******************************************************************************** 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/227/227.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10278 1.0000 500 11172 1.0000 500 1122 1.0000 500 1366 1.0000 500 20712 1.0000 500 20737 1.0000 500 20859 1.0000 500 21709 1.0000 500 22163 1.0000 500 22303 1.0000 500 23246 1.0000 500 23679 1.0000 500 24709 1.0000 500 24812 1.0000 500 24879 1.0000 500 25130 1.0000 500 25138 1.0000 500 25473 1.0000 500 25730 1.0000 500 264188 1.0000 500 264879 1.0000 500 268449 1.0000 500 269028 1.0000 500 269030 1.0000 500 32668 1.0000 500 32766 1.0000 500 32920 1.0000 500 34994 1.0000 500 35519 1.0000 500 36917 1.0000 500 38193 1.0000 500 38679 1.0000 500 42412 1.0000 500 4921 1.0000 500 5806 1.0000 500 6255 1.0000 500 7031 1.0000 500 7558 1.0000 500 9598 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/227/227.seqs.fa -oc motifs/227 -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= 39 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= 19500 N= 39 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.236 G 0.244 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.236 G 0.244 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 35 llr = 392 E-value = 1.2e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 6:3461:84355525512832 pos.-specific C 175623a14545174357157 probability G 1:::2::::::::1:1:1::: matrix T 332::6:1221:4:1241121 bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 * * Entropy 1.0 * * ** * (16.2 bits) 0.8 * * *** * ** * * 0.6 * ***** ***** ***** 0.4 *************** ***** 0.2 ********************* 0.0 --------------------- Multilevel ACCCATCAACAAACAACCACC consensus TTAACC CACCT CCTA AA sequence G TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 32668 435 2.09e-10 TTCACGTTCA ACTCATCAACCATCAACCACC ACCCACCTCC 38679 398 5.41e-10 CATAATGTCA ACCCATCAACACTCACCCATC ACGTCCTCTC 5806 473 2.84e-09 TTGGTGCACC TCCCATCAACACAACATCACC CAGCACA 264188 480 1.39e-08 ATGCGACGGC ACACATCAAAACACATCAACC 10278 86 1.91e-08 CCAATGAGCC ATCCAACAACAAACAATCACC GGACACTGAC 23679 407 1.09e-07 GATCGATGAA ACACCACAAACAACAACCACC CCCACAACCA 1122 416 1.42e-07 CTCCAACCGA ACCCATCACTCATCAATCCCT TTCCATCACG 269030 477 3.80e-07 GTTCACAGTC ACCCATCATCAACACATCAAC CAC 21709 127 5.38e-07 TCCCATCACC CTCAATCACTACACAATCAAC CGTCTCTTCG 34994 421 6.72e-07 ACCCACCGAC GCCAGCCACCCAACCACAAAC GCAACACAAA 24709 354 7.51e-07 CTAGACCGCC TCCCGTCCACAAACACCCATA TCACACCAAC 264879 256 1.04e-06 ACGGTTCTAC ACAAATCAACCCTCCTTCCAA AGTCTCGATA 25130 475 1.28e-06 TCATCAATAG ACACATCACACATCAACTAAT CCATC 4921 473 1.42e-06 TCAGCACCAC ATCACCCATCAAACCATCAAT CCCCATC 11172 428 1.42e-06 AAGCTCCGTA