******************************************************************************** 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/396/396.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11307 1.0000 500 1197 1.0000 500 12084 1.0000 500 1275 1.0000 500 1900 1.0000 500 20869 1.0000 500 21405 1.0000 500 23903 1.0000 500 24327 1.0000 500 24482 1.0000 500 24796 1.0000 500 24920 1.0000 500 24940 1.0000 500 25373 1.0000 500 25442 1.0000 500 25656 1.0000 500 261225 1.0000 500 262157 1.0000 500 263642 1.0000 500 264774 1.0000 500 268867 1.0000 500 269261 1.0000 500 3043 1.0000 500 36303 1.0000 500 8734 1.0000 500 8915 1.0000 500 9018 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/396/396.seqs.fa -oc motifs/396 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.233 G 0.237 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.233 G 0.237 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 27 llr = 270 E-value = 8.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4861:74:7:741:3:14:1: pos.-specific C 511811221713324714722 probability G :1119:28:23::7::3:151 matrix T 1:2::22:11:2613342227 bits 2.1 1.9 1.7 1.5 * Relative 1.3 * * Entropy 1.1 ** * * (14.4 bits) 0.8 * ** **** * * * 0.6 * *** **** ** * * * 0.4 ****** **** **** ** * 0.2 ****** ************** 0.0 --------------------- Multilevel CAACGAAGACAATGCCTACGT consensus A T TC GGCC ATGC C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 24327 428 2.21e-11 GGTGAATGAA AAACGAAGACAATGTCTCCGT TTCTCCCCTC 269261 90 3.51e-08 CCAGAAATGT CAACGACGACAATGACGATGG AGGTGAGACA 263642 173 1.25e-07 CTCCAAGCGC CAACGATGAGATTCCCTACGC CGATATTTCT 8734 220 1.87e-07 TCGAGGGGAG AAACGGAGACATTGTCTTCGT TTTTCATTCA 25373 290 1.87e-07 TATCCACGTT CAACGAAGATGCCGCCACCCT AACACTCATC 24940 288 2.41e-07 AAGACACTAA CAACGAGGACACCGATTCTGG TGCAATGATG 1197 12 5.07e-07 TAGTACTCGA TGACGACGACGACGACGACGT GCATCTCCTA 3043 419 7.23e-07 CTCTCTCTGT CAACGAACACAAGTCCTCCCT GCCTCAAGTT 20869 264 1.28e-06 TGTTCCGGCC AATGGAAGACAATCCTTACTT GGAAATGACG 23903 83 1.42e-06 GTGATGCCAG CACCGTTGACGCTGTTGTCGT CATCGCCATC 9018 228 5.44e-06 CTACTCCAGT CATCCATCTCACTGCTGCCCT CCAACGGCAA 25656 203 5.99e-06 ACAAAATCAT CATCGTCGTCGTCGTCGTCGT CGTCTCGTCG 24920 258 7.24e-06 CACCAACAAC AAACGAAGCTGCTTCCTCTGT ACATCACCTC 1275 326 7.95e-06 TTTCTGCATT CAACGCAGAGAACTTTCACTT CAATCCGAAC 8915 3 1.05e-05 GA CAGCGAGCCGAACGACGACTT CTGCGTCTTG 21405 49 1.05e-05 AATATCATAC AAACGACGTCAACCTCTAGTC TTCATAGCAT 24796 94 1.93e-05 CAACGAAGAG CACCGACGACGGAGCCGAGGT TGTTGGTAGT 268867 474 2.48e-05 TGACAGTGAC ACAACAAGAGGATGCTTCCGC CGCCGA 261225 330 2.70e-05 ACGACAAACC TTACGCTGACACTGCCGAGCT CGTTTGCGAT 25442 306 2.70e-05 GCTGCTCTTC CATCGTACACATTGACACTTC AGGTCTTCCA 