******************************************************************************** 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/107/107.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 20648 1.0000 500 20740 1.0000 500 21677 1.0000 500 21897 1.0000 500 22846 1.0000 500 24376 1.0000 500 25157 1.0000 500 25171 1.0000 500 25386 1.0000 500 25523 1.0000 500 26470 1.0000 500 264776 1.0000 500 268054 1.0000 500 268124 1.0000 500 268160 1.0000 500 268217 1.0000 500 268453 1.0000 500 269135 1.0000 500 269541 1.0000 500 34850 1.0000 500 36099 1.0000 500 4026 1.0000 500 42320 1.0000 500 5563 1.0000 500 6323 1.0000 500 7349 1.0000 500 7887 1.0000 500 928 1.0000 500 bd1182 1.0000 500 bd1790 1.0000 500 bd885 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/107/107.seqs.fa -oc motifs/107 -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= 31 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= 15500 N= 31 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.229 G 0.249 T 0.262 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.229 G 0.249 T 0.262 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 31 llr = 311 E-value = 4.0e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 441737:29:61711614113 pos.-specific C :13:1:211111121:2:12: probability G 42535267:918:68:35247 matrix T 241:112:::2:22145153: bits 2.1 1.9 1.7 * 1.5 ** Relative 1.3 ** Entropy 1.1 * ** * (14.5 bits) 0.9 * *** * ** * 0.6 * ***** ** ** * * 0.4 * ************* * * 0.2 ********************* 0.0 --------------------- Multilevel GAGAGAGGAGAGAGGATGTGG consensus ATCGA TGAGTA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 928 235 1.62e-10 TCCTTGTTGT GAGGGAGGAGAGAGGAGGTGG GTAGATGGGT 25171 169 8.56e-09 ATGGACGGAA GTCAGAGGAGAGATGATGCTG TGAGGTCTGC 22846 170 1.47e-07 TGGGATGAGG GTGAGATGAGTGAGGTTTTGG CAAGGACGGA 36099 364 1.68e-07 TTCTGACGAA GGCAAAGGAGAGAGTAGATGG TCCTCCTACA 268054 202 1.68e-07 GGAGAGCTCG GAGAGATGAGACATGATGTTG AGGGTGTTGA 4026 34 2.83e-07 GAGACATGAG ATGATGGGAGAGAGGAGGCCG ATGAGAATGG bd1790 125 3.64e-07 GTTCTCATCG TTGAGAGGAGGGTGGAGGGGA AGATCAACGT 7349 112 3.64e-07 GTTCTCATCG TTGAGAGGAGGGTGGAGGGGA AGATCAACGT 5563 308 9.44e-07 GAGGTCCAGG AAGAGGTGCGGGAGGTTGTGG TTGGACACAC 269135 287 1.06e-06 GAGGTGTTTG TACGGAGGAGAGAGTTCATCG TTGAGTAGTT 24376 390 1.06e-06 GCGTATTGGT GTCGGTGGAGTGAGGATAGGA GGTCCATGAT 20648 330 1.33e-06 ATAAATAATA TTGAGAGAAGAGAAAATATGG GACCATTGAA 20740 198 2.28e-06 GAGGCGGAGG AGAAGAGGAGGGACGATAGTA GAAAATGTTT 26470 286 3.12e-06 AAATGGTGTG AAGAGAGGAGAGCTGTTGAAG GTTGTGTTGG 269541 275 3.46e-06 