******************************************************************************** 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/463/463.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10518 1.0000 500 10811 1.0000 500 11480 1.0000 500 12025 1.0000 500 1957 1.0000 500 22304 1.0000 500 23665 1.0000 500 23770 1.0000 500 24165 1.0000 500 24243 1.0000 500 24991 1.0000 500 25647 1.0000 500 25648 1.0000 500 267946 1.0000 500 269233 1.0000 500 269325 1.0000 500 30804 1.0000 500 31166 1.0000 500 31499 1.0000 500 3313 1.0000 500 3477 1.0000 500 3632 1.0000 500 36679 1.0000 500 36927 1.0000 500 38672 1.0000 500 3949 1.0000 500 4095 1.0000 500 4306 1.0000 500 5708 1.0000 500 7845 1.0000 500 8147 1.0000 500 8274 1.0000 500 bd861 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/463/463.seqs.fa -oc motifs/463 -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= 33 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= 16500 N= 33 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.270 C 0.239 G 0.233 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.270 C 0.239 G 0.233 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 28 llr = 262 E-value = 6.3e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 364:a55a1844 pos.-specific C 723a:55:9236 probability G ::::::::::1: matrix T :14:::::::3: bits 2.1 * 1.9 ** * 1.7 ** * 1.5 ** ** Relative 1.3 ** *** Entropy 1.0 * *** *** * (13.5 bits) 0.8 * ******* * 0.6 ** ******* * 0.4 ********** * 0.2 ********** * 0.0 ------------ Multilevel CAACACCACAAC consensus ACT AA TA sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 3313 482 2.05e-07 CACCACCAAA CACCACCACAAC ACAAACC bd861 483 6.59e-07 ATCCTACCTG CAACACAACAAC ATTCAA 38672 67 6.59e-07 AGACCGACCA CAACAACACAAC GTAGCAAGCA 36679 483 6.59e-07 GACGCCTGCA CAACACAACAAC GATAGT 12025 460 1.53e-06 CCCTCCGCCT CAACAACACATC ATGATGTGGA 3477 419 3.76e-06 AAACTACCAA CACCAACACAAA CCGCTACGTC 25647 466 5.28e-06 TCATTGATAC CACCAACACATA AACAATCATA 24991 450 8.55e-06 TTCCAGATCC AACCAACACAAC GCGAACTCTC 30804 488 9.86e-06 AAGAGAACAC AAACAAAACAAC C 1957 473 1.10e-05 TTGTATCAAC AACCACAACATC AGCACCAACC 5708 377 1.53e-05 ACTGGAAGTA CACCACCACAGA AGTTTACAGA 10811 461 1.71e-05 AACTAACCTC CCTCACAACATA GGGCTGCAAC 7845 47 1.94e-05 TCTCACACAC CCTCACAACACA AAAACTGCAG 25648 328 1.94e-05 AATACAGCTA CCTCACAACACA ATATTTGCAC 23770 470 1.94e-05 TCTGATACCT CTACACCACATC TAACCGCCAT 4095 167 2.36e-05 TCGATCTCGC CTTCAACACATC TCCGCGTCAC 31499 254 2.36e-05 GTTGTTTCAT AAACAAAACATA CAAAACATAC 8147 484 2.54e-05 ATACACCAAG CCACACAACAGC AAATC 31166 488 3.35e-05 CTACCGACGT AAACAACACCAC C 24243 457 3.35e-05 CATCACTACC CTTCACCACACA TCTGTCCATT 3632 36 3.63e-05 GAAGGGAAAC CATCAACACCGC ACATTCGCAA 23665 60 3.94e-05 TCGCTGTATG CCCCACAACCTC CTTCGCACCC 3949 408 4.30e-05 