262157 400 2.92e-05 CCCCCCCCCA ACTAGTGGACATTGACCCCCT TCAGGACTGG 1900 305 3.71e-05 TCAAATCTTG GAAGGTTGAGAACGCTCACGT GGAACAAACC 12084 97 4.69e-05 ATCTCGTCTT TATCCAACTCAATGTCAACAT CATCCTCGGG 11307 381 1.55e-04 CCCAAGTACC AACCCAAGACCCTCACTCAAT ACCCAATACC 264774 134 1.76e-04 AAGTTCCTCT CAAAGATGATCCAGATTATGC GAAGTTCTTT 36303 339 2.26e-04 CTGGCCTTTG AGGAGAGGAGACCCCCTTCAT GATGTCAAGA 24482 447 2.86e-04 GATATGAACT ACACGCGCCCAATGATCTCCG CCATTTGCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24327 2.2e-11 427_[+1]_52 269261 3.5e-08 89_[+1]_390 263642 1.3e-07 172_[+1]_307 8734 1.9e-07 219_[+1]_260 25373 1.9e-07 289_[+1]_190 24940 2.4e-07 287_[+1]_192 1197 5.1e-07 11_[+1]_468 3043 7.2e-07 418_[+1]_61 20869 1.3e-06 263_[+1]_216 23903 1.4e-06 82_[+1]_397 9018 5.4e-06 227_[+1]_252 25656 6e-06 202_[+1]_277 24920 7.2e-06 257_[+1]_222 1275 7.9e-06 325_[+1]_154 8915 1e-05 2_[+1]_477 21405 1e-05 48_[+1]_431 24796 1.9e-05 93_[+1]_386 268867 2.5e-05 473_[+1]_6 261225 2.7e-05 329_[+1]_150 25442 2.7e-05 305_[+1]_174 262157 2.9e-05 399_[+1]_80 1900 3.7e-05 304_[+1]_175 12084 4.7e-05 96_[+1]_383 11307 0.00015 380_[+1]_99 264774 0.00018 133_[+1]_346 36303 0.00023 338_[+1]_141 24482 0.00029 446_[+1]_33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=27 24327 ( 428) AAACGAAGACAATGTCTCCGT 1 269261 ( 90) CAACGACGACAATGACGATGG 1 263642 ( 173) CAACGATGAGATTCCCTACGC 1 8734 ( 220) AAACGGAGACATTGTCTTCGT 1 25373 ( 290) CAACGAAGATGCCGCCACCCT 1 24940 ( 288) CAACGAGGACACCGATTCTGG 1 1197 ( 12) TGACGACGACGACGACGACGT 1 3043 ( 419) CAACGAACACAAGTCCTCCCT 1 20869 ( 264) AATGGAAGACAATCCTTACTT 1 23903 ( 83) CACCGTTGACGCTGTTGTCGT 1 9018 ( 228) CATCCATCTCACTGCTGCCCT 1 25656 ( 203) CATCGTCGTCGTCGTCGTCGT 1 24920 ( 258) AAACGAAGCTGCTTCCTCTGT 1 1275 ( 326) CAACGCAGAGAACTTTCACTT 1 8915 ( 3) CAGCGAGCCGAACGACGACTT 1 21405 ( 49) AAACGACGTCAACCTCTAGTC 1 24796 ( 94) CACCGACGACGGAGCCGAGGT 1 268867 ( 474) ACAACAAGAGGATGCTTCCGC 1 261225 ( 330) TTACGCTGACACTGCCGAGCT 1 25442 ( 306) CATCGTACACATTGACACTTC 1 262157 ( 400) ACTAGTGGACATTGACCCCCT 1 1900 ( 305) GAAGGTTGAGAACGCTCACGT 1 12084 ( 97) TATCCAACTCAATGTCAACAT 1 11307 ( 381) AACCCAAGACCCTCACTCAAT 1 264774 ( 134) CAAAGATGATCCAGATTATGC 1 36303 ( 339) AGGAGAGGAGACCCCCTTCAT 1 24482 ( 447) ACACGCGCCCAATGATCTCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 8.90388 E= 8.2e-002 48 105 -268 -125 155 -107 -168 -283 116 -107 -168 -25 -84 174 -168 -1140 -1140 -65 184 -1140 133 -107 -268 -51 62 -33 -36 -25 -1140 -7 171 -1140 148 -107 -1140 -84 -1140 152 -9 -125 133 -165 13 -1140 74 52 -268 -51 -184 52 -268 107 -1140 -33 157 -125 33 81 -1140 -3 -1140 152 -1140 33 -126 -65 32 75 74 67 -1140 -51 -284 152 -109 -51 -126 -7 102 -51 -1140 -33 -109 141 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 27 E= 8.2e-002 0.370370 0.481481 0.037037 0.111111 0.777778 0.111111 0.074074 0.037037 0.592593 0.111111 0.074074 0.222222 0.148148 0.777778 0.074074 0.000000 0.000000 0.148148 0.851852 0.000000 0.666667 0.111111 0.037037 0.185185 0.407407 0.185185 0.185185 0.222222 0.000000 0.222222 0.777778 0.000000 0.740741 0.111111 0.000000 0.148148 0.000000 0.666667 0.222222 0.111111 0.666667 0.074074 0.259259 0.000000 0.444444 0.333333 0.037037 0.185185 0.074074 0.333333 0.037037 0.555556 0.000000 0.185185 0.703704 0.111111 0.333333 0.407407 0.000000 0.259259 0.000000 0.666667 0.000000 0.333333 0.111111 0.148148 0.296296 0.444444 0.444444 0.370370 0.000000 0.185185 0.037037 0.666667 0.111111 0.185185 0.111111 0.222222 0.481481 0.185185 0.000000 0.185185 0.111111 0.703704 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]A[AT]CGA[AT][GC]A[CG][AG][AC][TC]G[CAT][CT][TG][AC]C[GC]T -------------------------------------------------------------------------------- Time 6.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 24 llr = 231 E-value = 1.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :21:6:31:15322:: pos.-specific C ::1:11:1:121:1:2 probability G 81:a:25:38353368 matrix T 288:37387::1544: bits 2.1 * 1.9 * 1.7 * 1.5 * Relative 1.3 * * Entropy 1.1 * ** *** ** (13.9 bits) 0.8 **** * *** ** 0.6 ****** **** ** 0.4 ************* ** 0.2 ************* ** 0.0 ---------------- Multilevel GTTGATGTTGAGTTGG consensus T TGA G GAGGT sequence T AA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 23903 266 1.19e-09 AAAGCATCGA GTTGATGTTGAGGGGG GTTGATTGAT 8734 151 3.53e-07 GAGTAGGGCA GTTGAGGTTGGATGTG GCTTGACGTC 24796 325 6.40e-07 ATTCGTTTCT GTTGATGTGAAGTGGG TGCATGATGT 24327 68 1.56e-06 GTGGTTCATT GTTGATTTGGGAAAGG AGCAGTAATG 12084 268 2.85e-06 CCATTGATGT GTTGTTGTTGATTTGC TCTTCGCGAC 20869 319 3.96e-06 AATAGAGGAT GTCGAGATTGAGTTTG GGAGATGAAT 36303 470 4.45e-06 AACTTCTCCA TTTGATTTGGAGGCTG CTTGCTTTGG 263642 27 7.46e-06 CAGTGGGGGG GATGATGCTGACTTGG ATGCTGCATG 261225 247 7.46e-06 TCAGCCCCTT TTTGATGTTTAGTTTG AGGTAGTCCC 269261 376 9.10e-06 CAAAGACGAC TTTGACTTTGCGATGG ATTCATTCGG 24920 122 9.10e-06 CTGCCAAGTC GATGATATGGCGATTG TAGACACTTC 268867 167 1.12e-05 GGCCGCCTTC GTTGTTTTTGGCGGGC GGCGGGCGTC 24940 12 1.24e-05 TTGAATGGAT TGTGATGTGGGAGGGG ATGTCTGCGA 21405 23 1.93e-05 ATTTGCTTCC GTTGTCATTGAAACTG AATATCATAC 11307 199 1.93e-05 AAGCAAGGGT ATTGATATGGGGAAGG GCCTCGGCAT 3043 114 2.53e-05 TGATGGCTGT GGAGATGTGGCGGTGG AGGACGTTCA 262157 166 2.75e-05 CTGTTCGAGA GTTGTTATTCAGTATC TGGCGAACCA 1197 452 2.98e-05 CGGGAACGTG GTTGTCACTGGAGTTG ACCTTCTGTC 25656 357 3.79e-05 TTGAAGTGCG GTTGTGGCTACGTTGG