TCGCACAAAC AACAAAGAAGAGTGCACATCG TCGTCGTCCT 264776 287 5.17e-06 TTGATACAAA GTCGGACGACAGACGATGACG AAAGAGTTCT 34850 246 6.91e-06 GGATGGCAAA GATGAACGAGAGAGGAAATTA AGTGAATTAG 25386 164 6.91e-06 AAGTCAACGA AACATGTCAGAGAGGTGGTGA GAGAACTTAC 21897 301 6.91e-06 TTGAGTTGGA AAGAAGTAAGACAGGTTATTG GTTGGGCGTT bd885 206 1.58e-05 GAGGCAGTTC GTAAAGCGAGAGAGGTCAACA TGATATGTAT 268160 63 3.66e-05 TGATATTCAT TGAAGAGGAGAAAGATTGGAG AGGCATGACC 268217 159 4.29e-05 GTAAGAAGTT GGCAGAGGAGAGACCACCAGA TGAGAACGGA 25157 267 5.85e-05 GACGTGTAAC ATAAGAGGAGAACTGTCTTTG TTCATAGTGA 42320 289 7.89e-05 TACATGTTGT GTTGAAGAACAGTTGATGGTG TCAGTTTGCT 268124 116 9.12e-05 GCTGTCTAAC ATGGTACAAGTGGGGATATGA TCGAGGAGGA 25523 224 1.13e-04 TAGTAGGAGG ACTAGAGAAGCGAGGAGGCGT TCGTCGTTCA bd1182 243 1.21e-04 TCAAAAAAGC AAGAACGGAGTATCGAAGTCG CTCACGAATG 7887 40 1.21e-04 TGCTGATGAA GCGACATCAGCGACGTCGGCG TCGGCCGGCG 21677 9 1.39e-04 CAATCGCA GACGCTGGAGCAACAATGTTG CCAAGATTGC 6323 174 1.70e-04 GGGGGAATAG AAGACTCGCGAGTGGCGATGG TGTATCCCGT 268453 278 1.70e-04 TGCGTCATAA TGCAAGGCCGTGAAGTTGTTG TATCCATCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 928 1.6e-10 234_[+1]_245 25171 8.6e-09 168_[+1]_311 22846 1.5e-07 169_[+1]_310 36099 1.7e-07 363_[+1]_116 268054 1.7e-07 201_[+1]_278 4026 2.8e-07 33_[+1]_446 bd1790 3.6e-07 124_[+1]_355 7349 3.6e-07 111_[+1]_368 5563 9.4e-07 307_[+1]_172 269135 1.1e-06 286_[+1]_193 24376 1.1e-06 389_[+1]_90 20648 1.3e-06 329_[+1]_150 20740 2.3e-06 197_[+1]_282 26470 3.1e-06 285_[+1]_194 269541 3.5e-06 274_[+1]_205 264776 5.2e-06 286_[+1]_193 34850 6.9e-06 245_[+1]_234 25386 6.9e-06 163_[+1]_316 21897 6.9e-06 300_[+1]_179 bd885 1.6e-05 205_[+1]_274 268160 3.7e-05 62_[+1]_417 268217 4.3e-05 158_[+1]_321 25157 5.9e-05 266_[+1]_213 42320 7.9e-05 288_[+1]_191 268124 9.1e-05 115_[+1]_364 25523 0.00011 223_[+1]_256 bd1182 0.00012 242_[+1]_237 7887 0.00012 39_[+1]_440 21677 0.00014 8_[+1]_471 6323 0.00017 173_[+1]_306 268453 0.00017 277_[+1]_202 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=31 928 ( 235) GAGGGAGGAGAGAGGAGGTGG 1 25171 ( 169) GTCAGAGGAGAGATGATGCTG 1 22846 ( 170) GTGAGATGAGTGAGGTTTTGG 1 36099 ( 364) GGCAAAGGAGAGAGTAGATGG 1 268054 ( 202) GAGAGATGAGACATGATGTTG 1 4026 ( 34) ATGATGGGAGAGAGGAGGCCG 1 bd1790 ( 125) TTGAGAGGAGGGTGGAGGGGA 1 7349 ( 112) TTGAGAGGAGGGTGGAGGGGA 1 5563 ( 308) AAGAGGTGCGGGAGGTTGTGG 1 269135 ( 287) TACGGAGGAGAGAGTTCATCG 1 24376 ( 390) GTCGGTGGAGTGAGGATAGGA 1 20648 ( 330) TTGAGAGAAGAGAAAATATGG 1 20740 ( 198) AGAAGAGGAGGGACGATAGTA 1 26470 ( 286) AAGAGAGGAGAGCTGTTGAAG 1 269541 ( 275) AACAAAGAAGAGTGCACATCG 