******************************************************************************** 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/454/454.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10198 1.0000 500 11691 1.0000 500 16926 1.0000 500 22120 1.0000 500 22388 1.0000 500 22900 1.0000 500 2312 1.0000 500 23177 1.0000 500 23388 1.0000 500 23886 1.0000 500 260937 1.0000 500 261261 1.0000 500 261771 1.0000 500 262029 1.0000 500 263929 1.0000 500 264326 1.0000 500 269416 1.0000 500 30882 1.0000 500 3180 1.0000 500 3693 1.0000 500 3824 1.0000 500 3854 1.0000 500 5304 1.0000 500 5499 1.0000 500 6491 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/454/454.seqs.fa -oc motifs/454 -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= 25 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= 12500 N= 25 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.264 C 0.229 G 0.240 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.229 G 0.240 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 25 llr = 241 E-value = 1.2e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 16314::24:33:54: pos.-specific C 9148:795:a5383:9 probability G :3::32121:12:::: matrix T ::2131:25:121261 bits 2.1 1.9 * 1.7 * * * 1.5 * * * * Relative 1.3 * * * * * Entropy 1.1 * * * * * * (13.9 bits) 0.9 * * ** * * ** 0.6 * * ** * **** 0.4 ** **** *** **** 0.2 *********** **** 0.0 ---------------- Multilevel CACCACCCTCCACATC consensus GA GG GA AC CA sequence T T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 5304 459 1.48e-08 AGTCATCGTC CACCTCCCTCCTCATC CACCACTCCT 269416 249 2.40e-08 GGACCTCAAA CGCCGCCCACCACATC CACGGTCTTA 22388 482 3.71e-08 CTTCTCGTCT CACCTCCCACACCATC ATA 264326 403 1.04e-06 GCCAGCCGAA CGCCACGCTCCGCAAC GAACAACCAA 2312 397 1.68e-06 CTATGGGCCT CACCGCCGACGTCAAC GAGTTCACAA 3693 227 1.88e-06 ACCGAACTGC CGCCTGCTACCCCAAC ACATCAACAT 262029 63 2.94e-06 GCAACAATGG CAACACCTGCAGCAAC ATTCAGAGCC 16926 446 6.76e-06 ACCAATCAGC CCTCTCCCTCCACTAC ACAACACTAC 3180 458 8.22e-06 ATTGGCTCTA CGCCAGGCACCACCAC TGACAAAGAA 260937 402 8.22e-06 ACGATGTCAT CACAACCCTCCGTCTC TGGAGCAACT 5499 10 9.06e-06 GAGTGTCAT CATCGGCATCATCATC TTGACGGACG 10198 282 9.06e-06 TTCTTCGGTT CACCGTCTTCCCCTTC CTGGAGGTAG 261771 46 1.31e-05 TTGACTTTTG CAAAGCCTACCTCAAC GAACACCACA 22900 484 1.31e-05 CAGCCGGAAC AAACACCGGCCACCAC C 23886 143 1.57e-05 CACTTGACAG CAACGCCATCACCAAT ATCACATCAC 22120 374 2.04e-05 AAACCGAAAG CAACAGCAGCCTCTTC TGCCAAAAGG 261261 191 2.41e-05 