GCGTTGGGGG 9018 432 4.47e-05 GCAAACAGCT TTTGAGTTTGAGGAGA TTGTACAGCT 24482 26 5.63e-05 AGTGCACTGA GTAGTGTATGAGTGGG AGTAAAACAG 8915 167 6.04e-05 TGCTGTGGTT GTTGCTGTTCGTTCGG CTGTCGTCCG 1900 43 6.49e-05 GTTCAATCGT GATGATAATGAATGTC TTGGTGCACG 1275 10 6.98e-05 GATGAAGAC GACGCTGTTGGAGAGG ATATCTGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23903 1.2e-09 265_[+2]_219 8734 3.5e-07 150_[+2]_334 24796 6.4e-07 324_[+2]_160 24327 1.6e-06 67_[+2]_417 12084 2.8e-06 267_[+2]_217 20869 4e-06 318_[+2]_166 36303 4.5e-06 469_[+2]_15 263642 7.5e-06 26_[+2]_458 261225 7.5e-06 246_[+2]_238 269261 9.1e-06 375_[+2]_109 24920 9.1e-06 121_[+2]_363 268867 1.1e-05 166_[+2]_318 24940 1.2e-05 11_[+2]_473 21405 1.9e-05 22_[+2]_462 11307 1.9e-05 198_[+2]_286 3043 2.5e-05 113_[+2]_371 262157 2.8e-05 165_[+2]_319 1197 3e-05 451_[+2]_33 25656 3.8e-05 356_[+2]_128 9018 4.5e-05 431_[+2]_53 24482 5.6e-05 25_[+2]_459 8915 6e-05 166_[+2]_318 1900 6.5e-05 42_[+2]_442 1275 7e-05 9_[+2]_475 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=24 23903 ( 266) GTTGATGTTGAGGGGG 1 8734 ( 151) GTTGAGGTTGGATGTG 1 24796 ( 325) GTTGATGTGAAGTGGG 1 24327 ( 68) GTTGATTTGGGAAAGG 1 12084 ( 268) GTTGTTGTTGATTTGC 1 20869 ( 319) GTCGAGATTGAGTTTG 1 36303 ( 470) TTTGATTTGGAGGCTG 1 263642 ( 27) GATGATGCTGACTTGG 1 261225 ( 247) TTTGATGTTTAGTTTG 1 269261 ( 376) TTTGACTTTGCGATGG 1 24920 ( 122) GATGATATGGCGATTG 1 268867 ( 167) GTTGTTTTTGGCGGGC 1 24940 ( 12) TGTGATGTGGGAGGGG 1 21405 ( 23) GTTGTCATTGAAACTG 1 11307 ( 199) ATTGATATGGGGAAGG 1 3043 ( 114) GGAGATGTGGCGGTGG 1 262157 ( 166) GTTGTTATTCAGTATC 1 1197 ( 452) GTTGTCACTGGAGTTG 1 25656 ( 357) GTTGTGGCTACGTTGG 1 9018 ( 432) TTTGAGTTTGAGGAGA 1 24482 ( 26) GTAGTGTATGAGTGGG 1 8915 ( 167) GTTGCTGTTCGTTCGG 1 1900 ( 43) GATGATAATGAATGTC 1 1275 ( 10) GACGCTGTTGGAGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13095 bayes= 9.53728 E= 1.0e+001 -267 -1123 166 -34 -67 -1123 -151 150 -167 -148 -1123 166 -1123 -1123 208 -1123 123 -148 -1123 14 -1123 -90 -19 133 13 -1123 95 -8 -167 -90 -1123 158 -1123 -1123 30 142 -167 -148 174 -266 91 -48 49 -1123 13 -148 119 -166 -35 -1123 49 79 -35 -90 30 50 -1123 -1123 140 50 -267 -48 174 -1123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 24 E= 1.0e+001 0.041667 0.000000 0.750000 0.208333 0.166667 0.000000 0.083333 0.750000 0.083333 0.083333 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.625000 0.083333 0.000000 0.291667 0.000000 0.125000 0.208333 0.666667 0.291667 0.000000 0.458333 0.250000 0.083333 0.125000 0.000000 0.791667 0.000000 0.000000 0.291667 0.708333 0.083333 0.083333 0.791667 0.041667 0.500000 0.166667 0.333333 0.000000 0.291667 0.083333 0.541667 0.083333 0.208333 0.000000 0.333333 0.458333 0.208333 0.125000 0.291667 0.375000 0.000000 0.000000 0.625000 0.375000 0.041667 0.166667 0.791667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]TTG[AT][TG][GAT]T[TG]G[AG][GA][TGA][TGA][GT]G -------------------------------------------------------------------------------- Time 13.45 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 12 llr = 150 E-value = 2.