******************************************************************************** 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/448/448.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11938 1.0000 500 12645 1.0000 500 1322 1.0000 500 1629 1.0000 500 17910 1.0000 500 21537 1.0000 500 22112 1.0000 500 22269 1.0000 500 23497 1.0000 500 23895 1.0000 500 23971 1.0000 500 24224 1.0000 500 24335 1.0000 500 24544 1.0000 500 24827 1.0000 500 25272 1.0000 500 261392 1.0000 500 262797 1.0000 500 264276 1.0000 500 267997 1.0000 500 268593 1.0000 500 269773 1.0000 500 2865 1.0000 500 3286 1.0000 500 35410 1.0000 500 38317 1.0000 500 4312 1.0000 500 8408 1.0000 500 9103 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/448/448.seqs.fa -oc motifs/448 -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 0.264 C 0.228 G 0.243 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.228 G 0.243 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 22 llr = 257 E-value = 2.6e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :4:3365:751652651251 pos.-specific C 93a22249:393382395:8 probability G 1::33::13::::::2:31: matrix T :3:3221::3::2:2:::31 bits 2.1 1.9 * 1.7 * * * 1.5 * * * * * * Relative 1.3 * * * * * * Entropy 1.1 * * ** * * * * (16.8 bits) 0.9 * * ** ** * * * 0.6 * * **** ** ** * * 0.4 *** ******* ******* 0.2 *** *************** 0.0 -------------------- Multilevel CACAAAACAACAACAACCAC consensus T GGCC GC CC C GT sequence C TC T T G A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 8408 481 1.77e-09 GTCAACCACT CTCGCAACACCAACAACGAC 262797 147 7.07e-09 TCCGGGAAAG CCCAAACCAACAACAGCAAC TCAGTATTTG 264276 469 1.80e-07 TCCTATTCGA CACAGACCACCACCACAGAC AACACCGTCA 38317 476 2.91e-07 ACTGAGATCA CACCCAACAACCCACACCAC CGACC 1629 383 3.26e-07 GGACCACTCA CTCAGAACACAACCAACAAC CAGCAACCAG 9103 477 4.57e-07 TCCACCTTGT CCCACCACAACCGCAACCTC CCAA 269773 451 4.57e-07 AATATCGAAG CTCGGACAAACATCAACGAC CAACGACGCG 23971 478 4.57e-07 ATATCGCCCT CTCTTCACAACATCTACCGC GTC 22269 420 6.30e-07 CATCCATACA CCCTCACCGACATCACCCTT CTTACCCAAT 17910 449 8.58e-07 TACCGGGCCA CACAGAACAACCACCCCTTC CACCCAACTG 24827 470 1.27e-06 CCAGGCCGGT CACGAAACACAAACAGACAC TCCTCCATCC 267997 337 1.40e-06 TCCTCAAACA GACAAACCGACCACACCATC GCAGAAAAGA 12645 359 1.40e-06 ATGAATCCGT CACGTCCGGTCCCCAACCAC CAGCCTCCTA 23497 422 2.41e-06 AAATATTGGA CACGATAGACCAACTCCCTC CCTTCTCTCC 22112 407 2.63e-06 TTAATGTTCC CTCCTTCCGTCAACCACGGC GGCCCTGCCT 35410 421 4.32e-06 CAAGTAATAG CCCTCTTCATCAACTGCGTC AACAAAATAC 11938 219 6.38e-06 GAGACAGCGT CTCTAAACATCATCCGCAGT ATTTCTCTAA 3286 460 6.88e-06 GGTCCATAGA CACGGTACACCTTCAACGAT TCGGCCTCGC 23895 