ACTCACAACCACACACCCATC ACCATAACTT 23246 466 1.73e-06 TAGATATTGT TCCCGTCAACTCTCCCTAACA TCAGTTCCAT 42412 384 1.91e-06 TCCCTCAGCC ACTCACCACTACTCACTCTTC TCACATAACC 24812 426 2.81e-06 CCACCGTCCT TCCACCCTTCCCACAACCACT GCCATCAATG 35519 311 3.39e-06 CCCTCTCCAT ACTAGCCAACACAACCCGACC TCAGCAAGTA 268449 474 3.39e-06 CAGTCCTTCC TCAAACCACACAAACAAAACC ACAGAC 25473 20 3.39e-06 AAACCCGCGG ATCACTCCAACCAGCATCACC GTACTCATCA 7558 303 4.87e-06 GCTCCCAGCT GCTCACCACCACAGCAACAAC AACAACCCTT 36917 476 5.31e-06 CCTCCGACCT ATCACTCTCAAAACAACAACA ACCA 269028 457 8.82e-06 GCATCACCAC ACACCTCCTCACTCACCACTC CACACAAAAG 24879 461 8.82e-06 TGGTTTAACC TCACACCACACATGCTCCTCC CAGCCCTCTC 38193 471 9.57e-06 TTCACACCGC TTCCATCATTCATCATCGACA CCATCCAAT 20859 470 1.04e-05 GGACATCCAA GCCCCTCATCTCACCGCCACA AAAGCTTTCA 25138 459 1.22e-05 CAGACAGACA CCGCATCACCTCTCACACACC ACTCTTCTCT 32766 479 1.31e-05 CTGGATCTAT ACAAGCCAAAAGTACATCAAC A 6255 463 1.42e-05 GACCACTGTC TCCAATCCATAACCATTAAAC CAAAATCCGA 20712 144 1.53e-05 GTGTGCAAAA ATACATCTCCCAACAGTCCTC CCACTGCCAA 9598 474 1.78e-05 GACTTTGACC ACCAACCAAGCAATAACAACA GCCGTC 25730 446 1.78e-05 GTTTCATTCC TCCCGCCACACCTCTCTCCCT CGTACCACCA 1366 288 5.65e-05 TTCACCCTGT ATAAATCAATAATACTATAAC GGAGACAATT 22163 456 1.48e-04 CATCTAGTGA TTTCGTCCTTCCTCTCCCTCC GTCACCACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32668 2.1e-10 434_[+1]_45 38679 5.4e-10 397_[+1]_82 5806 2.8e-09 472_[+1]_7 264188 1.4e-08 479_[+1] 10278 1.9e-08 85_[+1]_394 23679 1.1e-07 406_[+1]_73 1122 1.4e-07 415_[+1]_64 269030 3.8e-07 476_[+1]_3 21709 5.4e-07 126_[+1]_353 34994 6.7e-07 420_[+1]_59 24709 7.5e-07 353_[+1]_126 264879 1e-06 255_[+1]_224 25130 1.3e-06 474_[+1]_5 4921 1.4e-06 472_[+1]_7 11172 1.4e-06 427_[+1]_52 23246 1.7e-06 465_[+1]_14 42412 1.9e-06 383_[+1]_96 24812 2.8e-06 425_[+1]_54 35519 3.4e-06 310_[+1]_169 268449 3.4e-06 473_[+1]_6 25473 3.4e-06 19_[+1]_460 7558 4.9e-06 302_[+1]_177 36917 5.3e-06 475_[+1]_4 269028 8.8e-06 456_[+1]_23 24879 8.8e-06 460_[+1]_19 38193 9.6e-06 470_[+1]_9 20859 1e-05 469_[+1]_10 25138 1.2e-05 458_[+1]_21 32766 1.3e-05 478_[+1]_1 6255 1.4e-05 462_[+1]_17 20712 1.5e-05 143_[+1]_336 9598 1.8e-05 473_[+1]_6 25730 1.8e-05 445_[+1]_34 1366 5.7e-05 287_[+1]_192 22163 0.00015 455_[+1]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=35 32668 ( 435) ACTCATCAACCATCAACCACC 1 38679 ( 398) ACCCATCAACACTCACCCATC 1 5806 ( 473) TCCCATCAACACAACATCACC 1 264188 ( 480) ACACATCAAAACACATCAACC 1 10278 ( 86) ATCCAACAACAAACAATCACC 1 23679 ( 407) ACACCACAAACAACAACCACC 1 1122 ( 416) ACCCATCACTCATCAATCCCT 1 269030 ( 477) ACCCATCATCAACACATCAAC 1 21709 ( 127) CTCAATCACTACACAATCAAC 1 34994 ( 421) GCCAGCCACCCAACCACAAAC 1 24709 ( 354) TCCCGTCCACAAACACCCATA 