCGCCATCA 1 263755 ( 150) AATACAGCAACA 1 25323 ( 245) ACAGCAACGACA 1 24231 ( 480) CATCCATCAGCA 1 5829 ( 171) CTAACAACAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 22005 bayes= 10.1764 E= 4.6e-008 76 124 -1160 -1160 -47 124 -191 -41 120 -126 -1160 17 -73 -126 -91 125 -1160 211 -1160 -1160 185 -1160 -291 -1160 41 -4 9 -68 -1160 211 -1160 -1160 175 -1160 -133 -1160 -47 -126 9 81 -1160 211 -1160 -1160 170 -1160 -91 -1160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 31 E= 4.6e-008 0.451613 0.548387 0.000000 0.000000 0.193548 0.548387 0.064516 0.193548 0.612903 0.096774 0.000000 0.290323 0.161290 0.096774 0.129032 0.612903 0.000000 1.000000 0.000000 0.000000 0.967742 0.000000 0.032258 0.000000 0.354839 0.225806 0.258065 0.161290 0.000000 1.000000 0.000000 0.000000 0.903226 0.000000 0.096774 0.000000 0.193548 0.096774 0.258065 0.451613 0.000000 1.000000 0.000000 0.000000 0.870968 0.000000 0.129032 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA]C[AT]TCA[AGC]CA[TG]CA -------------------------------------------------------------------------------- Time 32.42 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 21 llr = 243 E-value = 2.4e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::25:192:9215:1 pos.-specific C 32::3:1:::1::1:: probability G 1188:9818a:78239 matrix T 672:21:::::1:17: bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * **** * Entropy 1.1 ** ****** ** (16.7 bits) 0.8 *** ******** ** 0.6 **** ******** ** 0.4 **** ******** ** 0.2 **************** 0.0 ---------------- Multilevel TTGGAGGAGGAGGATG consensus C AC A GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 25603 190 9.61e-10 TGAGTATTGT TTGGAGGAGGAGGGTG TTGCTGCTCG bd705 86 5.11e-08 GTCGTCTTTC CTGGAGGAGGAAGAGG ATCTCCGTTC 21284 111 9.88e-08 ACCTGCTCTG CTCGAGGAGGAGGATG AACCGCCAAT 23587 11 1.61e-07 GTGGTTGTGG TTGGAGGCGGAGGAGG TCTTGCGTTC 20630 479 2.06e-07 ATCGATAACG TTGGTGGAGGAGATTG AGGGAC 9790 427 4.48e-07 ACACTGACAG TCGACGGAGGAGGGGG GGGGGCTGTA 22620 434 4.48e-07 GAGCTTCGAG TCGGGGGAGGAGGAGG AATTGAGTCG 21839 51 7.53e-07 GATGGGTGAT TTGGCGGAGGATGATT GGATGGTGAG 22426 154 8.37e-07 GGCTGTGGGT TTTGAGGAAGAGGATA GAGTGAGAGG 21997 43 1.35e-06 AGCGGATGCG TCGGTGGAGGCTGATG TATCGTCGTT 21364 47 1.49e-06 TGGTGACTTT GTTGCGGAGGAAGCTG TAGGTAGAGG 23494 66 2.55e-06 GTGATCTACC CTGGCTAAGGAGGGTG GATTGATGAT 25451 273 4.24e-06 GGCACTGCAA TTGGAGGAGGATCATA CTGCCTCGCC 263755 268 4.59e-06 AATCTATAAA GTGGAGGGGGCGAATG ATGCGATTGC 24783 439 4.97e-06 AGAGGTGTCA TTGGCTCAAGAGGTTG TGTGGAATCA 12570 13 6.29e-06 GGAACGAGCT GCGATGGAAGAGGCTG TTGCCGTTGC 269896 226 7.35e-06 TGTTCGCATG CTTGAGGAAGAAAAGG CGGTCCTGTT 21852 128 7.35e-06 AGAAGTTGAT