284 6.88e-06 AACTGCAACA CACCGACCAACCAAACACAA GCCCGCCTGT 25272 415 9.88e-06 TCCTCTGCTT CCTCAAACGTCCCAAACCAC CGACCCTCGT 1322 285 1.14e-05 TCCTCTCTCC CTCTTCCCGACACCAACACA ATGGAAGAGA 21537 36 4.10e-05 GTATTCTTGA GCCTTCTCATCAAATGCCTC CAACTCATCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8408 1.8e-09 480_[+1] 262797 7.1e-09 146_[+1]_334 264276 1.8e-07 468_[+1]_12 38317 2.9e-07 475_[+1]_5 1629 3.3e-07 382_[+1]_98 9103 4.6e-07 476_[+1]_4 269773 4.6e-07 450_[+1]_30 23971 4.6e-07 477_[+1]_3 22269 6.3e-07 419_[+1]_61 17910 8.6e-07 448_[+1]_32 24827 1.3e-06 469_[+1]_11 267997 1.4e-06 336_[+1]_144 12645 1.4e-06 358_[+1]_122 23497 2.4e-06 421_[+1]_59 22112 2.6e-06 406_[+1]_74 35410 4.3e-06 420_[+1]_60 11938 6.4e-06 218_[+1]_262 3286 6.9e-06 459_[+1]_21 23895 6.9e-06 283_[+1]_197 25272 9.9e-06 414_[+1]_66 1322 1.1e-05 284_[+1]_196 21537 4.1e-05 35_[+1]_445 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=22 8408 ( 481) CTCGCAACACCAACAACGAC 1 262797 ( 147) CCCAAACCAACAACAGCAAC 1 264276 ( 469) CACAGACCACCACCACAGAC 1 38317 ( 476) CACCCAACAACCCACACCAC 1 1629 ( 383) CTCAGAACACAACCAACAAC 1 9103 ( 477) CCCACCACAACCGCAACCTC 1 269773 ( 451) CTCGGACAAACATCAACGAC 1 23971 ( 478) CTCTTCACAACATCTACCGC 1 22269 ( 420) CCCTCACCGACATCACCCTT 1 17910 ( 449) CACAGAACAACCACCCCTTC 1 24827 ( 470) CACGAAACACAAACAGACAC 1 267997 ( 337) GACAAACCGACCACACCATC 1 12645 ( 359) CACGTCCGGTCCCCAACCAC 1 23497 ( 422) CACGATAGACCAACTCCCTC 1 22112 ( 407) CTCCTTCCGTCAACCACGGC 1 35410 ( 421) CCCTCTTCATCAACTGCGTC 1 11938 ( 219) CTCTAAACATCATCCGCAGT 1 3286 ( 460) CACGGTACACCTTCAACGAT 1 23895 ( 284) CACCGACCAACCAAACACAA 1 25272 ( 415) CCTCAAACGTCCCAAACCAC 1 1322 ( 285) CTCTTCCCGACACCAACACA 1 21537 ( 36) GCCTTCTCATCAAATGCCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 13949 bayes= 9.66176 E= 2.6e-009 -1110 200 -142 -1110 63 26 -1110 26 -1110 207 -1110 -254 5 -32 17 4 5 0 17 -23 116 0 -1110 -55 92 85 -1110 -155 -253 192 -142 -1110 146 -1110 17 -1110 79 26 -1110 4 -154 200 -1110 -1110 127 48 -1110 -254 79 26 -242 -23 -54 185 -1110 -1110 127 -32 -1110 -55 92 26 -10 -1110 -95 192 -1110 -1110 -21 100 17 -254 92 -232 -83 26 -154 176 -1110 -96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 22 E= 2.6e-009 0.000000 0.909091 0.090909 0.000000 0.409091 0.272727 0.000000 0.318182 0.000000 0.954545 0.000000 0.045455 0.272727 0.181818 0.272727 0.272727 0.272727 0.227273 0.272727 0.227273 0.590909 0.227273 0.000000 0.181818 0.500000 0.409091 0.000000 0.090909 0.045455 0.863636 0.090909 0.000000 0.727273 0.000000 0.272727 0.000000 0.454545 0.272727 0.000000 0.272727 0.090909 0.909091 0.000000 0.000000 0.636364 