******************************************************************************** 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/124/124.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42424 1.0000 500 42606 1.0000 500 42749 1.0000 500 9115 1.0000 500 8810 1.0000 500 9625 1.0000 500 32314 1.0000 500 43164 1.0000 500 43174 1.0000 500 43277 1.0000 500 13157 1.0000 500 13261 1.0000 500 46939 1.0000 500 47117 1.0000 500 42123 1.0000 500 47881 1.0000 500 48186 1.0000 500 48187 1.0000 500 38927 1.0000 500 15125 1.0000 500 15239 1.0000 500 43280 1.0000 500 43317 1.0000 500 43435 1.0000 500 43515 1.0000 500 18197 1.0000 500 18323 1.0000 500 18335 1.0000 500 33037 1.0000 500 15627 1.0000 500 23557 1.0000 500 50146 1.0000 500 51271 1.0000 500 43807 1.0000 500 44222 1.0000 500 24119 1.0000 500 17086 1.0000 500 44333 1.0000 500 18945 1.0000 500 33921 1.0000 500 44480 1.0000 500 44738 1.0000 500 44868 1.0000 500 44905 1.0000 500 12107 1.0000 500 45572 1.0000 500 35643 1.0000 500 12732 1.0000 500 46097 1.0000 500 4413 1.0000 500 36077 1.0000 500 48342 1.0000 500 42868 1.0000 500 48661 1.0000 500 49241 1.0000 500 32315 1.0000 500 47254 1.0000 500 45803 1.0000 500 34460 1.0000 500 37133 1.0000 500 47112 1.0000 500 48772 1.0000 500 33099 1.0000 500 43861 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/124/124.seqs.fa -oc motifs/124 -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= 64 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= 32000 N= 64 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.270 C 0.237 G 0.230 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.270 C 0.237 G 0.230 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 29 llr = 298 E-value = 2.7e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::a:5:1:a51 pos.-specific C 3:4:a::15::4 probability G 2:5::1a15:51 matrix T 5a:::4:7:::4 bits 2.1 * * 1.9 * ** * * 1.7 * ** * * 1.5 * ** * * Relative 1.3 * ** * * Entropy 1.1 * ** * ** (14.8 bits) 0.8 **** * *** 0.6 *********** 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel TTGACAGTGAAC consensus C C T C GT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43435 458 3.69e-07 ACGCTGCCGT TTGACAGTGAGT CTACCCACCT 45803 379 6.89e-07 GTTTGCCGTA TTCACAGTCAGC CAGAAACCTT 45572 300 1.02e-06 GCAACAAAAT TTGACTGTGAAC AACAGACAAA 43515 151 1.02e-06 ACCAAACGTT TTGACTGTGAAC CCCTGATTCT 46097 219 1.40e-06 GGAGTGGGCA TTGACTGTGAGT CCTGTCTACT 13261 160 1.40e-06 GTTGACAAGG TTGACTGTGAGT GGTGTGGAAC 44480 18 1.84e-06 TTACTTGATT CTGACAGTGAAC AACCAGCCCA 33921 458 1.84e-06 GTACTTGGAA TTGACTGTGAAT AGGTTTTTCA 32314 95 1.84e-06 CTCACCTGCA CTGACAGTGAAC TGATTGACTG 32315 374 2.65e-06 AGTCAATCAG TTCACTGTCAGT GCAGGTGAGA 42868 87 3.02e-06 TGACCGTGAT CTCACAGTCAAC GTCTAAAACC 42123 312 3.67e-06 AGGTAAGTTA CTGACTGTGAAT ATCTCTTTAC 4413 91 5.88e-06 TTTCGAATGA TTCACAGTCAGA GATCGGCCGA 33099 141 6.55e-06 CCTTACTAGT GTCACAGTCAAT TTCGACAAAT 49241 1 6.55e-06 . TTGACGGTGAGT GAGTGGGGAA 18323 53 7.21e-06 CGCGTCCGGA CTGACAGTGAGA AGGGTTTGGT 18945 69 1.03e-05 GGGATGTTTC CTGACTGTGAAA GCATTACGAC 48342 393 