1 264879 ( 256) ACAAATCAACCCTCCTTCCAA 1 25130 ( 475) ACACATCACACATCAACTAAT 1 4921 ( 473) ATCACCCATCAAACCATCAAT 1 11172 ( 428) ACTCACAACCACACACCCATC 1 23246 ( 466) TCCCGTCAACTCTCCCTAACA 1 42412 ( 384) ACTCACCACTACTCACTCTTC 1 24812 ( 426) TCCACCCTTCCCACAACCACT 1 35519 ( 311) ACTAGCCAACACAACCCGACC 1 268449 ( 474) TCAAACCACACAAACAAAACC 1 25473 ( 20) ATCACTCCAACCAGCATCACC 1 7558 ( 303) GCTCACCACCACAGCAACAAC 1 36917 ( 476) ATCACTCTCAAAACAACAACA 1 269028 ( 457) ACACCTCCTCACTCACCACTC 1 24879 ( 461) TCACACCACACATGCTCCTCC 1 38193 ( 471) TTCCATCATTCATCATCGACA 1 20859 ( 470) GCCCCTCATCTCACCGCCACA 1 25138 ( 459) CCGCATCACCTCTCACACACC 1 32766 ( 479) ACAAGCCAAAAGTACATCAAC 1 6255 ( 463) TCCAATCCATAACCATTAAAC 1 20712 ( 144) ATACATCTCCCAACAGTCCTC 1 9598 ( 474) ACCAACCAAGCAATAACAACA 1 25730 ( 446) TCCCGCCACACCTCTCTCCCT 1 1366 ( 288) ATAAATCAATAATACTATAAC 1 22163 ( 456) TTTCGTCCTTCCTCTCCCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18720 bayes= 9.88334 E= 1.2e-022 116 -204 -151 11 -1177 166 -1177 -4 16 113 -309 -63 54 141 -1177 -1177 123 -24 -29 -1177 -216 54 -1177 118 -316 204 -1177 -1177 160 -72 -1177 -163 75 66 -1177 -41 1 113 -309 -41 93 86 -1177 -163 93 104 -309 -1177 101 -204 -1177 69 -57 160 -151 -321 109 76 -1177 -221 93 28 -209 -63 -116 104 -1177 59 -16 148 -209 -221 160 -72 -1177 -163 16 120 -1177 -63 -35 148 -1177 -89 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 35 E= 1.2e-022 0.571429 0.057143 0.085714 0.285714 0.000000 0.742857 0.000000 0.257143 0.285714 0.514286 0.028571 0.171429 0.371429 0.628571 0.000000 0.000000 0.600000 0.200000 0.200000 0.000000 0.057143 0.342857 0.000000 0.600000 0.028571 0.971429 0.000000 0.000000 0.771429 0.142857 0.000000 0.085714 0.428571 0.371429 0.000000 0.200000 0.257143 0.514286 0.028571 0.200000 0.485714 0.428571 0.000000 0.085714 0.485714 0.485714 0.028571 0.000000 0.514286 0.057143 0.000000 0.428571 0.171429 0.714286 0.085714 0.028571 0.542857 0.400000 0.000000 0.057143 0.485714 0.285714 0.057143 0.171429 0.114286 0.485714 0.000000 0.400000 0.228571 0.657143 0.057143 0.057143 0.771429 0.142857 0.000000 0.085714 0.285714 0.542857 0.000000 0.171429 0.200000 0.657143 0.000000 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT][CT][CA][CA][ACG][TC]CA[ACT][CAT][AC][AC][AT]C[AC][AC][CT][CA]A[CA][CA] -------------------------------------------------------------------------------- Time 13.94 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 26 llr = 302 E-value = 9.8e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 322:7135::52::1:2::22 pos.