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 31a415:2:::81128 pos.-specific C 69::92a3:a6:355: probability G ::::::::7::21:31 matrix T 2::6:3:63:4:5411 bits 2.1 * * 1.9 * * * 1.7 ** * * * 1.5 ** * * * Relative 1.3 ** * * * * Entropy 1.1 ** * * **** * (18.0 bits) 0.8 **** * **** * 0.6 ***** ****** * * 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CCATCACTGCCATCCA consensus A A T CT T CTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 25373 355 2.06e-08 CAAAAGAATA CCAACACTGCCATCAA CAGAAACAAT 268867 361 3.42e-08 GATGAACCCC CCAACACTGCTACCGA TAGTAGGTCT 8915 311 5.37e-08 TTCTTCTATA CCATCACAGCTATTCA AGTGCACCAT 3043 480 2.80e-07 ACAGCTCCCA CCATAACTGCCACTCA AAATC 1900 483 4.69e-07 CATTAACGTA CCATCTCTTCTATACA TA 12084 249 6.24e-07 TGAAGCAGTG ACATCTCCTCCATTGA TGTGTTGTTG 21405 392 1.15e-06 GATGCGCGTT ACAACCCTGCCACCTA AAACTCAAAC 24920 206 1.47e-06 TAAAAATGAG ACATCTCTGCTAGCAA AGTATCAAAC 24482 185 1.59e-06 ATTACCATCC CCATCACATCCATCGG CCATCATCCA 1275 71 1.59e-06 ACGAGGCCGA TCATCTCTGCTATTCT ACGTCGGGTC 11307 434 3.21e-06 AGGATTCGTA TCAACACCGCCGACCA AGCGAGAGAA 24940 449 9.72e-06 CACAATAAAG CAAACCCCTCCGCTCA GTTCTCTGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25373 2.1e-08 354_[+3]_130 268867 3.4e-08 360_[+3]_124 8915 5.4e-08 310_[+3]_174 3043 2.8e-07 479_[+3]_5 1900 4.7e-07 482_[+3]_2 12084 6.2e-07 248_[+3]_236 21405 1.2e-06 391_[+3]_93 24920 1.5e-06 205_[+3]_279 24482 1.6e-06 184_[+3]_300 1275 1.6e-06 70_[+3]_414 11307 3.2e-06 433_[+3]_51 24940 9.7e-06 448_[+3]_36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=12 25373 ( 355) CCAACACTGCCATCAA 1 268867 ( 361) CCAACACTGCTACCGA 1 8915 ( 311) CCATCACAGCTATTCA 1 3043 ( 480) CCATAACTGCCACTCA 1 1900 ( 483) CCATCTCTTCTATACA 1 12084 ( 249) ACATCTCCTCCATTGA 1 21405 ( 392) ACAACCCTGCCACCTA 1 24920 ( 206) ACATCTCTGCTAGCAA 1 24482 ( 185) CCATCACATCCATCGG 1 1275 ( 71) TCATCTCTGCTATTCT 1 11307 ( 434) TCAACACCGCCGACCA 1 24940 ( 449) CAAACCCCTCCGCTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13095 bayes= 10.5383 E= 2.9e+001 -9 132 -1023 -67 -167 198 -1023 -1023 191 -1023 -1023 -1023 65 -1023 -1023 114 -167 198 -1023 -1023 91 -48 -1023 33 -1023 210 -1023 -1023 -67 10 -1023 114 -1023 -1023 149 33 -1023 210 -1023 -1023 -1023 132 -1023 66 165 -1023 -51 -1023 -167 52 -151 92 -167 