1 264776 ( 287) GTCGGACGACAGACGATGACG 1 34850 ( 246) GATGAACGAGAGAGGAAATTA 1 25386 ( 164) AACATGTCAGAGAGGTGGTGA 1 21897 ( 301) AAGAAGTAAGACAGGTTATTG 1 bd885 ( 206) GTAAAGCGAGAGAGGTCAACA 1 268160 ( 63) TGAAGAGGAGAAAGATTGGAG 1 268217 ( 159) GGCAGAGGAGAGACCACCAGA 1 25157 ( 267) ATAAGAGGAGAACTGTCTTTG 1 42320 ( 289) GTTGAAGAACAGTTGATGGTG 1 268124 ( 116) ATGGTACAAGTGGGGATATGA 1 25523 ( 224) ACTAGAGAAGCGAGGAGGCGT 1 bd1182 ( 243) AAGAACGGAGTATCGAAGTCG 1 7887 ( 40) GCGACATCAGCGACGTCGGCG 1 21677 ( 9) GACGCTGGAGCAACAATGTTG 1 6323 ( 174) AAGACTCGCGAGTGGCGATGG 1 268453 ( 278) TGCAAGGCCGTGAAGTTGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 8.90388 E= 4.0e-008 57 -1160 75 -44 57 -182 -63 56 -101 50 86 -144 151 -1160 5 -1160 -2 -124 114 -144 138 -282 -36 -144 -1160 -50 137 -44 -43 -124 151 -1160 179 -124 -1160 -1160 -1160 -182 191 -1160 123 -124 -95 -70 -101 -182 170 -1160 144 -182 -294 -44 -201 -24 122 -70 -143 -182 164 -202 123 -282 -1160 44 -201 -24 5 89 44 -282 114 -202 -101 -124 -14 107 -201 -2 75 15 15 -1160 144 -302 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 31 E= 4.0e-008 0.387097 0.000000 0.419355 0.193548 0.387097 0.064516 0.161290 0.387097 0.129032 0.322581 0.451613 0.096774 0.741935 0.000000 0.258065 0.000000 0.258065 0.096774 0.548387 0.096774 0.677419 0.032258 0.193548 0.096774 0.000000 0.161290 0.645161 0.193548 0.193548 0.096774 0.709677 0.000000 0.903226 0.096774 0.000000 0.000000 0.000000 0.064516 0.935484 0.000000 0.612903 0.096774 0.129032 0.161290 0.129032 0.064516 0.806452 0.000000 0.709677 0.064516 0.032258 0.193548 0.064516 0.193548 0.580645 0.161290 0.096774 0.064516 0.774194 0.064516 0.612903 0.032258 0.000000 0.354839 0.064516 0.193548 0.258065 0.483871 0.354839 0.032258 0.548387 0.064516 0.129032 0.096774 0.225806 0.548387 0.064516 0.225806 0.419355 0.290323 0.290323 0.000000 0.677419 0.032258 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA][AT][GC][AG][GA]AGGAGAGAGG[AT][TG][GA][TG][GTC][GA] -------------------------------------------------------------------------------- Time 9.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 31 llr = 306 E-value = 2.3e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:1:::2:22:62:35:63: pos.