-specific C 2:43::112::1:22::1:1: probability G 52273361195283192:a32 matrix T :52::5:371:6256169:36 bits 2.1 1.9 * 1.7 * * 1.5 * * * * Relative 1.3 * * * ** Entropy 1.0 ** * * * ** (16.8 bits) 0.8 ** * *** * * ** 0.6 * **** *** ** **** 0.4 ** **** *********** * 0.2 ** ****************** 0.0 --------------------- Multilevel GTCGATGATGGTGTTGTTGGT consensus AATCGGAT A G A T sequence CG A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 11172 98 6.74e-10 GATGGAACCT CTTCATGATGATGTTGTTGTT GTTCTATGAT 269030 134 1.01e-09 TCGGTGGTGT CTGGATGATGGTGTTGATGGT TTTCTTATAC 264188 169 2.81e-09 GCGGACTATG ATCGAGGATGATGCTGTTGAT GTGAGGCTCG 269028 19 9.73e-09 GAAATTGACT CTCCATGTTGGAGTTGTTGTT AGATGAGTCG 23679 185 2.71e-07 AGTAGTTGAA GTCGGGGGTGATTCTGTTGGT CCAGTTGTAG 20712 45 2.71e-07 ACTTCCCCTC CACCGTGATGATGCTGATGAT CGGTGTATGC 38679 87 5.29e-07 TGCCATTAGT GGTGGTGATGGAGGCGGTGTT TTGCTACTCA 1366 141 5.89e-07 CGGTGCTGGG GTTCATGCTGTTGTCGTTGGT GGTGAGATGG 20737 147 7.26e-07 TGCTGCTGCT GGCCATGCTGAGTTTGTTGAT TGTACGGCGG 35519 143 8.04e-07 CATGGTTGAG GAAGAGAGCGAGGTTGTTGTT GGGAGAAGGA 25130 114 1.92e-06 CAATGTGATG ATGCAGAATTGTGGTGTTGAA GCAGTGGCAA 25138 198 2.10e-06 CAGTGTTGAT ATTGGTGATGACGGCGATGGA GTAAAGCGGT 20859 318 2.51e-06 CTGTGGCTCG GGAGAGAACGGTGGGGATGGA ACGAGAGCGT 10278 245 2.74e-06 CTTCAACGGT GGGCATCTTGGTTTTGTTGGG CGAGACGTTG 38193 316 3.55e-06 AAATCGGGTG GTTGGAAGTGGTGTTGTTTGT GATACGTGTG 32668 33 3.55e-06 CTGGTGCCAC AGGGATATTGGGGTTGTCGTA TGATTGTTGT 7031 274 3.86e-06 ATTTGGCACG GTCCATGTTTGCGTCGTTGTG CTTTGTTCGT 22303 330 4.55e-06 GTCAGACTTT GAAGAGATCGGTGCTGGTGCT ACTTTCCCTA 25473 368 4.93e-06 TGATGTCTCG ATCGAGGTGGATGGTGGTGCG AGGCGAGTGG 268449 188 5.35e-06 CCTTTTGTTG AAACGTGAGGAGGTTGATGAT GCAGCAATCA 23246 97 6.26e-06 GGAGAGCGTA CTCGGAGCCAGTGTTGTTGGT GCTACTTTCT 24709 164 7.31e-06 TGTTTTGGTG GAAGAGATTGGAGGGGTCGTT CGCAGGGGGG 25730 290 7.88e-06 TATTAGGTTC ATCGAGAATGATGGGTGTGTG TGCTGGCTGG 5806 108 1.22e-05 CAGCATGCAT GGGGAAGATGAAGGCTTTGTA GTCATCGGCT 32766 427 1.51e-05 CCCTCGCGAA CACGATCACGGTGTAGTTGAC CAGAGCCCTC 24879 261 1.51e-05 GTCCCATTGT GTTGGTAATGATTTAGAGGGT GGAGCGTGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11172 6.7e-10 97_[+2]_382 269030 1e-09 133_[+2]_346 264188 2.8e-09 168_[+2]_311 269028 9.7e-09 18_[+2]_461 23679 2.7e-07 184_[+2]_295 20712 2.7e-07 44_[+2]_435 38679 5.3e-07 86_[+2]_393 1366 5.9e-07 140_[+2]_339 20737 7.3e-07 146_[+2]_333 35519 8e-07 142_[+2]_337 25130 1.9e-06 113_[+2]_366 25138 2.1e-06 197_[+2]_282 20859 2.5e-06 317_[+2]_162 10278 2.7e-06 244_[+2]_235 38193 3.5e-06 315_[+2]_164 32668 3.5e-06 32_[+2]_447 7031 3.9e-06 273_[+2]_206 22303 4.6e-06 329_[+2]_150 25473 4.9e-06 367_[+2]_112 268449 5.3e-06 187_[+2]_292 23246 6.3e-06 96_[+2]_383 24709 7.3e-06 163_[+2]_316 25730 7.9e-06 289_[+2]_190 5806 1.2e-05 107_[+2]_372 32766 1.5e-05 426_[+2]_53 24879 1.5e-05 