110 -1023 66 -67 110 8 -166 165 -1023 -151 -166 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 2.9e+001 0.250000 0.583333 0.000000 0.166667 0.083333 0.916667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.416667 0.000000 0.000000 0.583333 0.083333 0.916667 0.000000 0.000000 0.500000 0.166667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.166667 0.250000 0.000000 0.583333 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.583333 0.000000 0.416667 0.833333 0.000000 0.166667 0.000000 0.083333 0.333333 0.083333 0.500000 0.083333 0.500000 0.000000 0.416667 0.166667 0.500000 0.250000 0.083333 0.833333 0.000000 0.083333 0.083333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CA]CA[TA]C[AT]C[TC][GT]C[CT]A[TC][CT][CG]A -------------------------------------------------------------------------------- Time 19.40 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11307 1.14e-04 198_[+2(1.93e-05)]_219_\ [+3(3.21e-06)]_51 1197 1.80e-04 11_[+1(5.07e-07)]_179_\ [+1(4.34e-05)]_219_[+2(2.98e-05)]_33 12084 1.77e-06 96_[+1(4.69e-05)]_131_\ [+3(6.24e-07)]_3_[+2(2.85e-06)]_217 1275 1.44e-05 9_[+2(6.98e-05)]_45_[+3(1.59e-06)]_\ 239_[+1(7.95e-06)]_154 1900 1.78e-05 42_[+2(6.49e-05)]_246_\ [+1(3.71e-05)]_157_[+3(4.69e-07)]_2 20869 7.30e-05 263_[+1(1.28e-06)]_34_\ [+2(3.96e-06)]_166 21405 4.46e-06 22_[+2(1.93e-05)]_10_[+1(1.05e-05)]_\ 322_[+3(1.15e-06)]_93 23903 4.09e-08 82_[+1(1.42e-06)]_162_\ [+2(1.19e-09)]_219 24327 2.18e-09 67_[+2(1.56e-06)]_344_\ [+1(2.21e-11)]_52 24482 2.56e-04 25_[+2(5.63e-05)]_143_\ [+3(1.59e-06)]_300 24796 1.89e-04 93_[+1(1.93e-05)]_210_\ [+2(6.40e-07)]_160 24920 2.04e-06 121_[+2(9.10e-06)]_68_\ [+3(1.47e-06)]_36_[+1(7.24e-06)]_222 24940 6.89e-07 11_[+2(1.24e-05)]_260_\ [+1(2.41e-07)]_140_[+3(9.72e-06)]_36 25373 2.02e-07 289_[+1(1.87e-07)]_44_\ [+3(2.06e-08)]_94_[+3(8.01e-05)]_20 25442 4.62e-02 305_[+1(2.70e-05)]_174 25656 2.11e-03 202_[+1(5.99e-06)]_133_\ [+2(3.79e-05)]_128 261225 6.65e-04 246_[+2(7.46e-06)]_67_\ [+1(2.70e-05)]_150 262157 4.97e-03 165_[+2(2.75e-05)]_218_\ [+1(2.92e-05)]_80 263642 1.17e-05 26_[+2(7.46e-06)]_130_\ [+1(1.25e-07)]_307 264774 2.84e-01 500 268867 2.50e-07 29_[+3(2.20e-05)]_121_\ [+2(1.12e-05)]_178_[+3(3.42e-08)]_97_[+1(2.48e-05)]_6 269261 1.37e-06 89_[+1(3.51e-08)]_265_\ [+2(9.10e-06)]_70_[+1(8.72e-06)]_18 3043 1.43e-07 113_[+2(2.53e-05)]_289_\ [+1(7.23e-07)]_40_[+3(2.80e-07)]_5 36303 2.86e-03 469_[+2(4.45e-06)]_15 8734 1.13e-06 150_[+2(3.53e-07)]_53_\ [+1(1.87e-07)]_260 8915 7.86e-07 2_[+1(1.05e-05)]_143_[+2(6.04e-05)]_\ 128_[+3(5.37e-08)]_174 9018 1.54e-03 227_[+1(5.44e-06)]_183_\ [+2(4.47e-05)]_53 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************