******************************************************************************** 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/207/207.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10077 1.0000 500 10157 1.0000 500 10741 1.0000 500 11598 1.0000 500 1376 1.0000 500 14924 1.0000 500 1819 1.0000 500 22279 1.0000 500 2362 1.0000 500 24555 1.0000 500 2492 1.0000 500 25068 1.0000 500 261756 1.0000 500 264496 1.0000 500 269663 1.0000 500 31121 1.0000 500 31759 1.0000 500 3235 1.0000 500 3341 1.0000 500 35896 1.0000 500 37911 1.0000 500 38164 1.0000 500 40097 1.0000 500 4466 1.0000 500 4696 1.0000 500 4775 1.0000 500 5137 1.0000 500 7874 1.0000 500 9967 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/207/207.seqs.fa -oc motifs/207 -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 0.255 C 0.233 G 0.244 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.233 G 0.244 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 16 llr = 226 E-value = 2.5e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 14733741459:874852561 pos.-specific C 83385318651a:33148319 probability G 11::2::1::::2:3:::11: matrix T :2::::41::::11:21:12: bits 2.1 * 1.9 * 1.7 * * 1.5 ** * * Relative 1.3 * * ** * * Entropy 1.1 * ** * ****** * * * (20.4 bits) 0.8 * ** * ******* * * * 0.6 * ************ *** * 0.4 * ***************** * 0.2 ********************* 0.0 --------------------- Multilevel CAACCAACCAACAAAAACAAC consensus CCAACT AC CC C C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 7874 476 1.18e-10 CTGTACCTCC CACCCCACCCACAAGAACAAC AAAG 25068 397 1.59e-09 ACAACTACAA CCCACAACCCACAACAACCAC AACAATAGAA 269663 474 8.09e-09 CCTCCCTCCC CGACCCTCCCCCAACAACAAC CCCAAT 2492 385 1.65e-08 ACACAAACAA CAACAACACAACAAAAACAAC CAAAAGGTAC 2362 476 1.85e-08 CTCGTCCAGT CCACCAACACACAACAAACCC AAAC 264496 401 2.58e-08 GGGGGGGGCT CCAAGATCCAACAAGATCCAC ATGTCACCCA 4466 120 6.50e-08 GATAGTTTGT AAACCATCCCACGAAACCAGC TACAAACGGA 37911 269 1.25e-07 CTCGTCGTCT CAACACTCACACAAATCCAAA TCCCACCGTC 14924 398 1.78e-07 GCTGTACACC GACACAACCAACACCTCCAAC CTCTAACACC 4775 338 2.93e-07 CCTTCAATTT CAACCAATAAACGAAAACGTC TAAAGTTTCC 31121 353 3.17e-07 GCAACAGGAG CTACGAACCCACGAGTTCATC AAAAACAAAA 10157 475 5.83e-07 TAACAACAGC CGACGCTCCAACACGACCTCC AAATC 10077 420 7.23e-07 TCCCTCCCCG CTACACTCAAACTCAAACCGC CCGCCGCCAC 4696 405 7.76e-07 CTTAGTAGTC CCCCAAAGACACAAGACAGAC AGCACTACAT 261756 218 1.09e-06 TTCAAGAGTC GACAAATCAAACATAAACATC AGTACTATCA 35896 473 2.04e-06 CCCCTTCTAA CTACCACCCACCACCCCACAC TGGCAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7874 1.2e-10 475_[+1]_4 25068 1.6e-09 396_[+1]_83 269663 8.1e-09 473_[+1]_6 2492 1.7e-08 384_[+1]_95 2362 1.8e-08 475_[+1]_4 264496 2.6e-08 