-specific C 29:36545537258229318 probability G ::6:34132311::::1:3: matrix T 7136:233231132531:32 bits 2.1 1.9 1.7 * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 * * * * (14.2 bits) 0.9 ** ** * * ** * 0.6 ** ** * ** ** * 0.4 ****** * ******** * 0.2 ********* ********** 0.0 -------------------- Multilevel TCGTCCCCCCCACCTACAAC consensus TCGGTG G T AT CGT sequence AT T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 25386 423 4.02e-09 CCGTCAACAA TCGTCCCTCGCATCAACCGC GTAGCGTCTG 269541 296 6.10e-09 GTGCACATCG TCGTCGTCCTCATCATCATC TAACGTCCAA 268124 373 1.37e-07 ATATACAAAA TCGCCCACGACACCTTCCGC CACCTCCCCT 4026 460 2.11e-07 CTCCCAACGA TCGTCCAGACCACCCTCCAC GCAGTCGTGG bd1790 282 8.95e-07 CAACTTCGTG TCGTGGACTGCACTTACCAC GCTGATACAA 7349 269 8.95e-07 CAACTTCGTG TCGTGGACTGCACTTACCAC GCTGATACAA 6323 477 1.14e-06 CACCCTGTAC TCCTCCCCCCCACCACCAAT AACC bd1182 39 1.44e-06 ACCGTCACTG CCGTCGATGGCATCCACATC GTGCTCGTGA 25157 402 1.44e-06 ACTACAAAAG CCTTCCTTCACAACCACAAC TAAAAGATAT 36099 150 2.26e-06 GTGCATGGTG TCGTCCGCCACAATTACAGT TACTGTTCGT 21677 450 3.87e-06 AACTGCGTGT TCTTGTTTCCGACCTCCAAC CTCTACCTCA bd885 61 4.30e-06 ATCGTGATCA CCGTCCGGTGCATCCACCGC AAAGGGTTCG 5563 480 5.83e-06 GTATATCTGC TCACCCCTATCGCCTACCGC A 268453 30 7.10e-06 CCGCCAAGTC TCGCCGCTACCTTCATCAAT ATAATGCTGA 25171 375 1.04e-05 AAAAACACAG TCGTGCTCTCACCCAACATC AGTTCTCCAT 22846 47 1.14e-05 CTCTCCGTCG TCGTCGTCGTCAACTTGATT GGTAGGCTGT 264776 320 1.50e-05 AGAGTTCTCT TCACCCTCCAGTCCTACACC GAGCCATCGA 928 468 1.64e-05 CCTGAACCTA CCTCGCCGCTGAACAACATC TCTCTCATCC 7887 322 1.95e-05 TATTGTAGCT TCTCCGCGAGCTACTTCATT TACTTCAAAC 26470 128 2.32e-05 CGTCTCGCTG TCATTGCACTCACCTACCAC TCAATCATGG 268160 472 2.52e-05 TACACCACCA ACACCTGCCCCACCCACACC ACCCTAATC 24376 126 2.52e-05 TCTGGCATGG CCTCGGCCGCGACCACCAGC CCCTCCCTTC 268217 368 2.74e-05 TCACTAAACC TCTTGCCTCACCTCATTAAC GTCAAAGTCG 268054 34 2.74e-05 GGAACGTAAC TCGTCGTGAGCCTCTCCTTC GCATGCAGCC 269135 75 2.97e-05 CTTGGAGATG ACGCCCTCCCCGTCCAGAGC GGTACTTCTG 21897 396 2.97e-05 GTTGTAGCAG TCGTGACCCTTCTCATCAGC ATCTCCTAGT 20740 438 4.10e-05 TCGGTGCACG TCTCGTCGCGTTCCTACAGT CGACAGTCGC 25523 152 5.59e-05 CGTCCAAGAT ACGTCTTGCGCACTTCTATC GATGCTGGTA 42320 63 9.32e-05 GTGATTAACT TTGACTTGCCCACCAACCGT GAGAACTACA 34850 433 1.71e-04 ACTTATCATA ACTTAGACGTCCACTTCATC GTCGTATCGG 20648 293 1.94e-04 TGTCCATATT TTGTCCATTTTATTTTCCAC ATAAATAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25386 4e-09 422_[+2]_58 269541 6.1e-09 295_[+2]_185 268124 1.4e-07 372_[+2]_108 4026 2.1e-07 459_[+2]_21 bd1790 8.9e-07 281_[+2]_199 7349 8.9e-07 268_[+2]_212 6323 1.1e-06 476_[+2]_4 bd1182 1.4e-06 38_[+2]_442 25157 1.4e-06 401_[+2]_79 36099 2.3e-06 149_[+2]_331 21677 3.9e-06 449_[+2]_31 bd885 4.3e-06 60_[+2]_420 5563 5.8e-06 479_[+2]_1 268453 7.1e-06 29_[+2]_451 25171 1e-05 374_[+2]_106 22846 1.1e-05 46_[+2]_434 264776 1.5e-05 319_[+2]_161 928 1.6e-05 467_[+2]_13 7887 2e-05 