1.55e-05 GAGGGATCTT TTCACTGAGAGC TCCAAAACGC 51271 44 1.71e-05 GTGTTACTCA TTCACAGGCAAC GGATTATTTT 44222 368 2.04e-05 GTGTGGCTTT TTCACTGACAGT TACAGTTAGT 48187 391 2.22e-05 ACACTCCCAA CTCACAGCCAAT GTCACATTCC 43174 126 2.39e-05 TGATTTCACT GTCACGGTCAGT CAGTTTCCCA 47254 262 2.54e-05 TATGAGCACT TTTACAGTCAAC AGGAATGAAA 8810 351 2.72e-05 GAATGGTAAA GTCACAGCCAGC AAGAAGTTTG 47117 315 2.90e-05 GATTTTGATT GTGACAGGGAGC AAATCCTCCC 43280 410 3.32e-05 AGTTATTGTG CTCACAGTCACC GTCAATTGCT 18335 343 3.74e-05 TCACCATTGC CTGACGGTGAGG CTTCACGCGA 35643 422 5.26e-05 TACACAAAGT GTGACAGCCAAA CTTGTCCAAC 46939 110 5.46e-05 GTGACTGTTG TTCACTGACAAG CAATCAGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43435 3.7e-07 457_[+1]_31 45803 6.9e-07 378_[+1]_110 45572 1e-06 299_[+1]_189 43515 1e-06 150_[+1]_338 46097 1.4e-06 218_[+1]_270 13261 1.4e-06 159_[+1]_329 44480 1.8e-06 17_[+1]_471 33921 1.8e-06 457_[+1]_31 32314 1.8e-06 94_[+1]_394 32315 2.6e-06 373_[+1]_115 42868 3e-06 86_[+1]_402 42123 3.7e-06 311_[+1]_177 4413 5.9e-06 90_[+1]_398 33099 6.6e-06 140_[+1]_348 49241 6.6e-06 [+1]_488 18323 7.2e-06 52_[+1]_436 18945 1e-05 68_[+1]_420 48342 1.5e-05 392_[+1]_96 51271 1.7e-05 43_[+1]_445 44222 2e-05 367_[+1]_121 48187 2.2e-05 390_[+1]_98 43174 2.4e-05 125_[+1]_363 47254 2.5e-05 261_[+1]_227 8810 2.7e-05 350_[+1]_138 47117 2.9e-05 314_[+1]_174 43280 3.3e-05 409_[+1]_79 18335 3.7e-05 342_[+1]_146 35643 5.3e-05 421_[+1]_67 46939 5.5e-05 109_[+1]_379 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=29 43435 ( 458) TTGACAGTGAGT 1 45803 ( 379) TTCACAGTCAGC 1 45572 ( 300) TTGACTGTGAAC 1 43515 ( 151) TTGACTGTGAAC 1 46097 ( 219) TTGACTGTGAGT 1 13261 ( 160) TTGACTGTGAGT 1 44480 ( 18) CTGACAGTGAAC 1 33921 ( 458) TTGACTGTGAAT 1 32314 ( 95) CTGACAGTGAAC 1 32315 ( 374) TTCACTGTCAGT 1 42868 ( 87) CTCACAGTCAAC 1 42123 ( 312) CTGACTGTGAAT 1 4413 ( 91) TTCACAGTCAGA 1 33099 ( 141) GTCACAGTCAAT 1 49241 ( 1) TTGACGGTGAGT 1 18323 ( 53) CTGACAGTGAGA 1 18945 ( 69) CTGACTGTGAAA 1 48342 ( 393) TTCACTGAGAGC 1 51271 ( 44) TTCACAGGCAAC 1 44222 ( 368) TTCACTGACAGT 1 48187 ( 391) CTCACAGCCAAT 1 43174 ( 126) GTCACGGTCAGT 1 47254 ( 262) TTTACAGTCAAC 1 8810 ( 351) GTCACAGCCAGC 1 47117 ( 315) GTGACAGGGAGC 1 43280 ( 410) CTCACAGTCACC 1 18335 ( 343) CTGACGGTGAGG 1 35643 ( 422) GTGACAGCCAAA 1 46939 ( 110) TTCACTGACAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 31296 bayes= 11.7634 E= 2.7e-008 -1150 39 -41 97 -1150 -1150 -1150 192 -1150 92 117 -293 189 -1150 -1150 -1150 -1150 208 -1150 -1150 94 -1150 -115 53 -1150 -1150 212 -1150 -139 -119 -173 146 -1150 103 117 -1150 189 -1150 -1150 -1150 84 -278 107 -1150 -97 81 -173 53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 29 E= 2.7e-008 0.000000 0.310345 0.172414 0.517241 0.000000 0.000000 0.000000 1.000000 0.000000 0.448276 0.517241 0.034483 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.517241 0.000000 0.103448 0.379310 0.000000 0.000000 1.000000 0.000000 0.103448 0.103448 0.068966 0.724138 0.000000 0.482759 0.517241 0.000000 1.000000 0.000000 0.000000 0.000000 0.482759 0.034483 0.482759 0.000000 0.137931 0.413793 0.068966 0.379310 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]T[GC]AC[AT]GT[GC]A[AG][CT] -------------------------------------------------------------------------------- Time 37.16 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 20 llr = 232 E-value = 3.