AAACATCCCA AACCAAAACCAC CCACCGACGA 24165 484 5.70e-05 AAACGAGTTA CATCAAAAAACC AAAAC 4306 25 1.20e-04 CTGGCACTGT CCTCACCATACC GGCAATCTTC 22304 258 1.20e-04 CGACGACACA AGACACAACAAA CTCCATACCT 8274 230 1.41e-04 ATTGAATGTG AATCAATACACA TGAATTGCCA 36927 488 1.47e-04 CTCTCACCCG CATCACCAACCA C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3313 2.1e-07 481_[+1]_7 bd861 6.6e-07 482_[+1]_6 38672 6.6e-07 66_[+1]_422 36679 6.6e-07 482_[+1]_6 12025 1.5e-06 459_[+1]_29 3477 3.8e-06 418_[+1]_70 25647 5.3e-06 465_[+1]_23 24991 8.6e-06 449_[+1]_39 30804 9.9e-06 487_[+1]_1 1957 1.1e-05 472_[+1]_16 5708 1.5e-05 376_[+1]_112 10811 1.7e-05 460_[+1]_28 7845 1.9e-05 46_[+1]_442 25648 1.9e-05 327_[+1]_161 23770 1.9e-05 469_[+1]_19 4095 2.4e-05 166_[+1]_322 31499 2.4e-05 253_[+1]_235 8147 2.5e-05 483_[+1]_5 31166 3.3e-05 487_[+1]_1 24243 3.3e-05 456_[+1]_32 3632 3.6e-05 35_[+1]_453 23665 3.9e-05 59_[+1]_429 3949 4.3e-05 407_[+1]_81 24165 5.7e-05 483_[+1]_5 4306 0.00012 24_[+1]_464 22304 0.00012 257_[+1]_231 8274 0.00014 229_[+1]_259 36927 0.00015 487_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=28 3313 ( 482) CACCACCACAAC 1 bd861 ( 483) CAACACAACAAC 1 38672 ( 67) CAACAACACAAC 1 36679 ( 483) CAACACAACAAC 1 12025 ( 460) CAACAACACATC 1 3477 ( 419) CACCAACACAAA 1 25647 ( 466) CACCAACACATA 1 24991 ( 450) AACCAACACAAC 1 30804 ( 488) AAACAAAACAAC 1 1957 ( 473) AACCACAACATC 1 5708 ( 377) CACCACCACAGA 1 10811 ( 461) CCTCACAACATA 1 7845 ( 47) CCTCACAACACA 1 25648 ( 328) CCTCACAACACA 1 23770 ( 470) CTACACCACATC 1 4095 ( 167) CTTCAACACATC 1 31499 ( 254) AAACAAAACATA 1 8147 ( 484) CCACACAACAGC 1 31166 ( 488) AAACAACACCAC 1 24243 ( 457) CTTCACCACACA 1 3632 ( 36) CATCAACACCGC 1 23665 ( 60) CCCCACAACCTC 1 3949 ( 408) AACCAAAACCAC 1 24165 ( 484) CATCAAAAAACC 1 4306 ( 25) CCTCACCATACC 1 22304 ( 258) AGACACAACAAA 1 8274 ( 230) AATCAATACACA 1 36927 ( 488) CATCACCAACCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 16137 bayes= 9.7748 E= 6.3e-009 8 158 -1145 -1145 125 -16 -270 -127 41 26 -1145 47 -1145 206 -1145 -1145 189 -1145 -1145 -1145 78 116 -1145 -1145 78 106 -1145 -285 189 -1145 -1145 -1145 -192 190 -1145 -285 161 -42 -1145 -1145 41 6 -112 15 54 134 -1145 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 28 E= 6.3e-009 0.285714 0.714286 0.000000 0.000000 0.642857 0.214286 0.035714 0.107143 0.357143 0.285714 0.000000 0.357143 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.464286 0.535714 0.000000 0.000000 0.464286 0.500000 0.000000 0.035714 1.000000 0.000000 0.000000 0.000000 0.071429 0.892857 0.000000 0.035714 0.821429 0.178571 0.000000 0.000000 0.357143 0.250000 0.107143 0.285714 0.392857 0.607143 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][AC][ATC]CA[CA][CA]ACA[ATC][CA] -------------------------------------------------------------------------------- Time 8.55 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 17 llr = 233 E-value = 7.5e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 8215:12:4122::431:72: pos.