321_[+2]_159 26470 2.3e-05 127_[+2]_353 268160 2.5e-05 471_[+2]_9 24376 2.5e-05 125_[+2]_355 268217 2.7e-05 367_[+2]_113 268054 2.7e-05 33_[+2]_447 269135 3e-05 74_[+2]_406 21897 3e-05 395_[+2]_85 20740 4.1e-05 437_[+2]_43 25523 5.6e-05 151_[+2]_329 42320 9.3e-05 62_[+2]_418 34850 0.00017 432_[+2]_48 20648 0.00019 292_[+2]_188 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=31 25386 ( 423) TCGTCCCTCGCATCAACCGC 1 269541 ( 296) TCGTCGTCCTCATCATCATC 1 268124 ( 373) TCGCCCACGACACCTTCCGC 1 4026 ( 460) TCGTCCAGACCACCCTCCAC 1 bd1790 ( 282) TCGTGGACTGCACTTACCAC 1 7349 ( 269) TCGTGGACTGCACTTACCAC 1 6323 ( 477) TCCTCCCCCCCACCACCAAT 1 bd1182 ( 39) CCGTCGATGGCATCCACATC 1 25157 ( 402) CCTTCCTTCACAACCACAAC 1 36099 ( 150) TCGTCCGCCACAATTACAGT 1 21677 ( 450) TCTTGTTTCCGACCTCCAAC 1 bd885 ( 61) CCGTCCGGTGCATCCACCGC 1 5563 ( 480) TCACCCCTATCGCCTACCGC 1 268453 ( 30) TCGCCGCTACCTTCATCAAT 1 25171 ( 375) TCGTGCTCTCACCCAACATC 1 22846 ( 47) TCGTCGTCGTCAACTTGATT 1 264776 ( 320) TCACCCTCCAGTCCTACACC 1 928 ( 468) CCTCGCCGCTGAACAACATC 1 7887 ( 322) TCTCCGCGAGCTACTTCATT 1 26470 ( 128) TCATTGCACTCACCTACCAC 1 268160 ( 472) ACACCTGCCCCACCCACACC 1 24376 ( 126) CCTCGGCCGCGACCACCAGC 1 268217 ( 368) TCTTGCCTCACCTCATTAAC 1 268054 ( 34) TCGTCGTGAGCCTCTCCTTC 1 269135 ( 75) ACGCCCTCCCCGTCCAGAGC 1 21897 ( 396) TCGTGACCCTTCTCATCAGC 1 20740 ( 438) TCTCGTCGCGTTCCTACAGT 1 25523 ( 152) ACGTCTTGCGCACTTCTATC 1 42320 ( 63) TTGACTTGCCCACCAACCGT 1 34850 ( 433) ACTTAGACGTCCACTTCATC 1 20648 ( 293) TTGTCCATTTTATTTTCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 14911 bayes= 8.90689 E= 2.3e-008 -101 -50 -1160 144 -1160 203 -1160 -202 -101 -282 122 -2 -301 50 -1160 130 -301 150 22 -302 -301 98 51 -70 -21 63 -136 30 -301 98 5 -2 -69 118 -63 -70 -69 35 22 -2 -301 170 -95 -144 131 -50 -195 -102 -43 108 -1160 30 -1160 188 -1160 -70 31 -24 -1160 89 98 -50 -1160 30 -1160 193 -195 -202 131 50 -1160 -302 31 -182 37 15 -1160 176 -1160 -21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 31 E= 2.3e-008 0.129032 0.161290 0.000000 0.709677 0.000000 0.935484 0.000000 0.064516 0.129032 0.032258 0.580645 0.258065 0.032258 0.322581 0.000000 0.645161 0.032258 0.645161 0.290323 0.032258 0.032258 0.451613 0.354839 0.161290 0.225806 0.354839 0.096774 0.322581 0.032258 0.451613 0.258065 0.258065 0.161290 0.516129 0.161290 0.161290 0.161290 0.290323 0.290323 0.258065 0.032258 0.741935 0.129032 0.096774 0.645161 0.161290 0.064516 0.129032 0.193548 0.483871 0.000000 0.322581 0.000000 0.838710 0.000000 0.161290 0.322581 0.193548 0.000000 0.483871 0.516129 