******************************************************************************** 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/7/7.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1000 1.0000 500 11174 1.0000 500 11183 1.0000 500 11831 1.0000 500 11833 1.0000 500 1238 1.0000 500 20405 1.0000 500 21194 1.0000 500 22677 1.0000 500 25662 1.0000 500 263800 1.0000 500 264285 1.0000 500 2678 1.0000 500 270222 1.0000 500 270296 1.0000 500 2944 1.0000 500 36928 1.0000 500 3914 1.0000 500 40655 1.0000 500 41166 1.0000 500 4131 1.0000 500 5098 1.0000 500 5957 1.0000 500 5958 1.0000 500 5971 1.0000 500 6757 1.0000 500 8414 1.0000 500 9405 1.0000 500 9412 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/7/7.seqs.fa -oc motifs/7 -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= 29 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= 14500 N= 29 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.218 G 0.254 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.218 G 0.254 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 26 llr = 291 E-value = 1.0e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 242536:23233:3::6:151 pos.-specific C :21::1:::132::21:11:2 probability G 73736:954742a1191:85: matrix T 21:2131331:3:68:39::7 bits 2.2 2.0 1.8 * 1.5 * * * Relative 1.3 * * * ** Entropy 1.1 * * * ** (16.1 bits) 0.9 * * ** *** 0.7 * * *** ********* 0.4 * * ******* ********* 0.2 *********** ********* 0.0 --------------------- Multilevel GAGAGAGGGGGAGTTGATGGT consensus GAGAT TA AT A T A sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 11183 62 1.80e-10 AGATGGATCG GAGAGAGGAGGTGTTGTTGGT GGTGATGGCT 5098 186 2.02e-09 ATCATGATTC GGAGGAGGGGAAGTTGATGGT CTCTGAGTGT 9405 4 1.75e-08 GCG GAGAGTGATGATGATGATGAT TGCGAGGAAG 1000 408 5.86e-08 GAAAGAAATG GCAAGAGGAGGAGTTGGTGGT AGTTCAGGCG 270296 206 3.14e-07 GTGCCTGTAA ACGTGTGTAGCAGTTGTTGAT TGACTGCTGG 20405 207 3.14e-07 GTGCCTGTAA ACGTGTGTAGCAGTTGTTGAT TGACTGCTGG 4131 133 4.97e-07 CTGCTGATTG GTGAGAGTGAGAGACGATGAT GGCGTCGCAT 264285 355 4.97e-07 GTGTGCTCAT GAGAACGGTGATGTTGATGGG TGATGGTTTC 9412 29 1.06e-06 TGAGACGAAA TAGAAAGGAGGAGTTGACGGA TCAGCGAGCC 5957 384 1.06e-06 CTGTAAAAGA AAGTGAGTGGCCGGTGATGGC ATGCATCAGA 263800 335 1.30e-06 CGTGACATTT GTGAATGGTGGTGTGGTTGAT GTAGAGTAGT 270222 88 1.58e-06 CGAAGGCATT GAGGGAGGTGGTGGTCTTGGC AACCTGAACA 5958 140 1.74e-06 TGAACGCAAG GCGAACGAGGACGATGACGAT GAGGATGACA 41166 77 2.11e-06 CGACGATAGC GCTGATGGTGAGGATGATGGT GATGGTCACC 11833 44 2.55e-06 GCTATTTCCT GTGAGATTGACCGTTGTTGAT CGACAAGGCG 11831 140 3.67e-06 GGGAAGGAAG GAGAAAGAATCGGATGATGGA