-specific C 2:::4::11::12::::1::1 probability G 15922:6919543a:495382 matrix T :3:349214:335:63:4::6 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * * * * * Relative 1.3 * * * * * * * Entropy 1.0 * * * * * ** * ** (19.8 bits) 0.8 * * *** * ** * *** 0.6 * * *** ** *** ***** 0.4 ******** ** ********* 0.2 ********************* 0.0 --------------------- Multilevel AGGACTGGAGGGTGTGGGAGT consensus T TT T TTG AA TG G sequence A GG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 269325 146 1.57e-09 CAGCCCTCGC ATGGCTGGTGAGTGAGGGAGT GACAGGGGAG 23665 146 1.57e-09 CAGCCCTCGC ATGGCTGGTGAGTGAGGGAGT GACAGACGAG 3949 114 1.82e-08 TGCCCGCCGT AGGGCTGGTGGCCGTGGCAGT ATCGCTGTTT 24165 87 3.31e-08 GAGTTTGTGT AGGATTAGGGTGTGTGGTGGT GTTGGCCGAA bd861 11 3.71e-08 GTATTGCATT ATGATTTGTGTGGGAGGGAGG CCATCACGGA 269233 152 5.17e-08 TTCACTCCGT AAGTCTTGAGGTGGTTGGAGG AGGGCTGACG 4306 295 6.40e-08 GCGGAGCGAA AGGAGAGGAGGAGGAGGGGGT TTTGTCCTGT 3477 141 2.24e-07 CCATGGCATG AGAACTGGTGGTTGTAATAGT GACGGGTCAG 31166 138 2.91e-07 TCCCAGTCAA AAGATTGGAGATGGAGGTGGC GTTATGAACC 1957 36 3.44e-07 AACTCACCTA CAGTTTTGAGGGTGATGGAGC TCATCTCGTT 31499 435 3.74e-07 ACAAGAGATC AGGAGTAGAGGCCGTAGTAAT TCACGAGAGA 24991 19 3.74e-07 TGGTTGTATG ATGTTTGGTAGTCGTAGCAGT GTGATGAGGA 30804 167 6.99e-07 TTGGAGACAA GTGTGTGGAAGATGTTGGAGT GGATGTGAAT 267946 416 6.99e-07 TGCATCCTGC CGGAGTGTCGTGTGTAGGAGT ATTGTTGGAG 5708 29 1.23e-06 ATGTTTTCAG AAGTTAAGAGTGTGTTGTGGG TGTAACCAAG 10811 351 1.50e-06 ATTTCTTTGA AGAGCTGGGGGATGAAGTGAT TTTGCTTCAT 36679 274 1.61e-06 ACTAGTACTT CGGACTGCTGTTGGTTGGAAG TGTGTCCTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 269325 1.6e-09 145_[+2]_334 23665 1.6e-09 145_[+2]_334 3949 1.8e-08 113_[+2]_366 24165 3.3e-08 86_[+2]_393 bd861 3.7e-08 10_[+2]_469 269233 5.2e-08 151_[+2]_328 4306 6.4e-08 294_[+2]_185 3477 2.2e-07 140_[+2]_339 31166 2.9e-07 137_[+2]_342 1957 3.4e-07 35_[+2]_444 31499 3.7e-07 434_[+2]_45 24991 3.7e-07 18_[+2]_461 30804 7e-07 166_[+2]_313 267946 7e-07 415_[+2]_64 5708 1.2e-06 28_[+2]_451 10811 1.5e-06 350_[+2]_129 36679 1.6e-06 273_[+2]_206 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=17 269325 ( 146) ATGGCTGGTGAGTGAGGGAGT 1 23665 ( 146) ATGGCTGGTGAGTGAGGGAGT 1 3949 ( 114) AGGGCTGGTGGCCGTGGCAGT 1 24165 ( 87) AGGATTAGGGTGTGTGGTGGT 1 bd861 ( 11) ATGATTTGTGTGGGAGGGAGG 1 269233 ( 152) AAGTCTTGAGGTGGTTGGAGG 1 4306 ( 295) AGGAGAGGAGGAGGAGGGGGT 1 3477 ( 141) AGAACTGGTGGTTGTAATAGT 1 31166 ( 138) AAGATTGGAGATGGAGGTGGC 1 1957 ( 36) CAGTTTTGAGGGTGATGGAGC 1 31499 ( 435) AGGAGTAGAGGCCGTAGTAAT 1 24991 ( 19) ATGTTTGGTAGTCGTAGCAGT 1 30804 ( 