0.318182 0.000000 0.045455 0.454545 0.272727 0.045455 0.227273 0.181818 0.818182 0.000000 0.000000 0.636364 0.181818 0.000000 0.181818 0.500000 0.272727 0.227273 0.000000 0.136364 0.863636 0.000000 0.000000 0.227273 0.454545 0.272727 0.045455 0.500000 0.045455 0.136364 0.318182 0.090909 0.772727 0.000000 0.136364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[ATC]C[AGT][AGCT][AC][AC]C[AG][ACT]C[AC][ACT]CA[ACG]C[CGA][AT]C -------------------------------------------------------------------------------- Time 7.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 27 llr = 254 E-value = 2.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::24::3:11:2:: pos.-specific C :22::4:41:31142 probability G a3:8::a1:6:4613 matrix T :58:66:19364146 bits 2.1 * 1.9 * * 1.7 * * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * ***** * (13.6 bits) 0.9 * ***** * 0.6 * ***** **** * 0.4 ******* ******* 0.2 *************** 0.0 --------------- Multilevel GTTGTTGCTGTTGTT consensus G AC A TCGACG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 24224 31 4.77e-08 TCTGCTTAGT GTTGTTGCTGTGGCG GAGGTTACAG 22269 82 7.59e-08 GTCGCCTGTT GTTGTCGCTGTGGTG GAGCTTGAAG 38317 249 1.10e-06 GAGATGTAGA GTTGTCGCTGTGAGT GTCGTGCTTG 21537 271 4.72e-06 ACATGAACTC GGTGATGACGTTGTT CGAATTGCTT 17910 234 5.34e-06 TAGACGCACT GCTGTTGCTTCGACT GCTGTTGCCT 24827 339 8.72e-06 TTCTTTGTGT GGTGTCGTTTTTACT TTATGTCTAG 9103 85 9.76e-06 TGCAAGTATT GTTATCGCTGTCATT GTTTCTTTCG 22112 271 9.76e-06 TCTCGTCGTC GTCGTTGATGTCGTC GGGGGCCGCT 261392 416 1.21e-05 GCCACATTAC GGTATTGTTGCGGCT AAGCTCAAGG 35410 102 1.35e-05 AGAAGTGGAA GTTGTTCCTGCTGCT CCTTCGGCAG 11938 311 1.35e-05 CACTCCCAAC GCTGACGCTGTGTTC CTCCACCGAC 8408 175 1.66e-05 GGTGGAAAGT GTTGATGATATTGGT TTGGTATTTG 24544 139 1.66e-05 TGTTTGCGCA GTTGATGTCGTTGCG CGATGCACTC 23971 102 1.84e-05 ACCGAACTTC GTTGTCGGTGTGTTG GGGTGTGGGC 2865 364 2.03e-05 ACGCACACTC GTTGATGATTCGCCT CCTCTTCCTA 3286 371 2.44e-05 GCACCGAATT GCCGTTGCCGTTGCG CAGCAGCAAT 268593 378 2.44e-05 TGTTCACACT GTTGATGCTTATCCT TCATTAGCGG 12645 208 2.44e-05 TTGATATGTT GGTATTGATTTGTTT GTTTGGGTTG 269773 314 2.93e-05 GTTTTGTGGG GTTGTTGTTGATTTG GAAGCTTGCT 1629 85 2.93e-05 GGTTGAAGTG GTTGACGGTGATGTG CGGCTCTCGT 24335 363 3.48e-05 GGTAGGTGTA GGCGTTGATTTGAGT GCTTTCTGCA 4312 361 3.80e-05 TTATTGTGTC GTTTACGATTTTGCT GCAACCGTGT 25272 113 3.80e-05 GTGTCTACCA GCCGACGATGCCGTT ACCGCTGATA 23497 152 6.07e-05 GTTTGGCGGA GGCGTTGCTACTGTC AGAGTCGTAA 264276 254 9.19e-05 TACCTTGGTC GGTATCGCTTATATC CTGACTTGCA 23895 447 9.19e-05 GCCAGCCAGC GCTATTGCTTCGGAT TACGACCAGC 1322 185 9.19e-05 GGTGATGGGA GGTGACGACGTCGGC TAATGGAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24224 