TACACTTCAT CGTCTCCCAACACCAC AAAATCACAA 3824 478 2.84e-05 GTTTCCTTTG CGACGCCGTCACGCTC CTCCGTC 3854 14 3.08e-05 AAAGATTGAA CTCCACCGTCGGCTTC ATTGTGTTTG 11691 18 3.33e-05 TTCATGAATG CAGCACCCTCTCTATC TCTCTATCTC 263929 419 4.21e-05 GTGACGTTCA CGCTAGCAACAACAAC AACGATACCA 30882 350 4.54e-05 CGACAACGAA AGTCTTCCTCCGCCTC CTGGTCCTCC 23177 479 1.14e-04 ATACACCAAC CAACTACCACAAAATC GAAGCA 23388 484 1.90e-04 ACACAACAAC AATTACCGACGGCCTC C 6491 376 2.70e-04 GAGCATGTTG CCACACCCTCTCTCTT CTCTTATTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5304 1.5e-08 458_[+1]_26 269416 2.4e-08 248_[+1]_236 22388 3.7e-08 481_[+1]_3 264326 1e-06 402_[+1]_82 2312 1.7e-06 396_[+1]_88 3693 1.9e-06 226_[+1]_258 262029 2.9e-06 62_[+1]_422 16926 6.8e-06 445_[+1]_39 3180 8.2e-06 457_[+1]_27 260937 8.2e-06 401_[+1]_83 5499 9.1e-06 9_[+1]_475 10198 9.1e-06 281_[+1]_203 261771 1.3e-05 45_[+1]_439 22900 1.3e-05 483_[+1]_1 23886 1.6e-05 142_[+1]_342 22120 2e-05 373_[+1]_111 261261 2.4e-05 190_[+1]_294 3824 2.8e-05 477_[+1]_7 3854 3.1e-05 13_[+1]_471 11691 3.3e-05 17_[+1]_467 263929 4.2e-05 418_[+1]_66 30882 4.5e-05 349_[+1]_135 23177 0.00011 478_[+1]_6 23388 0.00019 483_[+1]_1 6491 0.00027 375_[+1]_109 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=25 5304 ( 459) CACCTCCCTCCTCATC 1 269416 ( 249) CGCCGCCCACCACATC 1 22388 ( 482) CACCTCCCACACCATC 1 264326 ( 403) CGCCACGCTCCGCAAC 1 2312 ( 397) CACCGCCGACGTCAAC 1 3693 ( 227) CGCCTGCTACCCCAAC 1 262029 ( 63) CAACACCTGCAGCAAC 1 16926 ( 446) CCTCTCCCTCCACTAC 1 3180 ( 458) CGCCAGGCACCACCAC 1 260937 ( 402) CACAACCCTCCGTCTC 1 5499 ( 10) CATCGGCATCATCATC 1 10198 ( 282) CACCGTCTTCCCCTTC 1 261771 ( 46) CAAAGCCTACCTCAAC 1 22900 ( 484) AAACACCGGCCACCAC 1 23886 ( 143) CAACGCCATCACCAAT 1 22120 ( 374) CAACAGCAGCCTCTTC 1 261261 ( 191) CGTCTCCCAACACCAC 1 3824 ( 478) CGACGCCGTCACGCTC 1 3854 ( 14) CTCCACCGTCGGCTTC 1 11691 ( 18) CAGCACCCTCTCTATC 1 263929 ( 419) CGCTAGCAACAACAAC 1 30882 ( 350) AGTCTTCCTCCGCCTC 1 23177 ( 479) CAACTACCACAAAATC 1 23388 ( 484) AATTACCGACGGCCTC 1 6491 ( 376) CCACACCCTCTCTCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 12125 bayes= 8.91886 E= 1.2e-006 -114 194 -1129 -1129 109 -151 42 -274 28 94 -258 -42 -172 188 -1129 -174 74 -1129 22 6 -272 157 -26 -174 -1129 201 -158 -1129 -72 107 -26 -74 60 -1129 -100 84 -272 207 -1129 -1129 9 118 -100 -174 9 29 0 -42 -272 181 -258 -116 98 48 -1129 -74 74 -1129 -1129 106 -1129 201 -1129 -174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 