CGGATGGAGGAAGTTG TAAGACTAAC 6922 188 8.51e-06 TGTGAGGCGA CTGACGCGGGAGGGGG GAAACAGGGG 5829 345 1.06e-05 CTTGGGAGGA TGGAAGAAGGCGGGTG AAGAGTGATT 260818 141 1.60e-05 GCCGACTTTG TTTGAGCAAGAGTCTG AATCTCTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25603 9.6e-10 189_[+3]_295 bd705 5.1e-08 85_[+3]_399 21284 9.9e-08 110_[+3]_374 23587 1.6e-07 10_[+3]_474 20630 2.1e-07 478_[+3]_6 9790 4.5e-07 426_[+3]_58 22620 4.5e-07 433_[+3]_51 21839 7.5e-07 50_[+3]_434 22426 8.4e-07 153_[+3]_331 21997 1.4e-06 42_[+3]_442 21364 1.5e-06 46_[+3]_438 23494 2.5e-06 65_[+3]_419 25451 4.2e-06 272_[+3]_212 263755 4.6e-06 267_[+3]_217 24783 5e-06 438_[+3]_46 12570 6.3e-06 12_[+3]_472 269896 7.3e-06 225_[+3]_259 21852 7.3e-06 127_[+3]_357 6922 8.5e-06 187_[+3]_297 5829 1.1e-05 344_[+3]_140 260818 1.6e-05 140_[+3]_344 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=21 25603 ( 190) TTGGAGGAGGAGGGTG 1 bd705 ( 86) CTGGAGGAGGAAGAGG 1 21284 ( 111) CTCGAGGAGGAGGATG 1 23587 ( 11) TTGGAGGCGGAGGAGG 1 20630 ( 479) TTGGTGGAGGAGATTG 1 9790 ( 427) TCGACGGAGGAGGGGG 1 22620 ( 434) TCGGGGGAGGAGGAGG 1 21839 ( 51) TTGGCGGAGGATGATT 1 22426 ( 154) TTTGAGGAAGAGGATA 1 21997 ( 43) TCGGTGGAGGCTGATG 1 21364 ( 47) GTTGCGGAGGAAGCTG 1 23494 ( 66) CTGGCTAAGGAGGGTG 1 25451 ( 273) TTGGAGGAGGATCATA 1 263755 ( 268) GTGGAGGGGGCGAATG 1 24783 ( 439) TTGGCTCAAGAGGTTG 1 12570 ( 13) GCGATGGAAGAGGCTG 1 269896 ( 226) CTTGAGGAAGAAAAGG 1 21852 ( 128) CGGATGGAGGAAGTTG 1 6922 ( 188) CTGACGCGGGAGGGGG 1 5829 ( 345) TGGAAGAAGGCGGGTG 1 260818 ( 141) TTTGAGCAAGAGTCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 21825 bayes= 10.3251 E= 2.4e-005 -1104 30 -76 115 -1104 -28 -135 147 -1104 -228 165 -44 -17 -1104 165 -1104 83 30 -235 -44 -1104 -1104 190 -144 -149 -70 165 -1104 168 -228 -135 -1104 -17 -1104 165 -1104 -1104 -1104 204 -1104 168 -70 -1104 -1104 -49 -1104 146 -85 -90 -228 165 -243 83 -70 -3 -85 -1104 -1104 24 147 -149 -1104 182 -243 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 21 E= 2.4e-005 0.000000 0.285714 0.142857 0.571429 0.000000 0.190476 0.095238 0.714286 0.000000 0.047619 0.761905 0.190476 0.238095 0.000000 0.761905 0.000000 0.476190 0.285714 0.047619 0.190476 0.000000 0.000000 0.904762 0.095238 0.095238 0.142857 0.761905 0.000000 0.857143 0.047619 0.095238 0.000000 0.238095 0.000000 0.761905 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.190476 0.000000 0.666667 0.142857 0.142857 0.047619 0.761905 0.047619 0.476190 0.142857 0.238095 0.142857 0.000000 0.000000 0.285714 0.714286 0.095238 0.000000 0.857143 0.047619 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC]TG[GA][AC]GGA[GA]GAGG[AG][TG]G -------------------------------------------------------------------------------- Time 47.55 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10626 1.58e-02 109_[+2(3.63e-06)]_138_\ [+2(3.03e-05)]_229 12570 1.23e-05 12_[+3(6.29e-06)]_[+1(6.17e-08)]_\ 451 1732 3.08e-02 317_[+2(5.64e-06)]_171 20630 4.48e-06 410_[+1(1.69e-06)]_47_\ [+3(2.06e-07)]_6 20925 7.09e-01 500 21284 1.59e-09 110_[+3(9.88e-08)]_117_\ [+1(1.92e-10)]_236 21364 2.84e-06 46_[+3(1.49e-06)]_121_\ [+1(1.42e-06)]_181_[+1(1.99e-05)]_39_[+2(6.68e-05)]_43 21839 3.81e-06 50_[+3(7.53e-07)]_36_[+1(3.36e-07)]_\ 377 21852 3.36e-04 127_[+3(7.35e-06)]_192_\ [+2(8.27e-06)]_153 21997 1.43e-08 9_[+2(6.00e-07)]_21_[+3(1.35e-06)]_\ 92_[+1(5.04e-07)]_329 22023 7.60e-02 433_[+2(3.62e-05)]_55 22333 3.25e-05 290_[+2(3.01e-07)]_135_\ [+1(3.87e-06)]_42 22426 5.70e-06 51_[+1(1.97e-07)]_81_[+3(8.37e-07)]_\ 331 22620 2.35e-09 57_[+1(3.03e-07)]_160_\ [+1(3.30e-06)]_33_[+2(4.26e-07)]_129_[+3(4.48e-07)]_51 22922 8.02e-05 44_[+1(4.89e-06)]_12_[+2(1.52e-05)]_\ 411 23494 1.73e-05 65_[+3(2.55e-06)]_2_[+1(8.17e-07)]_\ 396 23587 2.41e-09 10_[+3(1.61e-07)]_44_[+1(3.36e-07)]_\ 386_[+2(1.09e-06)]_11 23602 1.40e-04 171_[+1(2.20e-07)]_253_\ [+2(8.70e-05)]_43 24231 9.41e-02 479_[+2(9.82e-05)]_9 24618 9.50e-02 429_[+2(7.19e-05)]_59 24633 2.38e-01 485_[+2(7.72e-05)]_3 24753 4.65e-03 57_[+1(1.84e-06)]_422 24783 7.12e-06 120_[+2(6.69e-06)]_226_\ [+1(1.17e-05)]_59_[+3(4.97e-06)]_46 24877 8.25e-04 2_[+1(1.77e-07)]_477 24997 4.02e-04 7_[+2(1.52e-05)]_316_[+1(3.30e-06)]_\ 144 25323 1.60e-07 8_[+1(2.44e-10)]_215_[+2(9.28e-05)]_\ 244 25397 1.64e-03 191_[+1(1.97e-07)]_288 25451 1.17e-05 84_[+2(2.27e-05)]_112_\ [+2(7.19e-05)]_52_[+3(4.24e-06)]_114_[+1(7.11e-06)]_77 25600 1.03e-03 88_[+1(8.17e-07)]_286_\ [+2(8.17e-05)]_93 25603 9.50e-08 189_[+3(9.61e-10)]_58_\ [+2(2.26e-06)]_204_[+2(3.92e-05)]_9 25617 1.76e-02 91_[+2(9.82e-05)]_382_\ [+2(8.27e-06)]_3 25640 2.86e-02 476_[+2(4.25e-06)]_12 25911 1.06e-01 467_[+2(3.03e-05)]_21 260818 5.77e-05 2_[+1(2.40e-05)]_117_[+3(1.60e-05)]_\ 322_[+2(1.10e-05)]_10 262120 1.53e-01 500 263755 8.33e-05 149_[+2(9.28e-05)]_61_\ [+1(1.53e-05)]_24_[+3(4.59e-06)]_217 269724 9.56e-02 14_[+2(6.68e-05)]_474 269896 6.85e-05 225_[+3(7.35e-06)]_50_\ [+2(8.27e-06)]_139_[+2(4.25e-06)]_46 4347 3.51e-01 500 5829 5.49e-05 27_[+1(3.30e-06)]_296_\ [+3(1.06e-05)]_140 6922 2.90e-06 133_[+1(3.36e-07)]_33_\ [+3(8.51e-06)]_279_[+2(5.02e-05)]_6 7121 9.66e-01 500 8733 6.62e-01 500 9790 1.80e-04 407_[+2(2.09e-05)]_7_[+3(4.48e-07)]_\ 58 bd705 1.66e-09 15_[+1(1.02e-05)]_19_[+1(1.42e-06)]_\ 9_[+3(5.11e-08)]_111_[+2(5.47e-07)]_276 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************