CTCTCTTGCA 2944 298 4.01e-06 GGTTTGCGTG GGCGGTGGGCGAGTTGATCGT TCCCGACCAT 5971 306 6.14e-06 TGAACACTCA AAGGAAGTAGACGACGATAAT GCGTGTTGCT 1238 208 8.50e-06 TCTGTTGAAC GGAGATTTGGCTGTTGTTGAC ACAATGAAAT 22677 337 9.20e-06 AGGGCTGCCA GAGGTCGGTCGGGTTGGTGGT TCGGGTTGGA 25662 302 1.16e-05 TTCCGTGCGC TGATGATAGGGGGTTGTTGAT TTGGCCTGTG 21194 27 1.80e-05 CGCAATGATT GGCCGAGATGAAGGCGATGGT ATCTATCGTA 2678 394 1.93e-05 GGCTGAGAAC GGAGAAGGAAGAGACGACGAC GCGAGGAAGG 40655 52 3.77e-05 TCCTACAGAA TAGAGAGGATAGTTTGATCGT TGTCTTCGCC 36928 35 4.82e-05 CGAGCAAACG TGATGAGTGAATGTGCATGAT ATGAATAAAA 6757 149 8.99e-05 AATAAAGTGT AAGATTGTGCCCGATCATAGT GCTCACGTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11183 1.8e-10 61_[+1]_418 5098 2e-09 185_[+1]_294 9405 1.8e-08 3_[+1]_476 1000 5.9e-08 407_[+1]_72 270296 3.1e-07 205_[+1]_274 20405 3.1e-07 206_[+1]_273 4131 5e-07 132_[+1]_347 264285 5e-07 354_[+1]_125 9412 1.1e-06 28_[+1]_451 5957 1.1e-06 383_[+1]_96 263800 1.3e-06 334_[+1]_145 270222 1.6e-06 87_[+1]_392 5958 1.7e-06 139_[+1]_340 41166 2.1e-06 76_[+1]_403 11833 2.5e-06 43_[+1]_436 11831 3.7e-06 139_[+1]_340 2944 4e-06 297_[+1]_182 5971 6.1e-06 305_[+1]_174 1238 8.5e-06 207_[+1]_272 22677 9.2e-06 336_[+1]_143 25662 1.2e-05 301_[+1]_178 21194 1.8e-05 26_[+1]_453 2678 1.9e-05 393_[+1]_86 40655 3.8e-05 51_[+1]_428 36928 4.8e-05 34_[+1]_445 6757 9e-05 148_[+1]_331 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=26 11183 ( 62) GAGAGAGGAGGTGTTGTTGGT 1 5098 ( 186) GGAGGAGGGGAAGTTGATGGT 1 9405 ( 4) GAGAGTGATGATGATGATGAT 1 1000 ( 408) GCAAGAGGAGGAGTTGGTGGT 1 270296 ( 206) ACGTGTGTAGCAGTTGTTGAT 1 20405 ( 207) ACGTGTGTAGCAGTTGTTGAT 1 4131 ( 133) GTGAGAGTGAGAGACGATGAT 1 264285 ( 355) GAGAACGGTGATGTTGATGGG 1 9412 ( 29) TAGAAAGGAGGAGTTGACGGA 1 5957 ( 384) AAGTGAGTGGCCGGTGATGGC 1 263800 ( 335) GTGAATGGTGGTGTGGTTGAT 1 270222 ( 88) GAGGGAGGTGGTGGTCTTGGC 1 5958 ( 140) GCGAACGAGGACGATGACGAT 1 41166 ( 77) GCTGATGGTGAGGATGATGGT 1 11833 ( 44) GTGAGATTGACCGTTGTTGAT 1 11831 ( 140) GAGAAAGAATCGGATGATGGA 1 2944 ( 298) GGCGGTGGGCGAGTTGATCGT 1 5971 ( 306) AAGGAAGTAGACGACGATAAT 1 1238 ( 208) GGAGATTTGGCTGTTGTTGAC 1 22677 ( 337) GAGGTCGGTCGGGTTGGTGGT 1 25662 ( 302) TGATGATAGGGGGTTGTTGAT 1 21194 ( 27) GGCCGAGATGAAGGCGATGGT 1 2678 ( 394) GGAGAAGGAAGAGACGACGAC 1 40655 ( 52) TAGAGAGGATAGTTTGATCGT 1 36928 ( 35) TGATGAGTGAATGTGCATGAT 1 6757 ( 149) AAGATTGTGCCCGATCATAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 9.59308 E= 1.0e-010 -43 -1134 136 -81 71 -18 8 -122 -17 -150 136 -280 83 -250 28 -48 42 -1134 118 -181 115 -91 -1134 19 -1134 -1134 180 -122 -43 -1134 86 