25 E= 1.2e-006 0.120000 0.880000 0.000000 0.000000 0.560000 0.080000 0.320000 0.040000 0.320000 0.440000 0.040000 0.200000 0.080000 0.840000 0.000000 0.080000 0.440000 0.000000 0.280000 0.280000 0.040000 0.680000 0.200000 0.080000 0.000000 0.920000 0.080000 0.000000 0.160000 0.480000 0.200000 0.160000 0.400000 0.000000 0.120000 0.480000 0.040000 0.960000 0.000000 0.000000 0.280000 0.520000 0.120000 0.080000 0.280000 0.280000 0.240000 0.200000 0.040000 0.800000 0.040000 0.120000 0.520000 0.320000 0.000000 0.160000 0.440000 0.000000 0.000000 0.560000 0.000000 0.920000 0.000000 0.080000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AG][CAT]C[AGT][CG]C[CG][TA]C[CA][ACGT]C[AC][TA]C -------------------------------------------------------------------------------- Time 5.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 25 llr = 258 E-value = 5.4e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :45142:11:51242312::: pos.-specific C :2:12::11:1:12:1::1:: probability G 922722871832725:852a3 matrix T 123125117227:236128:6 bits 2.1 1.9 * 1.7 * * 1.5 * * Relative 1.3 * * * * * Entropy 1.1 * * * * * (14.9 bits) 0.9 * * * * * ** 0.6 * * **** ** * *** 0.4 * ** ***** ** *** *** 0.2 * ** ******** ******* 0.0 --------------------- Multilevel GAAGATGGTGATGAGTGGTGT consensus GT CA GGAGTA A G sequence CG GG TA T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 269416 83 1.68e-09 GTCTGACGGT GATGATGGTGATGAGTGTGGT GTGTTCTGGT 22900 39 1.29e-08 ACCAGCCAGT GGAGTTGGTGATGGGCGATGT AGTATCGATG 260937 39 1.50e-08 AGTGACAGTT GTAGCTGTTGAGGAGTGGTGT TGATTTGCGA 16926 110 1.10e-07 TGACCTCAGC GGAGATGGAGGTGGGTAGTGT CGAGTTACTG 262029 240 1.61e-07 TGGTTGGTTG GGAGGTGGCGATATGAGGTGT GGCTGTATCA 22388 38 4.77e-07 GGTCAACGCG GTGGAAGGAGATGGGAGGGGT GAAGACTTGC 3693 195 5.99e-07 AAGAGAAAGG GGAGAAGGTGTCAGGTGGTGT CACCGAACTG 6491 38 1.04e-06 AAGTAGTACA GTGGAGGGTGTTGATTTGTGG TTGCGAAGTA 3854 198 1.29e-06 ATGCGAGTGT GCACCGGATGATGTTTGGTGT GTACCGTTGC 23886 288 3.91e-06 ATGAATGACG GCGGTGTGTGGTGCAAGATGT CAGATCAGAT 10198 7 3.91e-06 TCGTAG GCAGTTGCTTGTCTGTGGTGG ATGACTTTGT 264326 25 5.71e-06 TATGCGAAGC GGTGATGGCTGAGATTGTTGT TGTGGATCGG 2312 122 8.21e-06 TTGGTTAGTG GAAAAGGGTGCTGGTTGTTGC AAAAGTGCAC 261261 71 9.81e-06 GTATCCTTGC GATGTTTTTGGTATTTGTTGT ATCGTCGCCT 263929 254 1.39e-05 GCATCGTGCT GCTTCTGCTCATGAGAGATGT TCTACTCGAT 23177 174 1.94e-05 TATCAAATGT GAGGATGTGGAAGTGTGACGT TTGGTACGAT 261771 456 2.10e-05 CAACTGGGAG GAAGGGGGGTTGGAAAGTTGG TATGTTTGCT 3824 172 