400_[+1]_79 4466 6.5e-08 119_[+1]_360 37911 1.3e-07 268_[+1]_211 14924 1.8e-07 397_[+1]_82 4775 2.9e-07 337_[+1]_142 31121 3.2e-07 352_[+1]_127 10157 5.8e-07 474_[+1]_5 10077 7.2e-07 419_[+1]_60 4696 7.8e-07 404_[+1]_75 261756 1.1e-06 217_[+1]_262 35896 2e-06 472_[+1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=16 7874 ( 476) CACCCCACCCACAAGAACAAC 1 25068 ( 397) CCCACAACCCACAACAACCAC 1 269663 ( 474) CGACCCTCCCCCAACAACAAC 1 2492 ( 385) CAACAACACAACAAAAACAAC 1 2362 ( 476) CCACCAACACACAACAAACCC 1 264496 ( 401) CCAAGATCCAACAAGATCCAC 1 4466 ( 120) AAACCATCCCACGAAACCAGC 1 37911 ( 269) CAACACTCACACAAATCCAAA 1 14924 ( 398) GACACAACCAACACCTCCAAC 1 4775 ( 338) CAACCAATAAACGAAAACGTC 1 31121 ( 353) CTACGAACCCACGAGTTCATC 1 10157 ( 475) CGACGCTCCAACACGACCTCC 1 10077 ( 420) CTACACTCAAACTCAAACCGC 1 4696 ( 405) CCCCAAAGACACAAGACAGAC 1 261756 ( 218) GACAAATCAAACATAAACATC 1 35896 ( 473) CTACCACCCACCACCCCACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 11.0861 E= 2.5e-009 -203 180 -96 -1064 78 10 -96 -51 143 42 -1064 -1064 -3 168 -1064 -1064 29 110 -38 -1064 143 42 -1064 -1064 78 -90 -1064 71 -203 180 -196 -210 56 142 -1064 -1064 97 110 -1064 -1064 178 -90 -1064 -1064 -1064 210 -1064 -1064 156 -1064 -38 -210 143 10 -1064 -210 56 42 36 -1064 156 -190 -1064 -51 97 69 -1064 -110 -44 180 -1064 -1064 97 42 -96 -210 114 -90 -96 -51 -203 201 -1064 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 2.5e-009 0.062500 0.812500 0.125000 0.000000 0.437500 0.250000 0.125000 0.187500 0.687500 0.312500 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.312500 0.500000 0.187500 0.000000 0.687500 0.312500 0.000000 0.000000 0.437500 0.125000 0.000000 0.437500 0.062500 0.812500 0.062500 0.062500 0.375000 0.625000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.187500 0.062500 0.687500 0.250000 0.000000 0.062500 0.375000 0.312500 0.312500 0.000000 0.750000 0.062500 0.000000 0.187500 0.500000 0.375000 0.000000 0.125000 0.187500 0.812500 0.000000 0.000000 0.500000 0.312500 0.125000 0.062500 0.562500 0.125000 0.125000 0.187500 0.062500 0.937500 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AC][AC][CA][CA][AC][AT]C[CA][AC]ACA[AC][ACG]A[AC]C[AC]AC -------------------------------------------------------------------------------- Time 7.56 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 27 llr = 291 E-value = 3.7e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 232:331:::22:4144343: pos.