167) GTGTGTGGAAGATGTTGGAGT 1 267946 ( 416) CGGAGTGTCGTGTGTAGGAGT 1 5708 ( 29) AAGTTAAGAGTGTGTTGTGGG 1 10811 ( 351) AGAGCTGGGGGATGAAGTGAT 1 36679 ( 274) CGGACTGCTGTTGGTTGGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15840 bayes= 11.2282 E= 7.5e-008 150 -44 -199 -1073 -20 -1073 101 19 -120 -1073 192 -1073 80 -1073 1 19 -1073 78 1 45 -120 -1073 -1073 177 -61 -1073 147 -55 -1073 -202 192 -213 61 -202 -99 67 -120 -1073 192 -1073 -61 -1073 118 19 -61 -102 82 19 -1073 -44 33 104 -1073 -1073 210 -1073 61 -1073 -1073 119 13 -1073 82 19 -219 -1073 201 -1073 -1073 -102 118 45 139 -1073 33 -1073 -61 -1073 182 -1073 -1073 -102 1 133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 7.5e-008 0.764706 0.176471 0.058824 0.000000 0.235294 0.000000 0.470588 0.294118 0.117647 0.000000 0.882353 0.000000 0.470588 0.000000 0.235294 0.294118 0.000000 0.411765 0.235294 0.352941 0.117647 0.000000 0.000000 0.882353 0.176471 0.000000 0.647059 0.176471 0.000000 0.058824 0.882353 0.058824 0.411765 0.058824 0.117647 0.411765 0.117647 0.000000 0.882353 0.000000 0.176471 0.000000 0.529412 0.294118 0.176471 0.117647 0.411765 0.294118 0.000000 0.176471 0.294118 0.529412 0.000000 0.000000 1.000000 0.000000 0.411765 0.000000 0.000000 0.588235 0.294118 0.000000 0.411765 0.294118 0.058824 0.000000 0.941176 0.000000 0.000000 0.117647 0.529412 0.352941 0.705882 0.000000 0.294118 0.000000 0.176471 0.000000 0.823529 0.000000 0.000000 0.117647 0.235294 0.647059 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[GTA]G[ATG][CTG]TGG[AT]G[GT][GT][TG]G[TA][GAT]G[GT][AG]G[TG] -------------------------------------------------------------------------------- Time 16.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 19 llr = 227 E-value = 7.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 115316121::44:3::47:2 pos.-specific C 3112::2:35:45:32112:3 probability G 5821935621a::a5194:75 matrix T 2:34112354:22::8:2131 bits 2.1 * * 1.9 * * * 1.7 * * * 1.5 * * * * Relative 1.3 * * * * * * Entropy 1.0 * * * * ** * (17.2 bits) 0.8 * * * * ** ** 0.6 * ** * ** * ** ** 0.4 ** **** ******** *** 0.2 ********************* 0.0 --------------------- Multilevel GGATGAGGTCGACGGTGAAGG consensus C TA GCTCT CA A GCTC sequence T C T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 23665 439 1.73e-08 AAGCCCCAAC GGAAGAGACCGCAGGTGTAGC TACAAACTTC 269325 439 2.01e-08 AAGCCCCAAC GGAAGAGACCGAAGGTGTAGC CACAAACTTC 1957 120 1.02e-07 ATGGAAATGT GGTCGAGGTCGCCGATCGAGG TCGCCGATCG 25647 367 2.06e-07 ATCAATGATG TGTCGACGTCGACGGTGGATC ATGAGTTGAA 22304 130 3.97e-07 TGTATTGGTT CAGAGAGGCCGTCGGTGTAGG GGCTTGCCTT 11480 283 4.40e-07 TTCAAGGGTT GGATGTGTTGGCTGGTGGAGA AGACTCGAGT 36927 11 5.40e-07 GAATGCAAGA CGATGACAACGCCGCTGACGG ACGTCGACGA 38672 134 8.00e-07 TAGAAGCAGC CGCTGGGTTCGTCGGTGGCTG