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 11:4::::29:::115 pos.-specific C :12:74::7::::172 probability G 33:2:1971::1a533 matrix T 6685461421a9:3:: bits 2.1 * 1.9 * * 1.7 * * * 1.5 * **** Relative 1.3 * * **** Entropy 1.1 * * ** **** (16.7 bits) 0.8 * **** **** * 0.6 * * ********* * 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TTTTCTGGCATTGGCA consensus GGCATC T TGG sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 34460 392 8.55e-08 CGAATAGACA TTTTCTGTCATTGCCA CTTTTTTGGG 43317 298 1.73e-07 TGCAATATAT TTTTCCTGCATTGGCA CACAGCGCAC 47112 359 1.98e-07 ACGTTATACG GGTACCGGCATTGGGA ATCACTACTC 46097 428 1.98e-07 CCCGTCCTCG TTCACCGGCATTGGGA GAGATGCGTG 44738 176 2.94e-07 GCCAACGTCA TTTTCCGTCATTGGAA AGGAACGATG 44333 282 4.77e-07 GACGGAAAGA TTTACTGTTATTGTCG TCCATAGAGG 18335 188 6.04e-07 TATGCATAGC TCTATTGGCATTGTCG AAGTGTGAAA 44480 181 9.35e-07 TCAGCACCCA TTTACTGGATTTGGCA GGGTCTTAGC 45803 158 1.15e-06 AAATACTAAC GGTATCGGTATTGGCA TCTCTGAAGC 13261 62 1.70e-06 GCAATAAACC TGTTCTGTGATTGTCA GGTTTGCTGC 47117 364 1.87e-06 TGAATCTATA TTTTCTTGCATTGGAG CCACCATGAT 48186 409 2.05e-06 GAGGACAACC ATTGTTGGCATTGTGA GATCCGTAAT 4413 190 2.69e-06 AATTGTTCCG GTTGCTGTAATTGTCC CAACTCGCCG 17086 164 3.49e-06 TGATGTTACG ATCGCTGGTATTGGCA CTGTCTTGGA 24119 55 3.49e-06 ACGGTGGGAG TGTTCCGTCATGGTCC AGTCCGGACA 50146 65 3.79e-06 GGGAGCCGAC GACTTTGGCATTGGCG TCGGAGATCC 46939 38 4.84e-06 CAGTGTTCTT GGTTTTGTCATTGAGG AAAATATGGT 38927 452 9.36e-06 CTCTTTCTTG TTCTTCGGCATGGACG ATATATACCC 13157 160 1.30e-05 GAAATTCAAA TTTGTTGGATTTGGGC TTGTGTCCCA 12732 189 1.66e-05 GTTACTCGCC GCTACGGGCATTGCCC TTTTGGGTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34460 8.5e-08 391_[+2]_93 43317 1.7e-07 297_[+2]_187 47112 2e-07 358_[+2]_126 46097 2e-07 427_[+2]_57 44738 2.9e-07 175_[+2]_309 44333 4.8e-07 281_[+2]_203 18335 6e-07 187_[+2]_297 44480 9.3e-07 180_[+2]_304 45803 1.1e-06 157_[+2]_327 13261 1.7e-06 61_[+2]_423 47117 1.9e-06 363_[+2]_121 48186 2.1e-06 408_[+2]_76 4413 2.7e-06 189_[+2]_295 17086 3.5e-06 163_[+2]_321 24119 3.5e-06 54_[+2]_430 50146 3.8e-06 64_[+2]_420 46939 4.8e-06 37_[+2]_447 38927 9.4e-06 451_[+2]_33 13157 1.3e-05 159_[+2]_325 12732 1.7e-05 188_[+2]_296 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=20 34460 ( 392) TTTTCTGTCATTGCCA 1 43317 ( 298) TTTTCCTGCATTGGCA 1 47112 ( 359) GGTACCGGCATTGGGA 1 46097 ( 428) TTCACCGGCATTGGGA 1 44738 ( 176) TTTTCCGTCATTGGAA 1 44333 ( 282) TTTACTGTTATTGTCG 1 18335 ( 188) TCTATTGGCATTGTCG 1 44480 ( 181) TTTACTGGATTTGGCA 1 45803 ( 158) GGTATCGGTATTGGCA 1 13261 ( 62) TGTTCTGTGATTGTCA 1 47117 ( 364) TTTTCTTGCATTGGAG 1 48186 ( 409) ATTGTTGGCATTGTGA 1 4413 ( 190) GTTGCTGTAATTGTCC 1 17086 ( 164) ATCGCTGGTATTGGCA 1 24119 ( 55) TGTTCCGTCATGGTCC 1 50146 ( 65) GACTTTGGCATTGGCG 