260_[+2]_219 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=26 11172 ( 98) CTTCATGATGATGTTGTTGTT 1 269030 ( 134) CTGGATGATGGTGTTGATGGT 1 264188 ( 169) ATCGAGGATGATGCTGTTGAT 1 269028 ( 19) CTCCATGTTGGAGTTGTTGTT 1 23679 ( 185) GTCGGGGGTGATTCTGTTGGT 1 20712 ( 45) CACCGTGATGATGCTGATGAT 1 38679 ( 87) GGTGGTGATGGAGGCGGTGTT 1 1366 ( 141) GTTCATGCTGTTGTCGTTGGT 1 20737 ( 147) GGCCATGCTGAGTTTGTTGAT 1 35519 ( 143) GAAGAGAGCGAGGTTGTTGTT 1 25130 ( 114) ATGCAGAATTGTGGTGTTGAA 1 25138 ( 198) ATTGGTGATGACGGCGATGGA 1 20859 ( 318) GGAGAGAACGGTGGGGATGGA 1 10278 ( 245) GGGCATCTTGGTTTTGTTGGG 1 38193 ( 316) GTTGGAAGTGGTGTTGTTTGT 1 32668 ( 33) AGGGATATTGGGGTTGTCGTA 1 7031 ( 274) GTCCATGTTTGCGTCGTTGTG 1 22303 ( 330) GAAGAGATCGGTGCTGGTGCT 1 25473 ( 368) ATCGAGGTGGATGGTGGTGCG 1 268449 ( 188) AAACGTGAGGAGGTTGATGAT 1 23246 ( 97) CTCGGAGCCAGTGTTGTTGGT 1 24709 ( 164) GAAGAGATTGGAGGGGTCGTT 1 25730 ( 290) ATCGAGAATGATGGGTGTGTG 1 5806 ( 108) GGGGAAGATGAAGGCTTTGTA 1 32766 ( 427) CACGATCACGGTGTAGTTGAC 1 24879 ( 261) GTTGGTAATGATTTAGAGGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18720 bayes= 10.6553 E= 9.8e-009 8 -3 104 -1134 -14 -1134 -8 102 -41 71 -34 -20 -1134 55 142 -1134 144 -1134 34 -1134 -114 -1134 51 102 44 -161 124 -1134 97 -103 -108 2 -1134 -29 -166 146 -273 -1134 186 -178 85 -1134 104 -278 -73 -161 -66 121 -1134 -1134 179 -79 -1134 -62 34 102 -173 -29 -108 121 -1134 -1134 192 -178 -14 -1134 -66 121 -1134 -161 -266 174 -1134 -1134 198 -278 -14 -161 51 38 -41 -261 -66 121 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 26 E= 9.8e-009 0.269231 0.230769 0.500000 0.000000 0.230769 0.000000 0.230769 0.538462 0.192308 0.384615 0.192308 0.230769 0.000000 0.346154 0.653846 0.000000 0.692308 0.000000 0.307692 0.000000 0.115385 0.000000 0.346154 0.538462 0.346154 0.076923 0.576923 0.000000 0.500000 0.115385 0.115385 0.269231 0.000000 0.192308 0.076923 0.730769 0.038462 0.000000 0.884615 0.076923 0.461538 0.000000 0.500000 0.038462 0.153846 0.076923 0.153846 0.615385 0.000000 0.000000 0.846154 0.153846 0.000000 0.153846 0.307692 0.538462 0.076923 0.192308 0.115385 0.615385 0.000000 0.000000 0.923077 0.076923 0.230769 0.000000 0.153846 0.615385 0.000000 0.076923 0.038462 0.884615 0.000000 0.000000 0.961538 0.038462 0.230769 0.076923 0.346154 0.346154 0.192308 0.038462 0.153846 0.615385 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GAC][TAG][CT][GC][AG][TG][GA][AT]TG[GA]TG[TG]TG[TA]TG[GTA]T -------------------------------------------------------------------------------- Time 26.13 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 25 llr = 283 E-value = 1.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 31:5:2a42441:7412:632 pos.