36 42 -1134 60 0 -75 -91 136 -181 42 31 60 -1134 42 -18 -40 0 -1134 -1134 192 -280 25 -1134 -114 110 -1134 -50 -172 151 -1134 -91 180 -1134 125 -1134 -172 19 -1134 -91 -1134 172 -175 -150 174 -1134 83 -1134 108 -1134 -175 -50 -272 144 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 26 E= 1.0e-010 0.192308 0.000000 0.653846 0.153846 0.423077 0.192308 0.269231 0.115385 0.230769 0.076923 0.653846 0.038462 0.461538 0.038462 0.307692 0.192308 0.346154 0.000000 0.576923 0.076923 0.576923 0.115385 0.000000 0.307692 0.000000 0.000000 0.884615 0.115385 0.192308 0.000000 0.461538 0.346154 0.346154 0.000000 0.384615 0.269231 0.153846 0.115385 0.653846 0.076923 0.346154 0.269231 0.384615 0.000000 0.346154 0.192308 0.192308 0.269231 0.000000 0.000000 0.961538 0.038462 0.307692 0.000000 0.115385 0.576923 0.000000 0.153846 0.076923 0.769231 0.000000 0.115385 0.884615 0.000000 0.615385 0.000000 0.076923 0.307692 0.000000 0.115385 0.000000 0.884615 0.076923 0.076923 0.846154 0.000000 0.461538 0.000000 0.538462 0.000000 0.076923 0.153846 0.038462 0.730769 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[AG][GA][AG][GA][AT]G[GT][GAT]G[GAC][AT]G[TA]TG[AT]TG[GA]T -------------------------------------------------------------------------------- Time 7.09 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 26 llr = 287 E-value = 9.7e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 42:::2:6413336423:259 pos.-specific C 31823582282544556775: probability G 2:235::::111:::::1::: matrix T 17:524224:4:3::3:21:1 bits 2.2 2.0 1.8 1.5 * * Relative 1.3 * * * * Entropy 1.1 * * * * * * (16.0 bits) 0.9 * * * ** *** 0.7 ** ** * * ******** 0.4 ** **** * ********** 0.2 ********** ********** 0.0 --------------------- Multilevel ATCTGCCAACTCCACCCCCAA consensus C GCTTCT AAACATA C sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5098 316 1.59e-11 AGTAGACACA ATCTGCCACCTCCCCCCCCCA ACCTGAAGCT 270296 85 5.33e-09 GCACATCATC GTCCGCCAACAACACCACCAA CACGCTATCA 20405 86 5.33e-09 GCACATCATC GTCCGCCAACAACACCACCAA CACGCTATCA 9412 117 7.60e-09 ACTAGAGCAA CTCCGCCATCTATCATCCCCA CCTTTCAAAC 11831 454 8.80e-08 AGCGCCCGTC AACTGTCACCCCACCCCTCCA TCTTCAAGTC 36928 432 3.98e-07 GCATCCTGCC CTCTTTCATCTCCAACCTTAA CTTACCTACC 5971 468 5.61e-07 AGTCTCCTTG ATCCTTCTACAAAAACACCAA CCCCGCAACA 11183 430 1.08e-06 GTTGAACAGA GTCGGTCACAACCCCCCGCCA ACAGACACTG 2678 15 1.32e-06 TTTCGTTCCT GTCTGACAACCGTCCAACCAA TGCAGTACCA 5957 322 1.79e-06 TTCTCTCGCT CTCGCCTCTCCCTCCTCGCCA GCACCTACTG 270222 439 2.64e-06 ATTTTGCTTT ATGGGTCATAAAAAACACCAA AGTTGTCGTC 6757 470 3.50e-06 CAAGCGGTCA