2.68e-05 GGTTAACAAA TAAATAGATGATGAATGATGT TTGAAGATAC 22120 17 2.90e-05 CTTTGTTGAA TAAGATGGTTGGCAATGATGG AGCTTCTGAT 5499 274 3.13e-05 AACACCAGAG GAGGGAGGGGGTAAGAGGGGA AGGAGGAACA 5304 334 3.66e-05 AGATGTAGGG GAATGTGGAGAGGGAAAGTGG TAGGTTTAGG 23388 368 4.95e-05 TTGGGGCAGG GGAGAGGGTGATACGTTTGAT ATGTAATTAG 30882 251 6.16e-05 GTTATGCTTT GCTTGAAGTGTTGAGTGGCGG ACGAAGGAGG 3180 73 6.62e-05 TGGTGGTGGT GTTGCTGCTGCTGCTGGCTGT TCATAGCTGT 11691 246 8.78e-05 TTACTTTTGA GTTCCATGTGAGGCTCGGTGG GCGTTCCCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 269416 1.7e-09 82_[+2]_397 22900 1.3e-08 38_[+2]_441 260937 1.5e-08 38_[+2]_441 16926 1.1e-07 109_[+2]_370 262029 1.6e-07 239_[+2]_240 22388 4.8e-07 37_[+2]_442 3693 6e-07 194_[+2]_285 6491 1e-06 37_[+2]_442 3854 1.3e-06 197_[+2]_282 23886 3.9e-06 287_[+2]_192 10198 3.9e-06 6_[+2]_473 264326 5.7e-06 24_[+2]_455 2312 8.2e-06 121_[+2]_358 261261 9.8e-06 70_[+2]_409 263929 1.4e-05 253_[+2]_226 23177 1.9e-05 173_[+2]_306 261771 2.1e-05 455_[+2]_24 3824 2.7e-05 171_[+2]_308 22120 2.9e-05 16_[+2]_463 5499 3.1e-05 273_[+2]_206 5304 3.7e-05 333_[+2]_146 23388 4.9e-05 367_[+2]_112 30882 6.2e-05 250_[+2]_229 3180 6.6e-05 72_[+2]_407 11691 8.8e-05 245_[+2]_234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=25 269416 ( 83) GATGATGGTGATGAGTGTGGT 1 22900 ( 39) GGAGTTGGTGATGGGCGATGT 1 260937 ( 39) GTAGCTGTTGAGGAGTGGTGT 1 16926 ( 110) GGAGATGGAGGTGGGTAGTGT 1 262029 ( 240) GGAGGTGGCGATATGAGGTGT 1 22388 ( 38) GTGGAAGGAGATGGGAGGGGT 1 3693 ( 195) GGAGAAGGTGTCAGGTGGTGT 1 6491 ( 38) GTGGAGGGTGTTGATTTGTGG 1 3854 ( 198) GCACCGGATGATGTTTGGTGT 1 23886 ( 288) GCGGTGTGTGGTGCAAGATGT 1 10198 ( 7) GCAGTTGCTTGTCTGTGGTGG 1 264326 ( 25) GGTGATGGCTGAGATTGTTGT 1 2312 ( 122) GAAAAGGGTGCTGGTTGTTGC 1 261261 ( 71) GATGTTTTTGGTATTTGTTGT 1 263929 ( 254) GCTTCTGCTCATGAGAGATGT 1 23177 ( 174) GAGGATGTGGAAGTGTGACGT 1 261771 ( 456) GAAGGGGGGTTGGAAAGTTGG 1 3824 ( 172) TAAATAGATGATGAATGATGT 1 22120 ( 17) TAAGATGGTTGGCAATGATGG 1 5499 ( 274) GAGGGAGGGGGTAAGAGGGGA 1 5304 ( 334) GAATGTGGAGAGGGAAAGTGG 1 23388 ( 368) GGAGAGGGTGATACGTTTGAT 1 30882 ( 251) GCTTGAAGTGTTGAGTGGCGG 1 3180 ( 73) GTTGCTGCTGCTGCTGGCTGT 1 11691 ( 246) GTTCCATGTGAGGCTCGGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12000 bayes= 8.90388 E= 5.4e-004 -1129 -1129 194 -174 45 -19 0 -42 98 -1129 -26 6 -172 -151 159 -116 60 -19 -26 -42 -14 -1129 0 96 -272 -1129 181 -116 -172 -93 150 -116 -114 -151 -100 134 -1129 -251 174 -74 86 -151 22 -74 -172 -251 -26 134 -40 -151 159 -1129 60 -52 0 -42 -40 -1129 112 6 9 -151 -258 116 -172 -1129 181 -174 -14 -251 100 -16 -1129 -151 -58 151 -272 -1129 200 -1129 -272 -251 22 126 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 25 E= 5.4e-004 0.000000 0.000000 0.920000 0.080000 0.360000 0.200000 0.240000 0.200000 0.520000 0.000000 0.200000 0.280000 0.080000 0.080000 0.720000 0.120000 0.400000 0.200000 0.200000 0.200000 0.240000 0.000000 0.240000 0.520000 0.040000 0.000000 0.840000 0.120000 0.080000 0.120000 0.680000 0.120000 0.120000 0.080000 0.120000 0.680000 0.000000 0.040000 0.800000 0.160000 0.480000 0.080000 0.280000 0.160000 0.080000 0.040000 0.200000 0.680000 0.200000 0.080000 0.720000 0.000000 0.400000 0.160000 0.240000 0.200000 0.200000 0.000000 0.520000 0.280000 0.280000 0.080000 0.040000 0.600000 0.080000 0.000000 0.840000 0.080000 0.240000 0.040000 0.480000 0.240000 0.000000 0.080000 0.160000 0.760000 0.040000 0.000000 0.960000 0.000000 0.040000 0.040000 0.280000 0.640000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AGCT][ATG]G[ACGT][TAG]GGTG[AG][TG][GA][AGT][GTA][TA]G[GAT]TG[TG] -------------------------------------------------------------------------------- Time 9.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 25 llr = 213 E-value = 2.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 221::::2232: pos.-specific C ::2::2:243:1 probability G 6::a::a144:6 matrix T 286:a8:5::83 bits 2.1 * * 1.9 * * 1.7 ** * 1.5 ** * Relative 1.3 * **** Entropy 1.1 * **** * (12.3 bits) 0.9 * **** * 0.6 ******* ** 0.4 ******* **** 0.2 ************ 0.0 ------------ Multilevel GTTGTTGTCGTG consensus TAC CGAAT sequence A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 23388 6 6.76e-08 TTTCC GTTGTTGTCGTG TCAGGCCGAG 10198 63 8.14e-07 TTTCAGCATG GTTGTTGCGGTG GTTGTGTACG 3824 210 4.28e-06 TACGTTGCAT GTTGTTGTAATG TAAAGAAAAA 2312 91 7.90e-06 TTGTTGCTTA GTTGTTGGGATG GGAGGTCCGT 5499 190 1.02e-05 CCACGAGTTT TTCGTTGTCCTG GCCATTCGTG 261771 218 1.02e-05 TCTTGAAGCA ATTGTTGTCGAG GGAAGAAAGA 3854 486 1.20e-05 CGTCAGTCTG GTCGTCGTCGTG CCT 263929 212 1.58e-05 AAATTCGTCA GTAGTTGTGCTG GCTGCATTTC 16926 140 1.58e-05 TCGAGTTACT GATGTTGACGTG GCTCATGGTG 260937 475 2.31e-05 CTGTGATGCA GTTGTTGAGGTC GTCTTTTTCA 23177 73 2.90e-05 AACACCATCA GTCGTTGCGATT TCCGTTCGGT 23886 12 3.24e-05 CATGTTGATG GATGTTGTAGTT CGTTTGGGTA 5304 74 3.65e-05 GAAACAAAGA GATGTTGTGGAT ATTGCAGCAC 264326 262 4.89e-05 CAAGGCTGAA TTTGTCGCGGTG GTCGGCAACG 6491 443 