-specific C ::::2::11:1::2:2::::: probability G 659468:45434a:4567438 matrix T 14122:::2234:12212:3: bits 2.1 1.9 * 1.7 * * * 1.5 * ** * Relative 1.3 * ** * * Entropy 1.0 * ** * * * (16.3 bits) 0.8 * * ** ** *** * 0.6 **** ** *** *** * 0.4 ******** * **** *** * 0.2 ********************* 0.0 --------------------- Multilevel GGGAGGAAGGAGGAAGGGAAG consensus AT GT GTAGT CGCATGGA sequence A T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 268449 350 8.51e-11 GGAAGGAGGA GGGAGGAATGAGGAAGGGAAG GGAAGGGAGG 23246 354 1.62e-08 GGAGGAACCA GAGTGGAAGGTGGAAGGGATG GGTGGTCTGG 42412 256 4.85e-08 TTGCCGTGTA AGGAGAAATGATGAGGGGGGG CTAACAGGGT 269028 101 5.61e-08 GACGACGATG AGGAGGAGGAGGGAAGAGGAA GCAGAGCTGT 20859 280 1.68e-07 ATCGGCGTCG ATGAGGAGGATGGAGTGTATG CCGTCGCCTG 7031 341 1.90e-07 AAGAAGACGA AGGTGGAGAAATGAATGGGTG GTTGAGGTGC 24709 189 5.55e-07 GTCGTTCGCA GGGGGGAGATGTGAGAGGAGA CACAGCATCT 1366 223 7.70e-07 TCTGGCTGGG GGGGGGAGCAGGGCTGGGAGA AAAGGCACTT 20737 102 1.43e-06 TGCTGTTGTT GTGGCGAATGTGGATTAGAAG TCTGTTGGTA 25473 330 2.31e-06 GAGGACTGCG GTGGCGATGAGTGAAAGGGTG TTGTGATTGA 11172 313 2.31e-06 TGTGGTTGCG AGGAGGAGGATTAATGGTATG AAGGTAAATG 25130 158 2.53e-06 GGTGACCTTC AGGAAAAAGGGTGAGCGGGGG AGGGGCTCGT 32766 31 3.32e-06 CAACTGAATG TGGAGGAAGGAGGAAGATGCG GTACAACAGC 10278 288 3.32e-06 AGCGAAGTGT GTGGTGAAGTGGGTGGTGAGG CACTTCCCGT 36917 359 3.63e-06 TAAAGAGGAG GGGAGGAGTGAGGTAGGCGAA ATAGCTCTAC 4921 72 4.31e-06 AGAGGCAACT GTGTTGACAAATGAACGTAAG GATACTGTGG 269030 307 4.69e-06 GGTGCAAGTA GGGGGAAAGGCAGCGCGGGAG GGCAGGGTGT 25730 249 5.10e-06 TCGACAGATT GAGATGAGGATAGCTCGGATG ACTTGATCAG 1122 304 5.10e-06 CAGTAAGTGA AGGGTGAAGAATGAAGAAAGA AGATTGAGAA 20712 235 6.53e-06 CGGCGCTGTA GTTTGGAAAGAGGAATAGGAG GATATTGGGA 5806 154 9.64e-06 GTACGCACTC ATGACGAGATTTGATAAGATG TTGTACGGTC 32668 229 1.04e-05 CAGCAGTAGC GGGAGAACTGTGGCGGTGAGA GGCAGCTTCA 35519 36 2.25e-05 AGGATGATGG GAGATGAACGATGTGCTGATG GCGTACGAGA 22303 417 3.11e-05 TCGGTACGTC GTGGCGTGGACTGCAGGTGGG TGTATCGTCG 22163 305 3.73e-05 AACTGGACTC TTTGGGACTTGAGAGGGGAAG CTCGCTTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 268449 8.5e-11 349_[+3]_130 23246 1.6e-08 353_[+3]_126 42412 4.8e-08 255_[+3]_224 269028 5.6e-08 100_[+3]_379 20859 1.7e-07 279_[+3]_200 7031 1.9e-07 340_[+3]_139 24709 5.5e-07 188_[+3]_291 1366 7.7e-07 222_[+3]_257 20737 1.4e-06 101_[+3]_378 25473 2.3e-06 329_[+3]_150 11172 2.3e-06 312_[+3]_167 25130 2.5e-06 157_[+3]_322 32766 3.3e-06 30_[+3]_449 10278 3.3e-06 287_[+3]_192 36917 3.6e-06 358_[+3]_121 4921 4.3e-06 71_[+3]_408 269030 4.7e-06 306_[+3]_173 25730 5.1e-06 248_[+3]_231 1122 5.1e-06 303_[+3]_176 20712 6.5e-06 234_[+3]_245 5806 9.6e-06 153_[+3]_326 32668 1e-05 228_[+3]_251 35519 2.3e-05 