TTCGTTGGCT 24991 94 9.67e-07 ATGGATACTT TGATGATGATGAAGACGAAGG TTCATCGGGC 25648 86 1.06e-06 TGTGGGTTGT CGAAGAGTGGGAAGGCGGAGA AAGGAAGGAC 24243 75 1.39e-06 TCATTAATCG GGATGGTTTCGTAGCTGATGC GGAGGGGAAT 267946 218 1.66e-06 CCAACGATGC TGTCAAGGGTGAAGGTGAAGG AGCCACCTTA 10811 321 2.98e-06 AAGGATGGGG GGAGGACGTTGCTGCTGTCTA TTTCTTTGAA 31499 144 3.23e-06 TTACCATTGG CATTGATGTTGCCGCTGCATG TGTATTTGGG 31166 17 3.23e-06 AACTGCTATC GGATGTCTTTGACGACGGCGA AGGCAACGTT 8274 94 3.78e-06 GCAGCGAACA CCGAGGGGTCGCCGATGAAGT CATATGACAG 30804 71 5.11e-06 GATTGGAAAA GGGAGGTGGTGACGGGGATGG TGGAAAGGTA 3477 221 6.36e-06 TGGAGACGAC AGTTGAAGCTGCTGCTGGATG GGCGAGACTT 24165 174 6.36e-06 TCGGTGGAAT GGCGTGGGCTGAAGATGAAGC CCATAGTTTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23665 1.7e-08 438_[+3]_41 269325 2e-08 438_[+3]_41 1957 1e-07 119_[+3]_360 25647 2.1e-07 366_[+3]_113 22304 4e-07 129_[+3]_350 11480 4.4e-07 282_[+3]_197 36927 5.4e-07 10_[+3]_469 38672 8e-07 133_[+3]_346 24991 9.7e-07 93_[+3]_386 25648 1.1e-06 85_[+3]_394 24243 1.4e-06 74_[+3]_405 267946 1.7e-06 217_[+3]_262 10811 3e-06 320_[+3]_159 31499 3.2e-06 143_[+3]_336 31166 3.2e-06 16_[+3]_463 8274 3.8e-06 93_[+3]_386 30804 5.1e-06 70_[+3]_409 3477 6.4e-06 220_[+3]_259 24165 6.4e-06 173_[+3]_306 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=19 23665 ( 439) GGAAGAGACCGCAGGTGTAGC 1 269325 ( 439) GGAAGAGACCGAAGGTGTAGC 1 1957 ( 120) GGTCGAGGTCGCCGATCGAGG 1 25647 ( 367) TGTCGACGTCGACGGTGGATC 1 22304 ( 130) CAGAGAGGCCGTCGGTGTAGG 1 11480 ( 283) GGATGTGTTGGCTGGTGGAGA 1 36927 ( 11) CGATGACAACGCCGCTGACGG 1 38672 ( 134) CGCTGGGTTCGTCGGTGGCTG 1 24991 ( 94) TGATGATGATGAAGACGAAGG 1 25648 ( 86) CGAAGAGTGGGAAGGCGGAGA 1 24243 ( 75) GGATGGTTTCGTAGCTGATGC 1 267946 ( 218) TGTCAAGGGTGAAGGTGAAGG 1 10811 ( 321) GGAGGACGTTGCTGCTGTCTA 1 31499 ( 144) CATTGATGTTGCCGCTGCATG 1 31166 ( 17) GGATGTCTTTGACGACGGCGA 1 8274 ( 94) CCGAGGGGTCGCCGATGAAGT 1 30804 ( 71) GGGAGGTGGTGACGGGGATGG 1 3477 ( 221) AGTTGAAGCTGCTGCTGGATG 1 24165 ( 174) GGCGTGGGCTGAAGATGAAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15840 bayes= 10.5999 E= 7.8e-001 -235 40 102 -71 -136 -218 185 -1089 81 -118 -56 3 23 -60 -115 71 -235 -1089 194 -229 123 -1089 17 -129 -235 -18 117 -29 -77 -1089 131 3 -136 14 -56 88 -1089 99 -115 71 -1089 -1089 210 -1089 64 82 -1089 -71 45 99 -1089 -71 -1089 -1089 210 -1089 -4 14 102 -1089 -1089 -60 -215 161 -1089 -218 202 -1089 45 -218 66 -29 134 -18 -1089 -129 -1089 -1089 166 3 -36 14 102 -229 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 19 E= 7.8e-001 0.052632 0.315789 0.473684 0.157895 0.105263 0.052632 0.842105 0.000000 0.473684 0.105263 0.157895 0.263158 0.315789 0.157895 0.105263 0.421053 0.052632 0.000000 0.894737 0.052632 0.631579 0.000000 0.263158 0.105263 0.052632 0.210526 0.526316 0.210526 