ATCCCTCCTCCGTAACAGCCA GAGCACAGCC 11833 127 3.50e-06 TCTACTATTC CTCTGTCATCTATCTCCACAA TTACACAGCG 8414 450 5.47e-06 ACCATGATAA ACCTTCCAAATCCAAACTCAA CCCTCTTCCC 5958 323 6.50e-06 GACTCACAGA CACTGCTAGCGAACCTCCCAA AGTCAACCGC 21194 414 7.70e-06 GTAGACTAAA CTCTGCTCACTCCACTGCCCT CGCTTGAACC 1238 451 7.70e-06 GCCGACGAGA AACGACCCTCACCAACACTCA TCCCTCATTG 41166 442 9.08e-06 CCTCCACCCT GCCGCTCCTCTCACAACCTCA ATTAATAGGA 40655 216 1.16e-05 CACTCCACGG CAGAGCTATCCACACCACCAA ACTAATCAGT 3914 385 1.46e-05 AAATTAATGT CTCTCCTTCCACAACTATAAA TCGGGGAAGA 22677 252 1.70e-05 ATCGGTAGGT CTGTGCCACGGATACTCTCCA GTCGTCTGTG 2944 476 1.97e-05 TCACGTTATC TTCTCTCAACGCTACACCATA CATC 25662 423 1.97e-05 GATTGACATT ACCGTACTACTCAAAACCACA ATCCAATATC 263800 40 2.45e-05 AATTGGTACG TTCCCATCACTCTCACTCCCA AAGAACTCTT 1000 98 2.83e-05 CTCTGATAGG AAGTGACGACTCAACTCCAAA GCTTTGCATT 264285 102 3.47e-05 GCAGGCCCCA ATCGCTCTTGAGCCACCCCAT CTCCATACTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5098 1.6e-11 315_[+2]_164 270296 5.3e-09 84_[+2]_395 20405 5.3e-09 85_[+2]_394 9412 7.6e-09 116_[+2]_363 11831 8.8e-08 453_[+2]_26 36928 4e-07 431_[+2]_48 5971 5.6e-07 467_[+2]_12 11183 1.1e-06 429_[+2]_50 2678 1.3e-06 14_[+2]_465 5957 1.8e-06 321_[+2]_158 270222 2.6e-06 438_[+2]_41 6757 3.5e-06 469_[+2]_10 11833 3.5e-06 126_[+2]_353 8414 5.5e-06 449_[+2]_30 5958 6.5e-06 322_[+2]_157 21194 7.7e-06 413_[+2]_66 1238 7.7e-06 450_[+2]_29 41166 9.1e-06 441_[+2]_38 40655 1.2e-05 215_[+2]_264 3914 1.5e-05 384_[+2]_95 22677 1.7e-05 251_[+2]_228 2944 2e-05 475_[+2]_4 25662 2e-05 422_[+2]_57 263800 2.5e-05 39_[+2]_440 1000 2.8e-05 97_[+2]_382 264285 3.5e-05 101_[+2]_378 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=26 5098 ( 316) ATCTGCCACCTCCCCCCCCCA 1 270296 ( 85) GTCCGCCAACAACACCACCAA 1 20405 ( 86) GTCCGCCAACAACACCACCAA 1 9412 ( 117) CTCCGCCATCTATCATCCCCA 1 11831 ( 454) AACTGTCACCCCACCCCTCCA 1 36928 ( 432) CTCTTTCATCTCCAACCTTAA 1 5971 ( 468) ATCCTTCTACAAAAACACCAA 1 11183 ( 430) GTCGGTCACAACCCCCCGCCA 1 2678 ( 15) GTCTGACAACCGTCCAACCAA 1 5957 ( 322) CTCGCCTCTCCCTCCTCGCCA 1 270222 ( 439) ATGGGTCATAAAAAACACCAA 1 6757 ( 470) ATCCCTCCTCCGTAACAGCCA 1 11833 ( 127) CTCTGTCATCTATCTCCACAA 1 8414 ( 450) ACCTTCCAAATCCAAACTCAA 1 5958 ( 323) CACTGCTAGCGAACCTCCCAA 1 21194 ( 414) CTCTGCTCACTCCACTGCCCT 1 1238 ( 451) AACGACCCTCACCAACACTCA 1 41166 ( 442) GCCGCTCCTCTCACAACCTCA 1 40655 ( 216) CAGAGCTATCCACACCACCAA 1 3914 ( 385) CTCTCCTTCCACAACTATAAA 1 22677 ( 252) CTGTGCCACGGATACTCTCCA 1 2944 ( 476) TTCTCTCAACGCTACACCATA 1 25662 ( 423) ACCGTACTACTCAAAACCACA 1 263800 ( 40) TTCCCATCACTCTCACTCCCA 1 1000 ( 98) AAGTGACGACTCAACTCCAAA 1 264285 ( 102) ATCGCTCTTGAGCCACCCCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 9.59308 E= 9.7e-009 57 67 -40 -181 -43 -91 -1134 136 -1134 196 -72 -1134 -275 9 8 78 -275 31 108 -81 -75 108 -1134 51 -1134 182 -1134 -22 115 9 -272 -81 57 -18 -272 51 -117 189 -172 -1134 25 -18 -114 51 42 131 -114 -1134 25 82 -1134 19 115 96 -1134 -1134 71 131 -1134 -280 -43 131 -1134 0 42 141 -272 -280 -275 159 -114 -48 -75 175 -1134 -122 95 108 -1134 -280 183 -1134 -1134 -181 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 26 E= 9.7e-009 0.384615 0.346154 0.192308 0.076923 0.192308 0.115385 0.000000 0.692308 0.000000 0.846154 0.153846 0.000000 0.038462 0.230769 0.269231 0.461538 0.038462 0.269231 0.538462 0.153846 0.153846 0.461538 0.000000 0.384615 0.000000 0.769231 0.000000 0.230769 0.576923 0.230769 0.038462 0.153846 0.384615 0.192308 0.038462 0.384615 0.115385 0.807692 0.076923 0.000000 0.307692 0.192308 0.115385 0.384615 0.346154 0.538462 0.115385 0.000000 0.307692 0.384615 0.000000 0.307692 0.576923 0.423077 0.000000 0.000000 0.423077 0.538462 0.000000 0.038462 0.192308 0.538462 0.000000 0.269231 0.346154 0.576923 0.038462 0.038462 0.038462 0.653846 0.115385 0.192308 0.153846 0.730769 0.000000 0.115385 0.500000 0.461538 0.000000 0.038462 0.923077 0.000000 0.000000 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC]TC[TGC][GC][CT][CT][AC][AT]C[TA][CA][CAT][AC][CA][CT][CA]CC[AC]A -------------------------------------------------------------------------------- Time 13.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 16 llr = 211 E-value = 2.7e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::91233:1:23:2::8:2: pos.-specific C :2:1411::21:13:::::: probability G 281516:a1663432a2289 matrix T 81:43:7:9215438:1811 bits 2.2 2.0 * * 1.8 * * 1.5 * * * * Relative 1.3 * * ** ** * * Entropy 1.1 *** ** ** * * (19.0 bits) 0.9 *** *** ****** 0.7 *** ***** ****** 0.4 **** ***** ** ****** 0.2 ************* ****** 0.0 -------------------- Multilevel TGAGCGTGTGGTGGTGATGG consensus TTAA ATC sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 11831 319 9.81e-09 GACTCTGCTG TGAGCATGTCGTGTTGGTGG AGTTGGATAT 5957 432 1.14e-08 GTGTGATGGC TGAGTGTGTGTTCCTGATGG CAATCTGACA 5971 16 8.62e-08 GTGAGGACAA GGAGGGTGTGTGTGTGATGG CTAGTGCAGA 270296 165 8.62e-08 ATCCATTCTG TGAGTCTGTGCTGCGGATGG ACTTACTTCC 20405 166 8.62e-08 ATCCATTCTG TGAGTCTGTGCTGCGGATGG ACTTACTTCC 8414 147 1.30e-07 GATTTTGTAC TGAACAAGTCGTTATGATGG TTCATTTCCA 2944 121 1.60e-07 GACATCATCG TCACCATGTGAAGGTGATGG CTGATGTCCA 22677 311 1.60e-07 