-specific C 1:1::1:::1::::3:1:12: probability G 64186219456293662741a matrix T :2521481642613::2:14: bits 2.1 * 1.9 * 1.7 * * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * *** * * * (15.6 bits) 0.8 * *** * * * * 0.6 * ** ***** * ** * * 0.4 ** ** ********** ** * 0.2 ***** *************** 0.0 --------------------- Multilevel GGTGGTTGTGGTGAGGAGATG consensus AAA AA GTTA TCAGAGA sequence G G G T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5137 134 1.14e-08 GTCGTCGTCG CGAGGTTGGGGTGTGGAGATG CATGGGAGAG 35896 287 4.81e-08 GTGATGAAAA GGAGGGTGTTGTGGGGTGAGG GGTCGCGATG 7874 216 6.68e-08 AGATGCGGTG GGAGGTTGGGAGGAGGAGACG CCAGAGGTTC 14924 76 1.44e-07 TCAAGGGGTA GAAGGAGGTTGTGTGGTGGTG ATTTCTAACT 31121 188 1.92e-07 TGGGTTCGAC AGAGACTGTTGTGTGGAGACG GGCGGCAGAA 4696 195 2.53e-07 AGCCAAGAGC GGTGGTTGTGGAGAAACGGCG AGCTGTCCAG 40097 296 3.32e-07 CAAGACCTCC GGTGATGGTTGTGTGAGAGAG CTCATATGTG 269663 219 7.08e-07 CATGTTGGGC GGTTGTTGTTGTGAAGTAGCG TAGCGTCCGT 264496 353 7.08e-07 GTTCGTCAGT GGAGTCTGTTGTGAGGCGGTG TTGGACGGTG 261756 155 1.01e-06 TTGAAATGAT GATGGTGGTGGTGTCGGATTG GTGGTGAGTT 9967 46 1.13e-06 TGATGAGCAG GTTTGTTGTGTGGTGAAAATG CTGCAAGAGA 31759 21 1.58e-06 AGACTGCCAG GATGAGAGTGGAGGGGAAGAG GCCTCCGTGG 25068 26 1.75e-06 TGCATCCAGT AATGAGTGGGTGGAGGAGGGG GCCAACTTCC 2362 50 2.66e-06 AATGCCATGG CTTGGTTGTTTGGAGGGGTTG TTGTTGTCGC 4775 274 3.24e-06 GTGCCGTATT GACGAATGGTATGTGAGAGTG AGCGAGAATG 1819 327 6.82e-06 TGTATGGAGT AGTGGAGGGGGGGTCAAGTAG GGGTTCGGAA 10741 158 8.11e-06 ACATGATGAT GATTGGTGGTGTTGCGTGACG ATAATGATGC 10077 196 9.61e-06 AAGGTAGGTG GAGGTGTGTTGTGGCAGGCAG TACAACGGCA 11598 340 1.44e-05 TTCTCCGTTC AGCTTTTGTGGTGACGAGCTG GCGACACGCT 3341 275 1.81e-05 TTTCTTGGCG CGGGATTTGGAGGAGGAGAAG CGGAGGCGGT 3235 160 1.81e-05 AGTCGGCTAT ACTGGTTGTGTTCGGAAGAAG CAGGAGTTGA 10157 256 1.81e-05 TATTTCCTTG GACGGATGGGAATGGGAGAGG CGGGATGAGT 2492 217 2.10e-05 GTTGGCTTGG GTTGGCTGGCTAGTAGTGGTG GAGAGGTCAC 37911 208 3.43e-05 TCATTATAGC GGGTAATGTTGTAACAAAACG GTAACAGCTG 1376 126 3.66e-05 AGCAAGAGCA GTGGGAAGTGAAGGAATGATG GAGAAAATTG 4466 177 4.74e-05 TCCAATTGGA CATGAATGTCGTGACACCGTG GGATAAGATT 22279 117 8.06e-05 CCCCGTATTG ATTGAGTTGTTAGGGAGAAAG AAAGTGGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5137 1.1e-08 133_[+2]_346 35896 4.8e-08 286_[+2]_193 7874 6.7e-08 215_[+2]_264 14924 1.4e-07 75_[+2]_404 31121 1.9e-07 187_[+2]_292 4696 2.5e-07 194_[+2]_285 40097 3.3e-07 295_[+2]_184 269663 7.1e-07 218_[+2]_261 264496 7.1e-07 352_[+2]_127 261756 1e-06 154_[+2]_325 9967 1.1e-06 45_[+2]_434 31759 1.6e-06 20_[+2]_459 25068 1.8e-06 25_[+2]_454 2362 2.7e-06 49_[+2]_430 4775 3.2e-06 273_[+2]_206 1819 6.8e-06 326_[+2]_153 10741 8.1e-06 157_[+2]_322 10077 9.6e-06 195_[+2]_284 11598 1.4e-05 339_[+2]_140 3341 1.8e-05 274_[+2]_205 3235 1.8e-05 159_[+2]_320 10157 1.8e-05 255_[+2]_224 2492 2.1e-05 216_[+2]_263 37911 3.4e-05 207_[+2]_272 1376 3.7e-05 125_[+2]_354 4466 4.7e-05 176_[+2]_303 22279 8.1e-05 116_[+2]_363 