5.36e-05 AATGACCTGA ATTGTTGGCCTT TATTTTCCCC 262029 12 5.36e-05 AGGGCTCCGT GTCGTCGTCATT CGACAAGCAA 30882 155 5.90e-05 GGGCTTCATC ATTGTTGCAATG CAAATTCTGC 269416 116 1.17e-04 GTTCTGGTGG TTTGTTGAACTT GGTCGGTATA 261261 434 1.17e-04 ACAGGGAGAG GTGGTTGTCAAG GAACACGCAC 22388 298 1.27e-04 AACAGTTTTG TTTGTTGGCATC TGTGGAGGGT 11691 1 1.46e-04 . GTTGTTGTTCAT GAATGCAGCA 22120 323 1.91e-04 GCATAGAAGC ATTGTCGCGCAG AATGAGCTAT 3693 53 2.04e-04 ACAAAACTCC TAAGTTGTGGTT GGTAGTATCG 3180 313 3.92e-04 CTCTCGCGAG TACGTTGTGCAC TTCCCACAGA 22900 63 4.13e-04 GCGATGTAGT ATCGATGACGTG GACGATAATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23388 6.8e-08 5_[+3]_483 10198 8.1e-07 62_[+3]_426 3824 4.3e-06 209_[+3]_279 2312 7.9e-06 90_[+3]_398 5499 1e-05 189_[+3]_299 261771 1e-05 217_[+3]_271 3854 1.2e-05 485_[+3]_3 263929 1.6e-05 211_[+3]_277 16926 1.6e-05 139_[+3]_349 260937 2.3e-05 474_[+3]_14 23177 2.9e-05 72_[+3]_416 23886 3.2e-05 11_[+3]_477 5304 3.6e-05 73_[+3]_415 264326 4.9e-05 261_[+3]_227 6491 5.4e-05 442_[+3]_46 262029 5.4e-05 11_[+3]_477 30882 5.9e-05 154_[+3]_334 269416 0.00012 115_[+3]_373 261261 0.00012 433_[+3]_55 22388 0.00013 297_[+3]_191 11691 0.00015 [+3]_488 22120 0.00019 322_[+3]_166 3693 0.0002 52_[+3]_436 3180 0.00039 312_[+3]_176 22900 0.00041 62_[+3]_426 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=25 23388 ( 6) GTTGTTGTCGTG 1 10198 ( 63) GTTGTTGCGGTG 1 3824 ( 210) GTTGTTGTAATG 1 2312 ( 91) GTTGTTGGGATG 1 5499 ( 190) TTCGTTGTCCTG 1 261771 ( 218) ATTGTTGTCGAG 1 3854 ( 486) GTCGTCGTCGTG 1 263929 ( 212) GTAGTTGTGCTG 1 16926 ( 140) GATGTTGACGTG 1 260937 ( 475) GTTGTTGAGGTC 1 23177 ( 73) GTCGTTGCGATT 1 23886 ( 12) GATGTTGTAGTT 1 5304 ( 74) GATGTTGTGGAT 1 264326 ( 262) TTTGTCGCGGTG 1 6491 ( 443) ATTGTTGGCCTT 1 262029 ( 12) GTCGTCGTCATT 1 30882 ( 155) ATTGTTGCAATG 1 269416 ( 116) TTTGTTGAACTT 1 261261 ( 434) GTGGTTGTCAAG 1 22388 ( 298) TTTGTTGGCATC 1 11691 ( 1) GTTGTTGTTCAT 1 22120 ( 323) ATTGTCGCGCAG 1 3693 ( 53) TAAGTTGTGGTT 1 3180 ( 313) TACGTTGTGCAC 1 22900 ( 63) ATCGATGACGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 12225 bayes= 8.93074 E= 2.1e-001 -40 -1129 122 -16 -40 -1129 -1129 158 -172 7 -258 126 -1129 -1129 206 -1129 -272 -1129 -1129 184 -1129 -52 -1129 165 -1129 -1129 206 -1129 -72 -19 -100 96 -72 81 74 -274 9 29 88 -1129 -14 -1129 -1129 151 -1129 -93 122 26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 25 E= 2.1e-001 0.200000 0.000000 0.560000 0.240000 0.200000 0.000000 0.000000 