GCATCTTGGC TCATCGTGTTGGTATGAGGG CTGCCAGAGG 264285 203 1.76e-07 TGCAACTAGT TGATCGTGTGGATTGGAGAG ACGTGCCAGA 1238 83 3.10e-07 TAGCTTCTCA TCATAGCGTGGTGGTGGTGG GAGATTGATC 9405 67 3.39e-07 TGTTGTTCTG TGAGAAAGGGGGTTTGATGG ATTGTTTACT 263800 385 7.28e-07 GGTATTGGTG TGGTTGTGTCGGTCTGGTGG TGTTGTGGTT 270222 186 8.55e-07 GTGGATGACG TGAGAGAGTTATTGTGAGAG GAGGTGGATG 40655 418 2.07e-06 ATCCTTTGCG TGATGGAGTTGTCTTGATGT ATGTTTGCAA 11183 119 2.89e-06 AGGTGATGAT GGATCGTGAGAAGGTGATTG ATGAGATCAT 1000 369 5.67e-06 GTTGTTTGTG GTAGCATGTGGAGATGTTAG TTTCCTTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11831 9.8e-09 318_[+3]_162 5957 1.1e-08 431_[+3]_49 5971 8.6e-08 15_[+3]_465 270296 8.6e-08 164_[+3]_316 20405 8.6e-08 165_[+3]_315 8414 1.3e-07 146_[+3]_334 2944 1.6e-07 120_[+3]_360 22677 1.6e-07 310_[+3]_170 264285 1.8e-07 202_[+3]_278 1238 3.1e-07 82_[+3]_398 9405 3.4e-07 66_[+3]_414 263800 7.3e-07 384_[+3]_96 270222 8.5e-07 185_[+3]_295 40655 2.1e-06 417_[+3]_63 11183 2.9e-06 118_[+3]_362 1000 5.7e-06 368_[+3]_112 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=16 11831 ( 319) TGAGCATGTCGTGTTGGTGG 1 5957 ( 432) TGAGTGTGTGTTCCTGATGG 1 5971 ( 16) GGAGGGTGTGTGTGTGATGG 1 270296 ( 165) TGAGTCTGTGCTGCGGATGG 1 20405 ( 166) TGAGTCTGTGCTGCGGATGG 1 8414 ( 147) TGAACAAGTCGTTATGATGG 1 2944 ( 121) TCACCATGTGAAGGTGATGG 1 22677 ( 311) TCATCGTGTTGGTATGAGGG 1 264285 ( 203) TGATCGTGTGGATTGGAGAG 1 1238 ( 83) TCATAGCGTGGTGGTGGTGG 1 9405 ( 67) TGAGAAAGGGGGTTTGATGG 1 263800 ( 385) TGGTTGTGTCGGTCTGGTGG 1 270222 ( 186) TGAGAGAGTTATTGTGAGAG 1 40655 ( 418) TGATGGAGTTGTCTTGATGT 1 11183 ( 119) GGATCGTGAGAAGGTGATTG 1 1000 ( 369) GTAGCATGTGGAGATGTTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 13949 bayes= 9.76622 E= 2.7e-005 -1064 -1064 -44 159 -1064 -21 156 -210 185 -1064 -202 -1064 -205 -180 98 48 -47 101 -102 -11 27 -80 115 -1064 -5 -180 -1064 135 -1064 -1064 198 -1064 -205 -1064 -202 170 -1064 -21 130 -52 -47 -80 115 -111 -5 -1064 -2 89 -1064 -80 78 70 -47 20 30 -11 -1064 -1064 -44 159 -1064 -1064 198 -1064 153 -1064 -44 -210 -1064 -1064 -44 159 -47 -1064 156 -210 -1064 -1064 188 -210 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 16 E= 2.7e-005 0.000000 0.000000 0.187500 0.812500 0.000000 0.187500 0.750000 0.062500 0.937500 0.000000 0.062500 0.000000 0.062500 0.062500 0.500000 0.375000 0.187500 0.437500 0.125000 0.250000 0.312500 0.125000 0.562500 0.000000 0.250000 0.062500 0.000000 0.687500 0.000000 0.000000 1.000000 0.000000 0.062500 0.000000 0.062500 0.875000 0.000000 0.187500 0.625000 0.187500 0.187500 0.125000 0.562500 0.125000 0.250000 