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=27 5137 ( 134) CGAGGTTGGGGTGTGGAGATG 1 35896 ( 287) GGAGGGTGTTGTGGGGTGAGG 1 7874 ( 216) GGAGGTTGGGAGGAGGAGACG 1 14924 ( 76) GAAGGAGGTTGTGTGGTGGTG 1 31121 ( 188) AGAGACTGTTGTGTGGAGACG 1 4696 ( 195) GGTGGTTGTGGAGAAACGGCG 1 40097 ( 296) GGTGATGGTTGTGTGAGAGAG 1 269663 ( 219) GGTTGTTGTTGTGAAGTAGCG 1 264496 ( 353) GGAGTCTGTTGTGAGGCGGTG 1 261756 ( 155) GATGGTGGTGGTGTCGGATTG 1 9967 ( 46) GTTTGTTGTGTGGTGAAAATG 1 31759 ( 21) GATGAGAGTGGAGGGGAAGAG 1 25068 ( 26) AATGAGTGGGTGGAGGAGGGG 1 2362 ( 50) CTTGGTTGTTTGGAGGGGTTG 1 4775 ( 274) GACGAATGGTATGTGAGAGTG 1 1819 ( 327) AGTGGAGGGGGGGTCAAGTAG 1 10741 ( 158) GATTGGTGGTGTTGCGTGACG 1 10077 ( 196) GAGGTGTGTTGTGGCAGGCAG 1 11598 ( 340) AGCTTTTGTGGTGACGAGCTG 1 3341 ( 275) CGGGATTTGGAGGAGGAGAAG 1 3235 ( 160) ACTGGTTGTGTTCGGAAGAAG 1 10157 ( 256) GACGGATGGGAATGGGAGAGG 1 2492 ( 217) GTTGGCTGGCTAGTAGTGGTG 1 37911 ( 208) GGGTAATGTTGTAACAAAACG 1 1376 ( 126) GTGGGAAGTGAAGGAATGATG 1 4466 ( 177) CATGAATGTCGTGACACCGTG 1 22279 ( 117) ATTGAGTTGTTAGGGAGAAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 9.57712 E= 3.7e-009 -20 -65 137 -1140 39 -265 86 -53 -20 -107 -72 95 -1140 -1140 174 -53 39 -1140 119 -127 2 -107 -14 60 -178 -1140 -72 154 -1140 -1140 192 -185 -1140 -1140 60 123 -1140 -165 98 73 -46 -1140 128 -27 -20 -1140 -14 105 -278 -265 180 -185 54 -1140 28 32 -78 15 128 -1140 68 -1140 128 -1140 80 -107 -14 -27 22 -265 145 -1140 80 -165 60 -127 2 -7 -113 60 -1140 -1140 203 -1140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 27 E= 3.7e-009 0.222222 0.148148 0.629630 0.000000 0.333333 0.037037 0.444444 0.185185 0.222222 0.111111 0.148148 0.518519 0.000000 0.000000 0.814815 0.185185 0.333333 0.000000 0.555556 0.111111 0.259259 0.111111 0.222222 0.407407 0.074074 0.000000 0.148148 0.777778 0.000000 0.000000 0.925926 0.074074 0.000000 0.000000 0.370370 0.629630 0.000000 0.074074 0.481481 0.444444 0.185185 0.000000 0.592593 0.222222 0.222222 0.000000 0.222222 0.555556 0.037037 0.037037 0.851852 0.074074 0.370370 0.000000 0.296296 0.333333 0.148148 0.259259 0.592593 0.000000 0.407407 0.000000 0.592593 0.000000 0.444444 0.111111 0.222222 0.222222 0.296296 0.037037 0.666667 0.000000 0.444444 0.074074 0.370370 0.111111 0.259259 0.222222 0.111111 0.407407 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA][GA][TA]G[GA][TAG]TG[TG][GT][GT][TAG]G[ATG][GC][GA][AGT][GA][AG][TAC]G -------------------------------------------------------------------------------- Time 14.28 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 16 llr = 184 E-value = 1.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::1:::1:::::1:: pos.