35_[+3]_444 22303 3.1e-05 416_[+3]_63 22163 3.7e-05 304_[+3]_175 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=25 268449 ( 350) GGGAGGAATGAGGAAGGGAAG 1 23246 ( 354) GAGTGGAAGGTGGAAGGGATG 1 42412 ( 256) AGGAGAAATGATGAGGGGGGG 1 269028 ( 101) AGGAGGAGGAGGGAAGAGGAA 1 20859 ( 280) ATGAGGAGGATGGAGTGTATG 1 7031 ( 341) AGGTGGAGAAATGAATGGGTG 1 24709 ( 189) GGGGGGAGATGTGAGAGGAGA 1 1366 ( 223) GGGGGGAGCAGGGCTGGGAGA 1 20737 ( 102) GTGGCGAATGTGGATTAGAAG 1 25473 ( 330) GTGGCGATGAGTGAAAGGGTG 1 11172 ( 313) AGGAGGAGGATTAATGGTATG 1 25130 ( 158) AGGAAAAAGGGTGAGCGGGGG 1 32766 ( 31) TGGAGGAAGGAGGAAGATGCG 1 10278 ( 288) GTGGTGAAGTGGGTGGTGAGG 1 36917 ( 359) GGGAGGAGTGAGGTAGGCGAA 1 4921 ( 72) GTGTTGACAAATGAACGTAAG 1 269030 ( 307) GGGGGAAAGGCAGCGCGGGAG 1 25730 ( 249) GAGATGAGGATAGCTCGGATG 1 1122 ( 304) AGGGTGAAGAATGAAGAAAGA 1 20712 ( 235) GTTTGGAAAGAGGAATAGGAG 1 5806 ( 154) ATGACGAGATTTGATAAGATG 1 32668 ( 229) GGGAGAACTGTGGCGGTGAGA 1 35519 ( 36) GAGATGAACGATGTGCTGATG 1 22303 ( 417) GTGGCGTGGACTGCAGGTGGG 1 22163 ( 305) TTTGGGACTTGAGAGGGGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 18720 bayes= 10.0371 E= 1.8e-003 33 -1129 130 -173 -109 -1129 109 44 -1129 -1129 192 -173 91 -1129 56 -73 -267 -56 130 -41 -67 -1129 178 -1129 191 -1129 -1129 -273 79 -97 71 -273 -35 -156 98 -14 65 -1129 85 -73 50 -156 20 8 -109 -1129 85 73 -267 -1129 198 -1129 141 -24 -1129 -114 79 -1129 56 -41 -109 -24 109 -73 -9 -1129 139 -114 -267 -256 156 -41 123 -1129 71 -1129 33 -256 39 27 -9 -1129 164 -1129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 25 E= 1.8e-003 0.320000 0.000000 0.600000 0.080000 0.120000 0.000000 0.520000 0.360000 0.000000 0.000000 0.920000 0.080000 0.480000 0.000000 0.360000 0.160000 0.040000 0.160000 0.600000 0.200000 0.160000 0.000000 0.840000 0.000000 0.960000 0.000000 0.000000 0.040000 0.440000 0.120000 0.400000 0.040000 0.200000 0.080000 0.480000 0.240000 0.400000 0.000000 0.440000 0.160000 0.360000 0.080000 0.280000 0.280000 0.120000 0.000000 0.440000 0.440000 0.040000 0.000000 0.960000 0.000000 0.680000 0.200000 0.000000 0.120000 0.440000 0.000000 0.360000 0.200000 0.120000 0.200000 0.520000 0.160000 0.240000 0.000000 0.640000 0.120000 0.040000 0.040000 0.720000 0.200000 0.600000 0.000000 0.400000 0.000000 0.320000 0.040000 0.320000 0.320000 0.240000 0.000000 0.760000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][GT]G[AG][GT]GA[AG][GTA][GA][AGT][GT]G[AC][AGT][GC][GA][GT][AG][AGT][GA] -------------------------------------------------------------------------------- Time 39.90 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10278 6.34e-09 85_[+1(1.91e-08)]_138_\ [+2(2.74e-06)]_22_[+3(3.32e-06)]_64_[+1(2.56e-05)]_6_[+1(8.13e-06)]_80 