0.000000 0.250000 0.500000 0.000000 0.125000 0.437500 0.437500 0.187500 0.250000 0.312500 0.250000 0.000000 0.000000 0.187500 0.812500 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.187500 0.062500 0.000000 0.000000 0.187500 0.812500 0.187500 0.000000 0.750000 0.062500 0.000000 0.000000 0.937500 0.062500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TGA[GT][CT][GA][TA]GTGG[TAG][GT][GCT]TGATGG -------------------------------------------------------------------------------- Time 20.05 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1000 2.43e-07 97_[+2(2.83e-05)]_250_\ [+3(5.67e-06)]_19_[+1(5.86e-08)]_72 11174 5.34e-01 500 11183 3.07e-11 61_[+1(1.80e-10)]_15_[+1(1.93e-05)]_\ [+3(2.89e-06)]_84_[+1(6.14e-06)]_186_[+2(1.08e-06)]_50 11831 1.55e-10 139_[+1(3.67e-06)]_158_\ [+3(9.81e-09)]_115_[+2(8.80e-08)]_26 11833 2.04e-04 43_[+1(2.55e-06)]_62_[+2(3.50e-06)]_\ 353 1238 4.91e-07 82_[+3(3.10e-07)]_105_\ [+1(8.50e-06)]_222_[+2(7.70e-06)]_29 20405 8.58e-12 85_[+2(5.33e-09)]_59_[+3(8.62e-08)]_\ 21_[+1(3.14e-07)]_273 21194 1.63e-03 26_[+1(1.80e-05)]_366_\ [+2(7.70e-06)]_66 22677 5.91e-07 251_[+2(1.70e-05)]_38_\ [+3(1.60e-07)]_6_[+1(9.20e-06)]_143 25662 2.47e-04 301_[+1(1.16e-05)]_100_\ [+2(1.97e-05)]_57 263800 5.52e-07 39_[+2(2.45e-05)]_227_\ [+1(3.32e-05)]_26_[+1(1.30e-06)]_29_[+3(7.28e-07)]_96 264285 8.72e-08 101_[+2(3.47e-05)]_80_\ [+3(1.76e-07)]_132_[+1(4.97e-07)]_125 2678 1.19e-04 14_[+2(1.32e-06)]_358_\ [+1(1.93e-05)]_86 270222 1.02e-07 87_[+1(1.58e-06)]_77_[+3(8.55e-07)]_\ 233_[+2(2.64e-06)]_41 270296 8.58e-12 84_[+2(5.33e-09)]_59_[+3(8.62e-08)]_\ 21_[+1(3.14e-07)]_274 2944 3.19e-07 120_[+3(1.60e-07)]_121_\ [+3(3.01e-05)]_16_[+1(4.01e-06)]_157_[+2(1.97e-05)]_4 36928 6.08e-05 34_[+1(4.82e-05)]_376_\ [+2(3.98e-07)]_48 3914 5.00e-02 384_[+2(1.46e-05)]_95 40655 1.45e-05 51_[+1(3.77e-05)]_143_\ [+2(1.16e-05)]_181_[+3(2.07e-06)]_63 41166 3.36e-04 76_[+1(2.11e-06)]_344_\ [+2(9.08e-06)]_38 4131 4.23e-03 132_[+1(4.97e-07)]_347 5098 2.95e-13 185_[+1(2.02e-09)]_109_\ [+2(1.59e-11)]_164 5957 9.21e-10 18_[+1(6.46e-05)]_282_\ [+2(1.79e-06)]_41_[+1(1.06e-06)]_27_[+3(1.14e-08)]_49 5958 3.68e-05 139_[+1(1.74e-06)]_162_\ [+2(6.50e-06)]_157 5971 1.04e-08 15_[+3(8.62e-08)]_270_\ [+1(6.14e-06)]_141_[+2(5.61e-07)]_12 6757 1.42e-03 148_[+1(8.99e-05)]_300_\ [+2(3.50e-06)]_10 8414 2.20e-05 146_[+3(1.30e-07)]_283_\ [+2(5.47e-06)]_30 9405 3.15e-07 3_[+1(1.75e-08)]_42_[+3(3.39e-07)]_\ 321_[+3(5.05e-05)]_73 9412 2.79e-07 28_[+1(1.06e-06)]_67_[+2(7.60e-09)]_\ 363 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************