0.161290 0.000000 0.322581 0.000000 0.870968 0.064516 0.064516 0.645161 0.322581 0.000000 0.032258 0.322581 0.064516 0.322581 0.290323 0.000000 0.774194 0.000000 0.225806 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TC[GT][TC][CG][CG][CTA][CGT]C[CGT]CA[CT]C[TA][AT]C[AC][AGT][CT] -------------------------------------------------------------------------------- Time 18.47 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 31 llr = 258 E-value = 5.4e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :113::::::11 pos.-specific C 1:4:1:14:2:2 probability G 153:71:2a::6 matrix T 85272994:891 bits 2.1 1.9 1.7 * 1.5 ** * Relative 1.3 ** *** Entropy 1.1 * *** *** (12.0 bits) 0.9 * **** *** 0.6 ** **** *** 0.4 ** ********* 0.2 ************ 0.0 ------------ Multilevel TTCTGTTCGTTG consensus GGA T C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 24376 84 4.32e-07 AGTTCATCGT TGGTGTTCGTTG ATGCTGGATA 20648 210 7.52e-07 GCTCATCGTG TTTTGTTCGTTG CGACGCAGCT 5563 91 2.04e-06 CTCTACGTTT TGGAGTTCGTTG TCATTGCCGT 25171 106 3.23e-06 AAGGTGTGGC TTTAGTTCGTTG CTTCGCGTTG 36099 170 5.85e-06 CAATTACAGT TACTGTTCGTTG TGATGGTGAC 26470 308 1.11e-05 CTGTTGAAGG TTGTGTTGGCTG CCAGGAGGAG 269541 65 1.29e-05 ATCGAATCGC TTCTCTTTGTTG AATCGTACAC 268160 341 1.29e-05 AGATACAATT CTCTGTTTGTTG TATCCAAATT 22846 15 1.63e-05 GGACTGTCGA TGCTGTTGGTAG CAGCCGCTGG 268217 5 1.83e-05 GAGT TGCAGTTGGCTG GATTCGTAGA 25523 277 1.83e-05 TTGGCTTCGG TGCTTTTTGTTC TGTGGCTGTG 25157 76 2.77e-05 CTCTTCGTCG TTATGTTCGTTC CGTCGTATTT bd1182 96 4.15e-05 GTGTGCATCA GTTTGTTCGCTG ATGGATCCGG 928 77 4.15e-05 TGCGATGTTA TGCTGTTGGCTA GGAGGATTGA 42320 160 4.15e-05 TGACCGAAGG TGATGTTCGTTA TCTCCGTGAT bd1790 361 5.03e-05 GTGATAATTG GTGTTTTTGTTG CATGTATATG 7349 348 5.03e-05 GTGATAATTG GTGTTTTTGTTG CATGTATATG 6323 132 5.51e-05 TTTCATCTGT TGCTGGTTGTTT GGGCTGTTAG 4026 110 6.11e-05 GAGGATCCAC TGCAGGTTGCTG CACCTCCAAA 20740 235 6.65e-05 GTTTCATGGT GGGTGTTCGTTT CCTATCGTCT 34850 300 7.28e-05 GGAATTGAAG TTGTGTTTGTAA AGTACTGTGC 268054 413 7.94e-05 GTGTGACAAG TGTTGTGTGTTG CGAGTGCCTC 268453 100 1.12e-04 CCAATTGATT TGCTTGTTGTTC CGTCAGACTT 268124 151 1.21e-04 GGAGGAGAGT TGTTTTTTGCTC TGTGCTCGTG 7887 200 1.31e-04 GTTGCCCTCG TATTGTTTGTAG TTCCTCTCTC 21677 172 1.31e-04 GTACCACCCT TTCATTCCGTTG GTGGTGCAAT bd885 378 1.42e-04 CGTCATCGTG CTGAGTTCGTTC CTCACAAAAC 21897 224 1.80e-04 TTGTCGATGC TTTAGTTGGCTA TACTACAACT 269135 155 2.24e-04 ATCCATCGAG TGGACGTCGTTG ACGTTGATGG 25386 232 2.24e-04 TGTAGCGTGG TTCCGTCCGTTG TCGTTTGGGT 264776 417 1.72e-03 CAGTTGACCA TTCAGTTGATAT CCATCTCGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24376 4.3e-07 83_[+3]_405 20648 7.5e-07 209_[+3]_279 5563 2e-06 90_[+3]_398 25171 3.2e-06 105_[+3]_383 36099 5.9e-06 169_[+3]_319 26470 1.1e-05 307_[+3]_181 269541 1.3e-05 64_[+3]_424 268160 1.3e-05 340_[+3]_148 22846 1.6e-05 14_[+3]_474 268217 1.8e-05 4_[+3]_484 25523 1.8e-05 276_[+3]_212 25157 2.8e-05 75_[+3]_413 bd1182 4.1e-05 95_[+3]_393 928 4.1e-05 76_[+3]_412 42320 4.1e-05 159_[+3]_329 bd1790 5e-05 360_[+3]_128 7349 5e-05 347_[+3]_141 6323 5.5e-05 131_[+3]_357 4026 6.1e-05 109_[+3]_379 20740 6.7e-05 234_[+3]_254 34850 7.3e-05 299_[+3]_189 268054 7.9e-05 412_[+3]_76 268453 0.00011 99_[+3]_389 268124 0.00012 150_[+3]_338 7887 0.00013 199_[+3]_289 21677 0.00013 171_[+3]_317 bd885 0.00014 377_[+3]_111 21897 0.00018 223_[+3]_265 269135 0.00022 154_[+3]_334 25386 0.00022 231_[+3]_257 264776 0.0017 416_[+3]_72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=31 24376 ( 84) TGGTGTTCGTTG 1 20648 ( 210) TTTTGTTCGTTG 1 5563 ( 91) TGGAGTTCGTTG 1 25171 ( 106) TTTAGTTCGTTG 1 36099 ( 170) TACTGTTCGTTG 1 26470 ( 308) TTGTGTTGGCTG 1 269541 ( 65) TTCTCTTTGTTG 1 268160 ( 341) CTCTGTTTGTTG 1 22846 ( 15) TGCTGTTGGTAG 1 268217 ( 5) TGCAGTTGGCTG 1 25523 ( 277) TGCTTTTTGTTC 1 25157 ( 76) TTATGTTCGTTC 1 bd1182 ( 96) GTTTGTTCGCTG 1 928 ( 77) TGCTGTTGGCTA 1 42320 ( 160) TGATGTTCGTTA 1 bd1790 ( 361) GTGTTTTTGTTG 1 7349 ( 348) GTGTTTTTGTTG 1 6323 ( 132) TGCTGGTTGTTT 1 4026 ( 110) TGCAGGTTGCTG 1 20740 ( 235) GGGTGTTCGTTT 1 34850 ( 300) TTGTGTTTGTAA 1 268054 ( 413) TGTTGTGTGTTG 1 268453 ( 100) TGCTTGTTGTTC 1 268124 ( 151) TGTTTTTTGCTC 1 7887 ( 200) TATTGTTTGTAG 1 21677 ( 172) TTCATTCCGTTG 1 bd885 ( 378) CTGAGTTCGTTC 1 21897 ( 224) TTTAGTTGGCTA 1 269135 ( 155) TGGACGTCGTTG 1 25386 ( 232) TTCCGTCCGTTG 1 264776 ( 417) TTCAGTTGATAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 15159 bayes= 8.93074 E= 5.4e-003 -1160 -182 -95 162 -201 -1160 86 89 -201 88 22 -21 15 -282 -1160 137 -1160 -182 158 -44 -1160 -1160 -95 173 -1160 -182 -294 179 -1160 88 -36 56 -301 -1160 196 -1160 -1160 -2 -1160 156 -101 -1160 -1160 173 -101 -50 130 -144 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 31 E= 5.4e-003 0.000000 0.064516 0.129032 0.806452 0.064516 0.000000 0.451613 0.483871 0.064516 0.419355 0.290323 0.225806 0.290323 0.032258 0.000000 0.677419 0.000000 0.064516 0.741935 0.193548 0.000000 0.000000 0.129032 0.870968 0.000000 0.064516 0.032258 0.903226 0.000000 0.419355 0.193548 0.387097 0.032258 0.000000 0.967742 0.000000 0.000000 0.225806 0.000000 0.774194 0.129032 0.000000 0.000000 