-specific C 7619464a3681:9: probability G ::4::2::5:1121: matrix T 3441634:34288:a bits 2.1 * 1.9 * * 1.7 * * ** 1.5 * * ** Relative 1.3 * * ** Entropy 1.1 ** ** * ** ** (16.6 bits) 0.8 ** ** * ****** 0.6 ** ***** ****** 0.4 ** ************ 0.2 *************** 0.0 --------------- Multilevel CCGCTCCCGCCTTCT consensus TTT CTT CT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 38164 44 3.99e-09 GGTGGATCTA CTGCTCCCGCCTTCT CCTACCTCCG 3341 78 2.32e-08 CTCACAGTCT CCTCTCCCCCCTTCT TACTGTCCCC 35896 456 3.52e-07 GACGTTAGCT CCACCCCCCCCTTCT AACTACCACC 37911 446 6.54e-07 AACTCACCCA CTGCTCTCTCTTTCT CTGCCCTCGT 10157 28 9.20e-07 GAAACGCAGT CTGCTCTCGCGTTCT TCTGCGATAT 4775 226 1.02e-06 GCTTATATAC CTTCTCCCCTTTTCT GGCTCTCGTG 31759 438 1.13e-06 GAAGCTCTCG CCGCCCTCCTCCTCT GGTGGTGTAC 24555 265 1.86e-06 CAAATTTGCA TCACCTTCGCCTTCT CTCATCCTTC 9967 417 2.25e-06 CAGCTTTGCC CTTCTTCCTTCTGCT AATCCTCGTC 22279 247 2.70e-06 GGTACGATTA CCGCCTCCTTCGTCT GTGGCTCTTG 264496 37 3.80e-06 TTGAAACTTC TCCCTGTCGTCTTCT CCAAATGGAT 11598 125 3.80e-06 AGCTCCCCCA TCTCCGTCGTCTGCT GATGATGGTG 14924 442 7.95e-06 GCCTACACCC TTGCTTACGCCGTCT GCGGCTTTTG 261756 307 1.40e-05 AACAATATCT CCGCTGCCTCTTTGT GCTTGCTACT 25068 461 1.40e-05 CACGAACACC CTTCTCACGCCCACT GACAACCATC 10741 63 1.48e-05 GAGAGCCTCA TCTTCCTCGTCTGCT TCTTCCTCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38164 4e-09 43_[+3]_442 3341 2.3e-08 77_[+3]_408 35896 3.5e-07 455_[+3]_30 37911 6.5e-07 445_[+3]_40 10157 9.2e-07 27_[+3]_458 4775 1e-06 225_[+3]_260 31759 1.1e-06 437_[+3]_48 24555 1.9e-06 264_[+3]_221 9967 2.3e-06 416_[+3]_69 22279 2.7e-06 246_[+3]_239 264496 3.8e-06 36_[+3]_449 11598 3.8e-06 124_[+3]_361 14924 8e-06 441_[+3]_44 261756 1.4e-05 306_[+3]_179 25068 1.4e-05 460_[+3]_25 10741 1.5e-05 62_[+3]_423 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=16 38164 ( 44) CTGCTCCCGCCTTCT 1 3341 ( 78) CCTCTCCCCCCTTCT 1 35896 ( 456) CCACCCCCCCCTTCT 1 37911 ( 446) CTGCTCTCTCTTTCT 1 10157 ( 28) CTGCTCTCGCGTTCT 1 4775 ( 226) CTTCTCCCCTTTTCT 1 31759 ( 438) CCGCCCTCCTCCTCT 1 24555 ( 265) TCACCTTCGCCTTCT 1 9967 ( 417) CTTCTTCCTTCTGCT 1 22279 ( 247) CCGCCTCCTTCGTCT 1 264496 ( 37) TCCCTGTCGTCTTCT 1 11598 ( 125) TCTCCGTCGTCTGCT 1 14924 ( 442) TTGCTTACGCCGTCT 1 261756 ( 307) CCGCTGCCTCTTTGT 1 25068 ( 461) CTTCTCACGCCCACT 1 10741 ( 63) TCTTCCTCGTCTGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 14094 bayes= 10.5188 E= 1.0e-001 -1064 156 -1064 22 -1064 127 -1064 71 -103 -190 84 49 -1064 201 -1064 -210 -1064 69 -1064 122 -1064 127 -38 -10 -103 91 -1064 71 -1064 210 -1064 -1064 -1064 10 103 -10 -1064 127 -1064 71 -1064 168 -196 -51 -1064 -90 -96 148 -203 -1064 -38 148 -1064 201 -196 -1064 -1064 -1064 -1064 190 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 