0.800000 0.080000 0.240000 0.040000 0.640000 0.000000 0.000000 1.000000 0.000000 0.040000 0.000000 0.000000 0.960000 0.000000 0.160000 0.000000 0.840000 0.000000 0.000000 1.000000 0.000000 0.160000 0.200000 0.120000 0.520000 0.160000 0.400000 0.400000 0.040000 0.280000 0.280000 0.440000 0.000000 0.240000 0.000000 0.000000 0.760000 0.000000 0.120000 0.560000 0.320000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GTA][TA][TC]GTTG[TC][CG][GAC][TA][GT] -------------------------------------------------------------------------------- Time 14.27 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10198 6.92e-07 6_[+2(3.91e-06)]_35_[+3(8.14e-07)]_\ 20_[+3(2.31e-05)]_175_[+1(9.06e-06)]_14_[+2(5.73e-05)]_168 11691 2.78e-03 17_[+1(3.33e-05)]_212_\ [+2(8.78e-05)]_234 16926 3.05e-07 109_[+2(1.10e-07)]_9_[+3(1.58e-05)]_\ 294_[+1(6.76e-06)]_39 22120 9.24e-04 16_[+2(2.90e-05)]_336_\ [+1(2.04e-05)]_111 22388 6.63e-08 8_[+2(8.78e-05)]_8_[+2(4.77e-07)]_\ 423_[+1(3.71e-08)]_3 22900 1.40e-06 38_[+2(1.29e-08)]_424_\ [+1(1.31e-05)]_1 2312 2.28e-06 90_[+3(7.90e-06)]_19_[+2(8.21e-06)]_\ 254_[+1(1.68e-06)]_88 23177 5.87e-04 72_[+3(2.90e-05)]_89_[+2(1.94e-05)]_\ 306 23388 1.05e-05 5_[+3(6.76e-08)]_350_[+2(4.95e-05)]_\ 112 23886 2.99e-05 11_[+3(3.24e-05)]_119_\ [+1(1.57e-05)]_129_[+2(3.91e-06)]_192 260937 8.42e-08 38_[+2(1.50e-08)]_288_\ [+1(7.07e-05)]_38_[+1(8.22e-06)]_57_[+3(2.31e-05)]_14 261261 2.87e-04 70_[+2(9.81e-06)]_99_[+1(2.41e-05)]_\ 294 261771 4.06e-05 45_[+1(1.31e-05)]_156_\ [+3(1.02e-05)]_226_[+2(2.10e-05)]_24 262029 6.11e-07 11_[+3(5.36e-05)]_39_[+1(2.94e-06)]_\ 161_[+2(1.61e-07)]_240 263929 1.13e-04 211_[+3(1.58e-05)]_30_\ [+2(1.39e-05)]_144_[+1(4.21e-05)]_66 264326 8.20e-07 24_[+2(5.71e-06)]_216_\ [+3(4.89e-05)]_129_[+1(1.04e-06)]_82 269416 2.24e-10 82_[+2(1.68e-09)]_145_\ [+1(2.40e-08)]_236 30882 1.29e-03 154_[+3(5.90e-05)]_84_\ [+2(6.16e-05)]_78_[+1(4.54e-05)]_135 3180 1.51e-03 72_[+2(6.62e-05)]_364_\ [+1(8.22e-06)]_27 3693 4.28e-06 194_[+2(5.99e-07)]_11_\ [+1(1.88e-06)]_139_[+1(1.31e-05)]_103 3824 4.59e-05 171_[+2(2.68e-05)]_17_\ [+3(4.28e-06)]_256_[+1(2.84e-05)]_7 3854 8.49e-06 13_[+1(3.08e-05)]_168_\ [+2(1.29e-06)]_267_[+3(1.20e-05)]_3 5304 4.83e-07 73_[+3(3.65e-05)]_248_\ [+2(3.66e-05)]_104_[+1(1.48e-08)]_26 5499 4.16e-05 9_[+1(9.06e-06)]_164_[+3(1.02e-05)]_\ 72_[+2(3.13e-05)]_206 6491 1.65e-04 37_[+2(1.04e-06)]_384_\ [+3(5.36e-05)]_46 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************