0.157895 0.000000 0.578947 0.263158 0.105263 0.263158 0.157895 0.473684 0.000000 0.473684 0.105263 0.421053 0.000000 0.000000 1.000000 0.000000 0.421053 0.421053 0.000000 0.157895 0.368421 0.473684 0.000000 0.157895 0.000000 0.000000 1.000000 0.000000 0.263158 0.263158 0.473684 0.000000 0.000000 0.157895 0.052632 0.789474 0.000000 0.052632 0.947368 0.000000 0.368421 0.052632 0.368421 0.210526 0.684211 0.210526 0.000000 0.105263 0.000000 0.000000 0.736842 0.263158 0.210526 0.263158 0.473684 0.052632 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC]G[AT][TA]G[AG][GCT][GT][TC][CT]G[AC][CA]G[GAC]TG[AGT][AC][GT][GCA] -------------------------------------------------------------------------------- Time 25.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10518 3.21e-01 500 10811 1.65e-06 320_[+3(2.98e-06)]_9_[+2(1.50e-06)]_\ 89_[+1(1.71e-05)]_28 11480 2.44e-03 282_[+3(4.40e-07)]_197 12025 2.55e-02 459_[+1(1.53e-06)]_29 1957 1.34e-08 35_[+2(3.44e-07)]_63_[+3(1.02e-07)]_\ 332_[+1(1.10e-05)]_16 22304 4.20e-04 129_[+3(3.97e-07)]_350 23665 5.65e-11 59_[+1(3.94e-05)]_74_[+2(1.57e-09)]_\ 272_[+3(1.73e-08)]_41 23770 4.61e-02 469_[+1(1.94e-05)]_19 24165 3.07e-07 86_[+2(3.31e-08)]_66_[+3(6.36e-06)]_\ 289_[+1(5.70e-05)]_5 24243 8.00e-04 74_[+3(1.39e-06)]_361_\ [+1(3.35e-05)]_32 24991 9.03e-08 18_[+2(3.74e-07)]_54_[+3(9.67e-07)]_\ 277_[+1(5.02e-05)]_46_[+1(8.55e-06)]_39 25647 2.45e-05 366_[+3(2.06e-07)]_78_\ [+1(5.28e-06)]_23 25648 3.65e-04 85_[+3(1.06e-06)]_221_\ [+1(1.94e-05)]_161 267946 3.33e-05 217_[+3(1.66e-06)]_177_\ [+2(6.99e-07)]_64 269233 1.52e-04 151_[+2(5.17e-08)]_328 269325 8.88e-10 88_[+2(9.30e-05)]_36_[+2(1.57e-09)]_\ 272_[+3(2.01e-08)]_41 30804 8.20e-07 70_[+3(5.11e-06)]_75_[+2(6.99e-07)]_\ 126_[+2(2.63e-05)]_153_[+1(9.86e-06)]_1 31166 7.37e-07 16_[+3(3.23e-06)]_100_\ [+2(2.91e-07)]_329_[+1(3.35e-05)]_1 31499 6.76e-07 143_[+3(3.23e-06)]_89_\ [+1(2.36e-05)]_8_[+1(5.02e-05)]_10_[+1(5.02e-05)]_7_[+1(5.02e-05)]_10_\ [+1(5.02e-05)]_86_[+2(3.74e-07)]_45 3313 1.92e-04 156_[+2(6.97e-05)]_304_\ [+1(2.05e-07)]_7 3477 1.49e-07 140_[+2(2.24e-07)]_59_\ [+3(6.36e-06)]_177_[+1(3.76e-06)]_70 3632 5.28e-02 35_[+1(3.63e-05)]_453 36679 2.44e-05 273_[+2(1.61e-06)]_188_\ [+1(6.59e-07)]_6 36927 4.23e-04 10_[+3(5.40e-07)]_183_\ [+3(3.74e-05)]_265 38672 1.39e-05 66_[+1(6.59e-07)]_55_[+3(8.00e-07)]_\ 346 3949 2.13e-06 113_[+2(1.82e-08)]_273_\ [+1(4.30e-05)]_81 4095 6.31e-02 166_[+1(2.36e-05)]_322 4306 1.41e-04 294_[+2(6.40e-08)]_185 5708 3.46e-04 28_[+2(1.23e-06)]_327_\ [+1(1.53e-05)]_112 7845 5.15e-02 46_[+1(1.94e-05)]_442 8147 2.60e-02 483_[+1(2.54e-05)]_5 8274 2.26e-03 93_[+3(3.78e-06)]_386 bd861 1.13e-06 10_[+2(3.71e-08)]_358_\ [+1(7.34e-06)]_81_[+1(6.59e-07)]_6 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************