16 E= 1.0e-001 0.000000 0.687500 0.000000 0.312500 0.000000 0.562500 0.000000 0.437500 0.125000 0.062500 0.437500 0.375000 0.000000 0.937500 0.000000 0.062500 0.000000 0.375000 0.000000 0.625000 0.000000 0.562500 0.187500 0.250000 0.125000 0.437500 0.000000 0.437500 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.500000 0.250000 0.000000 0.562500 0.000000 0.437500 0.000000 0.750000 0.062500 0.187500 0.000000 0.125000 0.125000 0.750000 0.062500 0.000000 0.187500 0.750000 0.000000 0.937500 0.062500 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][CT][GT]C[TC][CT][CT]C[GCT][CT]CTTCT -------------------------------------------------------------------------------- Time 21.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10077 1.17e-04 195_[+2(9.61e-06)]_203_\ [+1(7.23e-07)]_1_[+1(3.93e-05)]_38 10157 2.54e-07 27_[+3(9.20e-07)]_213_\ [+2(1.81e-05)]_198_[+1(5.83e-07)]_5 10741 1.62e-03 62_[+3(1.48e-05)]_80_[+2(8.11e-06)]_\ 322 11598 1.94e-04 124_[+3(3.80e-06)]_179_\ [+3(1.48e-05)]_6_[+2(1.44e-05)]_140 1376 2.63e-02 125_[+2(3.66e-05)]_354 14924 7.40e-09 75_[+2(1.44e-07)]_301_\ [+1(1.78e-07)]_23_[+3(7.95e-06)]_44 1819 1.18e-02 326_[+2(6.82e-06)]_153 22279 6.91e-04 [+3(8.88e-05)]_101_[+2(8.06e-05)]_\ 109_[+3(2.70e-06)]_239 2362 1.01e-06 49_[+2(2.66e-06)]_405_\ [+1(1.85e-08)]_4 24555 7.29e-03 264_[+3(1.86e-06)]_221 2492 7.01e-06 216_[+2(2.10e-05)]_147_\ [+1(1.65e-08)]_95 25068 1.61e-09 25_[+2(1.75e-06)]_350_\ [+1(1.59e-09)]_43_[+3(1.40e-05)]_25 261756 3.85e-07 154_[+2(1.01e-06)]_11_\ [+2(2.10e-05)]_10_[+1(1.09e-06)]_68_[+3(1.40e-05)]_179 264496 2.75e-09 36_[+3(3.80e-06)]_301_\ [+2(7.08e-07)]_27_[+1(2.58e-08)]_14_[+1(4.32e-05)]_44 269663 5.57e-08 218_[+2(7.08e-07)]_234_\ [+1(8.09e-09)]_6 31121 1.72e-06 187_[+2(1.92e-07)]_144_\ [+1(3.17e-07)]_127 31759 5.01e-05 20_[+2(1.58e-06)]_396_\ [+3(1.13e-06)]_48 3235 4.97e-03 159_[+2(1.81e-05)]_209_\ [+3(3.86e-05)]_96 3341 5.47e-06 77_[+3(2.32e-08)]_182_\ [+2(1.81e-05)]_205 35896 1.44e-09 286_[+2(4.81e-08)]_148_\ [+3(3.52e-07)]_2_[+1(2.04e-06)]_7 37911 8.17e-08 207_[+2(3.43e-05)]_40_\ [+1(1.25e-07)]_49_[+3(5.36e-05)]_92_[+3(6.54e-07)]_40 38164 5.22e-05 43_[+3(3.99e-09)]_442 40097 3.74e-03 295_[+2(3.32e-07)]_184 4466 2.15e-05 119_[+1(6.50e-08)]_36_\ [+2(4.74e-05)]_303 4696 4.98e-06 194_[+2(2.53e-07)]_42_\ [+2(5.69e-05)]_126_[+1(7.76e-07)]_75 4775 3.11e-08 225_[+3(1.02e-06)]_33_\ [+2(3.24e-06)]_43_[+1(2.93e-07)]_5_[+3(2.50e-05)]_122 5137 2.35e-05 133_[+2(1.14e-08)]_346 7874 4.99e-10 15_[+1(2.24e-05)]_137_\ [+2(1.33e-05)]_21_[+2(6.68e-08)]_239_[+1(1.18e-10)]_4 9967 8.68e-06 45_[+2(1.13e-06)]_350_\ [+3(2.25e-06)]_69 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************