11172 1.10e-10 97_[+2(6.74e-10)]_194_\ [+3(2.31e-06)]_94_[+1(1.42e-06)]_52 1122 2.30e-05 303_[+3(5.10e-06)]_91_\ [+1(1.42e-07)]_64 1366 6.00e-07 140_[+2(5.89e-07)]_61_\ [+3(7.70e-07)]_44_[+1(5.65e-05)]_192 20712 6.36e-07 44_[+2(2.71e-07)]_78_[+1(1.53e-05)]_\ 70_[+3(6.53e-06)]_245 20737 2.90e-05 101_[+3(1.43e-06)]_24_\ [+2(7.26e-07)]_333 20859 1.22e-07 129_[+3(8.55e-05)]_33_\ [+2(5.45e-05)]_75_[+3(1.68e-07)]_17_[+2(2.51e-06)]_131_[+1(1.04e-05)]_10 21709 3.05e-03 102_[+1(8.13e-06)]_3_[+1(5.38e-07)]_\ 353 22163 2.28e-02 304_[+3(3.73e-05)]_175 22303 1.97e-03 329_[+2(4.55e-06)]_66_\ [+3(3.11e-05)]_63 23246 6.41e-09 96_[+2(6.26e-06)]_236_\ [+3(1.62e-08)]_91_[+1(1.73e-06)]_14 23679 1.20e-06 184_[+2(2.71e-07)]_201_\ [+1(1.09e-07)]_73 24709 8.76e-08 163_[+2(7.31e-06)]_4_[+3(5.55e-07)]_\ 144_[+1(7.51e-07)]_126 24812 1.31e-02 425_[+1(2.81e-06)]_54 24879 1.68e-04 260_[+2(1.51e-05)]_179_\ [+1(8.82e-06)]_19 25130 1.68e-07 113_[+2(1.92e-06)]_23_\ [+3(2.53e-06)]_296_[+1(1.28e-06)]_5 25138 6.30e-05 197_[+2(2.10e-06)]_240_\ [+1(1.22e-05)]_21 25473 8.78e-07 19_[+1(3.39e-06)]_203_\ [+2(2.39e-05)]_65_[+3(2.31e-06)]_17_[+2(4.93e-06)]_112 25730 1.19e-05 248_[+3(5.10e-06)]_20_\ [+2(7.88e-06)]_135_[+1(1.78e-05)]_34 264188 1.28e-09 168_[+2(2.81e-09)]_42_\ [+2(5.96e-08)]_227_[+1(1.39e-08)] 264879 1.21e-03 255_[+1(1.04e-06)]_224 268449 7.88e-11 187_[+2(5.35e-06)]_141_\ [+3(8.51e-11)]_103_[+1(3.39e-06)]_6 269028 2.28e-10 18_[+2(9.73e-09)]_61_[+3(5.61e-08)]_\ 335_[+1(8.82e-06)]_23 269030 9.13e-11 133_[+2(1.01e-09)]_46_\ [+1(1.92e-05)]_60_[+2(3.66e-05)]_4_[+3(4.69e-06)]_149_[+1(3.80e-07)]_3 32668 3.53e-10 32_[+2(3.55e-06)]_175_\ [+3(1.04e-05)]_185_[+1(2.09e-10)]_45 32766 1.10e-05 30_[+3(3.32e-06)]_375_\ [+2(1.51e-05)]_31_[+1(1.31e-05)]_1 32920 4.31e-01 500 34994 1.16e-02 16_[+1(9.62e-05)]_359_\ [+1(2.32e-06)]_3_[+1(6.72e-07)]_59 35519 1.33e-06 35_[+3(2.25e-05)]_86_[+2(8.04e-07)]_\ 118_[+1(7.21e-05)]_8_[+1(3.39e-06)]_169 36917 1.66e-04 358_[+3(3.63e-06)]_96_\ [+1(5.31e-06)]_4 38193 2.43e-04 315_[+2(3.55e-06)]_134_\ [+1(9.57e-06)]_9 38679 4.67e-09 86_[+2(5.29e-07)]_290_\ [+1(5.41e-10)]_13_[+1(6.88e-06)]_16_[+1(1.53e-05)]_11 42412 6.15e-07 255_[+3(4.85e-08)]_107_\ [+1(1.91e-06)]_63_[+1(3.60e-05)]_12 4921 6.77e-05 71_[+3(4.31e-06)]_203_\ [+1(1.12e-05)]_156_[+1(1.42e-06)]_7 5806 1.16e-08 107_[+2(1.22e-05)]_25_\ [+3(9.64e-06)]_146_[+1(1.04e-05)]_131_[+1(2.84e-09)]_7 6255 1.21e-01 462_[+1(1.42e-05)]_17 7031 1.51e-05 250_[+3(5.29e-05)]_2_[+2(3.86e-06)]_\ 11_[+3(5.59e-05)]_14_[+3(1.90e-07)]_139 7558 1.30e-02 302_[+1(4.87e-06)]_102_\ [+1(4.68e-05)]_54 9598 8.01e-02 473_[+1(1.78e-05)]_6 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************