4.8e-08 30_[+2]_455 22269 7.6e-08 81_[+2]_404 38317 1.1e-06 248_[+2]_237 21537 4.7e-06 270_[+2]_215 17910 5.3e-06 233_[+2]_252 24827 8.7e-06 338_[+2]_147 9103 9.8e-06 84_[+2]_401 22112 9.8e-06 270_[+2]_215 261392 1.2e-05 415_[+2]_70 35410 1.3e-05 101_[+2]_384 11938 1.3e-05 310_[+2]_175 8408 1.7e-05 174_[+2]_311 24544 1.7e-05 138_[+2]_347 23971 1.8e-05 101_[+2]_384 2865 2e-05 363_[+2]_122 3286 2.4e-05 370_[+2]_115 268593 2.4e-05 377_[+2]_108 12645 2.4e-05 207_[+2]_278 269773 2.9e-05 313_[+2]_172 1629 2.9e-05 84_[+2]_401 24335 3.5e-05 362_[+2]_123 4312 3.8e-05 360_[+2]_125 25272 3.8e-05 112_[+2]_373 23497 6.1e-05 151_[+2]_334 264276 9.2e-05 253_[+2]_232 23895 9.2e-05 446_[+2]_39 1322 9.2e-05 184_[+2]_301 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=27 24224 ( 31) GTTGTTGCTGTGGCG 1 22269 ( 82) GTTGTCGCTGTGGTG 1 38317 ( 249) GTTGTCGCTGTGAGT 1 21537 ( 271) GGTGATGACGTTGTT 1 17910 ( 234) GCTGTTGCTTCGACT 1 24827 ( 339) GGTGTCGTTTTTACT 1 9103 ( 85) GTTATCGCTGTCATT 1 22112 ( 271) GTCGTTGATGTCGTC 1 261392 ( 416) GGTATTGTTGCGGCT 1 35410 ( 102) GTTGTTCCTGCTGCT 1 11938 ( 311) GCTGACGCTGTGTTC 1 8408 ( 175) GTTGATGATATTGGT 1 24544 ( 139) GTTGATGTCGTTGCG 1 23971 ( 102) GTTGTCGGTGTGTTG 1 2865 ( 364) GTTGATGATTCGCCT 1 3286 ( 371) GCCGTTGCCGTTGCG 1 268593 ( 378) GTTGATGCTTATCCT 1 12645 ( 208) GGTATTGATTTGTTT 1 269773 ( 314) GTTGTTGTTGATTTG 1 1629 ( 85) GTTGACGGTGATGTG 1 24335 ( 363) GGCGTTGATTTGAGT 1 4312 ( 361) GTTTACGATTTTGCT 1 25272 ( 113) GCCGACGATGCCGTT 1 23497 ( 152) GGCGTTGCTACTGTC 1 264276 ( 254) GGTATCGCTTATATC 1 23895 ( 447) GCTATTGCTTCGGAT 1 1322 ( 185) GGTGACGACGTCGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 14094 bayes= 9.59506 E= 2.1e-004 -1140 -1140 204 -1140 -1140 -30 29 96 -1140 -30 -1140 162 -51 -1140 168 -284 49 -1140 -1140 124 -1140 84 -1140 116 -1140 -262 199 -1140 34 97 -171 -84 -1140 -62 -1140 168 -183 -1140 129 33 -83 19 -1140 116 -1140 -62 75 74 -25 -162 119 -84 -283 70 -71 74 -1140 -30 9 106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 27 E= 2.1e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.185185 0.296296 0.518519 0.000000 0.185185 0.000000 0.814815 0.185185 0.000000 0.777778 0.037037 0.370370 0.000000 0.000000 0.629630 0.000000 0.407407 0.000000 0.592593 0.000000 0.037037 0.962963 0.000000 0.333333 0.444444 0.074074 0.148148 0.000000 0.148148 0.000000 0.851852 0.074074 0.000000 0.592593 0.333333 0.148148 0.259259 0.000000 0.592593 0.000000 0.148148 0.407407 0.444444 0.222222 0.074074 0.555556 0.148148 0.037037 0.370370 0.148148 0.444444 0.000000 0.185185 0.259259 0.555556 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TG]TG[TA][TC]G[CA]T[GT][TC][TG][GA][TC][TG] -------------------------------------------------------------------------------- Time 14.