0.870968 0.129032 0.161290 0.612903 0.096774 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TG][CGT][TA]GTT[CT]G[TC]TG -------------------------------------------------------------------------------- Time 26.80 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20648 3.65e-06 209_[+3(7.52e-07)]_108_\ [+1(1.33e-06)]_150 20740 7.94e-05 97_[+1(1.32e-05)]_79_[+1(2.28e-06)]_\ 16_[+3(6.65e-05)]_191_[+2(4.10e-05)]_43 21677 6.14e-04 449_[+2(3.87e-06)]_31 21897 3.60e-04 300_[+1(6.91e-06)]_74_\ [+2(2.97e-05)]_85 22846 6.53e-07 14_[+3(1.63e-05)]_20_[+2(1.14e-05)]_\ 28_[+2(6.50e-05)]_55_[+1(1.47e-07)]_168_[+2(4.80e-05)]_122 24376 2.99e-07 83_[+3(4.32e-07)]_30_[+2(2.52e-05)]_\ 244_[+1(1.06e-06)]_90 25157 3.39e-05 75_[+3(2.77e-05)]_179_\ [+1(5.85e-05)]_114_[+2(1.44e-06)]_79 25171 1.02e-08 105_[+3(3.23e-06)]_51_\ [+1(8.56e-09)]_185_[+2(1.04e-05)]_106 25386 1.63e-07 163_[+1(6.91e-06)]_238_\ [+2(4.02e-09)]_58 25523 9.49e-04 151_[+2(5.59e-05)]_105_\ [+3(1.83e-05)]_212 26470 1.33e-05 127_[+2(2.32e-05)]_138_\ [+1(3.12e-06)]_1_[+3(1.11e-05)]_181 264776 7.97e-04 286_[+1(5.17e-06)]_12_\ [+2(1.50e-05)]_161 268054 6.56e-06 33_[+2(2.74e-05)]_148_\ [+1(1.68e-07)]_190_[+3(7.94e-05)]_76 268124 2.25e-05 115_[+1(9.12e-05)]_236_\ [+2(1.37e-07)]_108 268160 1.40e-04 62_[+1(3.66e-05)]_257_\ [+3(1.29e-05)]_119_[+2(2.52e-05)]_9 268217 2.33e-04 4_[+3(1.83e-05)]_142_[+1(4.29e-05)]_\ 188_[+2(2.74e-05)]_113 268453 1.06e-03 29_[+2(7.10e-06)]_451 269135 8.57e-05 74_[+2(2.97e-05)]_117_\ [+1(2.23e-05)]_54_[+1(1.06e-06)]_193 269541 9.76e-09 64_[+3(1.29e-05)]_94_[+3(6.65e-05)]_\ 113_[+2(6.10e-09)]_46_[+2(5.59e-05)]_119 34850 7.30e-04 245_[+1(6.91e-06)]_33_\ [+3(7.28e-05)]_189 36099 6.73e-08 149_[+2(2.26e-06)]_[+3(5.85e-06)]_\ 182_[+1(1.68e-07)]_116 4026 1.04e-07 33_[+1(2.83e-07)]_55_[+3(6.11e-05)]_\ 338_[+2(2.11e-07)]_21 42320 2.12e-03 62_[+2(9.32e-05)]_77_[+3(4.15e-05)]_\ 137_[+3(5.51e-05)]_180 5563 2.92e-07 90_[+3(2.04e-06)]_205_\ [+1(9.44e-07)]_151_[+2(5.83e-06)]_1 6323 1.24e-04 131_[+3(5.51e-05)]_149_\ [+2(8.69e-05)]_164_[+2(1.14e-06)]_4 7349 4.08e-07 111_[+1(3.64e-07)]_136_\ [+2(8.95e-07)]_32_[+1(7.89e-05)]_6_[+3(5.03e-05)]_141 7887 2.11e-03 321_[+2(1.95e-05)]_159 928 4.18e-09 36_[+1(7.33e-05)]_19_[+3(4.15e-05)]_\ 146_[+1(1.62e-10)]_212_[+2(1.64e-05)]_13 bd1182 8.93e-05 38_[+2(1.44e-06)]_37_[+3(4.15e-05)]_\ 393 bd1790 4.08e-07 124_[+1(3.64e-07)]_136_\ [+2(8.95e-07)]_32_[+1(7.89e-05)]_6_[+3(5.03e-05)]_128 bd885 1.15e-04 60_[+2(4.30e-06)]_125_\ [+1(1.58e-05)]_274 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************