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 12 llr = 153 E-value = 8.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:3::31::::::1:: pos.-specific C 1614377:a:7945a2 probability G :::23:11:2:::1:: matrix T 84745:29:83163:8 bits 2.1 * * 1.9 * * 1.7 * * * 1.5 ** * * Relative 1.3 *** * ** Entropy 1.1 ** * ****** ** (18.4 bits) 0.9 ** * ****** ** 0.6 **** ******** ** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TCTCTCCTCTCCTCCT consensus TATCA T CT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 261392 328 1.57e-10 AGCTCTTCAC TCTCTCCTCTCCTCCT CTTTCCTCTC 3286 327 4.24e-08 ATCCCACATC TTTTTCCTCGCCTCCT TTGGTTACTC 23497 445 4.24e-08 CTCCCTCCCT TCTCTCCTCTCCCTCC CTGCACCACG 11938 21 5.57e-08 TACTAATGAA TCTTGACTCTTCTCCT GTTCGTTTCC 25272 395 1.00e-07 CACCTCCACC TTTTCCCTCTTCCTCT GCTTCCTCAA 2865 49 1.45e-07 CGAAAAAAGA TTACTCCTCGCCTCCT AAAACTCCAG 9103 196 1.89e-06 GAAGTGCTGT ATTCTACTCTCCTACT TACTGAAGAT 23971 183 2.18e-06 TACCCAGCTT TCAGGAGTCTCCCCCT AAAAGTTTAG 12645 327 2.49e-06 ATACAAGGCG TCTCTATTCTTTCCCT TTCACCATGA 22269 234 3.65e-06 CTCCCAGTCC TCTTCCTGCTCCTGCT GCCTTCCTCT 38317 64 5.15e-06 AGTATTGCTG TTCTGCATCTTCTTCT TGATCAGAGG 1322 262 5.15e-06 GGCTGCAAGC CCAGCCCTCTCCCTCC TCTCTCCCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261392 1.6e-10 327_[+3]_157 3286 4.2e-08 326_[+3]_158 23497 4.2e-08 444_[+3]_40 11938 5.6e-08 20_[+3]_464 25272 1e-07 394_[+3]_90 2865 1.5e-07 48_[+3]_436 9103 1.9e-06 195_[+3]_289 23971 2.2e-06 182_[+3]_302 12645 2.5e-06 326_[+3]_158 22269 3.6e-06 233_[+3]_251 38317 5.2e-06 63_[+3]_421 1322 5.2e-06 261_[+3]_223 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=12 261392 ( 328) TCTCTCCTCTCCTCCT 1 3286 ( 327) TTTTTCCTCGCCTCCT 1 23497 ( 445) TCTCTCCTCTCCCTCC 1 11938 ( 21) TCTTGACTCTTCTCCT 1 25272 ( 395) TTTTCCCTCTTCCTCT 1 2865 ( 49) TTACTCCTCGCCTCCT 1 9103 ( 196) ATTCTACTCTCCTACT 1 23971 ( 183) TCAGGAGTCTCCCCCT 1 12645 ( 327) TCTCTATTCTTTCCCT 1 22269 ( 234) TCTTCCTGCTCCTGCT 1 38317 ( 64) TTCTGCATCTTCTTCT 1 1322 ( 262) CCAGCCCTCTCCCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 14065 bayes= 11.2938 E= 8.2e+000 -166 -145 -1023 165 -1023 136 -1023 65 -8 -145 -1023 133 -1023 87 -54 65 -1023 14 4 91 34 155 -1023 -1023 -166 155 -154 -67 -1023 -1023 -154 179 -1023 213 -1023 -1023 -1023 -1023 -54 165 -1023 155 -1023 33 -1023 201 -1023 -167 -1023 87 -1023 113 -166 114 -154 33 -1023 213 -1023 -1023 -1023 -45 -1023 165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 8.2e+000 0.083333 0.083333 0.000000 0.833333 0.000000 0.583333 0.000000 0.416667 0.250000 0.083333 0.000000 0.666667 0.000000 0.416667 0.166667 0.416667 0.000000 0.250000 0.250000 0.500000 0.333333 0.666667 0.000000 0.000000 0.083333 0.666667 0.083333 0.166667 0.000000 0.000000 0.083333 0.916667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.666667 0.000000 0.333333 0.000000 0.916667 0.000000 0.083333 0.000000 0.416667 0.000000 0.583333 0.083333 0.500000 0.083333 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CT][TA][CT][TCG][CA]CTCT[CT]C[TC][CT]CT -------------------------------------------------------------------------------- Time 20.87 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11938 1.35e-07 20_[+3(5.57e-08)]_182_\ [+1(6.38e-06)]_72_[+2(1.35e-05)]_175 12645 1.82e-06 207_[+2(2.44e-05)]_104_\ [+3(2.49e-06)]_16_[+1(1.40e-06)]_122 1322 1.50e-05 184_[+2(9.19e-05)]_62_\ [+3(5.15e-06)]_7_[+1(1.14e-05)]_97_[+3(4.62e-05)]_83 1629 1.04e-04 84_[+2(2.93e-05)]_283_\ [+1(3.26e-07)]_98 17910 5.85e-05 233_[+2(5.34e-06)]_200_\ [+1(8.58e-07)]_32 21537 1.30e-03 35_[+1(4.10e-05)]_215_\ [+2(4.72e-06)]_215 22112 1.43e-04 112_[+2(5.63e-05)]_143_\ [+2(9.76e-06)]_121_[+1(2.63e-06)]_51_[+1(6.51e-05)]_3 22269 6.50e-09 81_[+2(7.59e-08)]_137_\ [+3(3.65e-06)]_170_[+1(6.30e-07)]_61 23497 1.69e-07 151_[+2(6.07e-05)]_255_\ [+1(2.41e-06)]_3_[+3(4.24e-08)]_40 23895 5.08e-03 283_[+1(6.88e-06)]_143_\ [+2(9.19e-05)]_39 23971 4.55e-07 44_[+2(7.01e-05)]_42_[+2(1.84e-05)]_\ 66_[+3(2.18e-06)]_279_[+1(4.57e-07)]_3 24224 4.94e-04 30_[+2(4.77e-08)]_455 24335 1.54e-01 362_[+2(3.48e-05)]_59_\ [+2(8.61e-05)]_49 24544 2.29e-02 138_[+2(1.66e-05)]_347 24827 2.18e-04 338_[+2(8.72e-06)]_116_\ [+1(1.27e-06)]_11 25272 8.71e-07 112_[+2(3.80e-05)]_267_\ [+3(1.00e-07)]_4_[+1(9.88e-06)]_66 261392 1.21e-08 327_[+3(1.57e-10)]_72_\ [+2(1.21e-05)]_70 262797 3.64e-05 146_[+1(7.07e-09)]_334 264276 9.64e-05 226_[+1(6.88e-06)]_7_[+2(9.19e-05)]_\ 200_[+1(1.80e-07)]_12 267997 1.66e-02 336_[+1(1.40e-06)]_144 268593 1.92e-02 377_[+2(2.44e-05)]_108 269773 2.87e-04 313_[+2(2.93e-05)]_122_\ [+1(4.57e-07)]_30 2865 2.72e-05 48_[+3(1.45e-07)]_299_\ [+2(2.03e-05)]_122 3286 1.94e-07 326_[+3(4.24e-08)]_28_\ [+2(2.44e-05)]_74_[+1(6.88e-06)]_21 35410 1.20e-04 101_[+2(1.35e-05)]_304_\ [+1(4.32e-06)]_60 38317 5.14e-08 63_[+3(5.15e-06)]_62_[+2(3.48e-05)]_\ 92_[+2(1.10e-06)]_212_[+1(2.91e-07)]_5 4312 1.29e-01 360_[+2(3.80e-05)]_125 8408 1.10e-06 174_[+2(1.66e-05)]_291_\ [+1(1.77e-09)] 9103 2.26e-07 84_[+2(9.76e-06)]_96_[+3(1.89e-06)]_\ 265_[+1(4.57e-07)]_4 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************