1 46939 ( 38) GGTTTTGTCATTGAGG 1 38927 ( 452) TTCTTCGGCATGGACG 1 13157 ( 160) TTTGTTGGATTTGGGC 1 12732 ( 189) GCTACGGGCATTGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 31040 bayes= 11.5428 E= 3.7e+000 -143 -1097 39 119 -243 -124 12 119 -1097 -24 -1097 160 37 -1097 -20 77 -1097 146 -1097 41 -1097 56 -220 119 -1097 -1097 197 -140 -1097 -1097 150 41 -85 146 -220 -81 173 -1097 -1097 -140 -1097 -1097 -1097 192 -1097 -1097 -120 177 -1097 -1097 212 -1097 -143 -124 112 19 -143 146 12 -1097 89 -24 39 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 20 E= 3.7e+000 0.100000 0.000000 0.300000 0.600000 0.050000 0.100000 0.250000 0.600000 0.000000 0.200000 0.000000 0.800000 0.350000 0.000000 0.200000 0.450000 0.000000 0.650000 0.000000 0.350000 0.000000 0.350000 0.050000 0.600000 0.000000 0.000000 0.900000 0.100000 0.000000 0.000000 0.650000 0.350000 0.150000 0.650000 0.050000 0.150000 0.900000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.100000 0.900000 0.000000 0.000000 1.000000 0.000000 0.100000 0.100000 0.500000 0.300000 0.100000 0.650000 0.250000 0.000000 0.500000 0.200000 0.300000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][TG][TC][TAG][CT][TC]G[GT]CATTG[GT][CG][AGC] -------------------------------------------------------------------------------- Time 74.88 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 16 llr = 220 E-value = 1.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 65a395a38386889184618 pos.-specific C 43:3:4:4:31432131633: probability G :1:41::2:2:1:1161:162 matrix T :1:::1:1221:::::::::: bits 2.1 1.9 * * 1.7 * * 1.5 * * * Relative 1.3 * * * * * * Entropy 1.1 * * * * * * * ** * (19.9 bits) 0.8 * * * * * * ******* * 0.6 * * *** * *********** 0.4 * ***** * *********** 0.2 ********* *********** 0.0 --------------------- Multilevel AAAGAAACAAAAAAAGACAGA consensus CC A C A C CC C ACC sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 49241 477 3.54e-11 GTACGCCGAG ACACACACACAAAAAGACAGA GCA 43317 255 1.64e-08 GGACAGCGTC CAACAAACAACAAAACACACA ATGAAAGATC 12732 266 1.86e-08 CAGTACACAT ACACACACACACACACACACA CGAGCTCCGA 43174 41 2.10e-08 TTTGTTCCGA AAAAAAAAAAAAAAAGAACAA GTTGATGCGA 46097 379 2.65e-08 AGGAGAGAGT AAACACACAAAAAGAGAACGA AGCTTCCCAT 48186 433 7.80e-08 GAGATCCGTA ATAAAAACACAAAACGAAAGA GTAGTAGCTA 42749 274 1.15e-07 GTGGATATTA AAAGAAAATCACAAAGGACGA AGCTCGCTTT 44738 316 1.39e-07 TCTCTGTCGT CCAGACAGATAGACAGACAGA TGGTTGATAC 24119 342 1.39e-07 CGCGTCGGGT ATACACACATACACACACACA CGCTCACAAG 8810 200 2.82e-07 CATCGTCGAT CAAGAAAAAGAAAAGCAAAGG AGGCTCATCG 43280 76 3.06e-07 AATGCCTTAC AAAAACAGTAAACAAGACCAA AGTTTTTTAT 37133 392 1.08e-06 GCAACATTAT CCAGAAATAGAACAACACGCA TATTTTACAT 15627 359 1.08e-06 CACAAACACT CAAGAAAATCTCCAAGGCACA ACCAAATGAT 43807 71 1.16e-06 ACACACACGG CCAAGCACATTAAAAGAAAGG TTGCCGTTTT 47254 14 1.92e-06 TCTCGTTGAT AAAGATAAAAACCAAAACCGG AGACCTTGTT 34460 478 2.16e-06 TTATCCTCAA CGAAAAAGAGCCAAAGCAAGA TA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49241 3.5e-11 476_[+3]_3 43317 1.6e-08 254_[+3]_225 12732 1.9e-08 265_[+3]_214 43174 2.1e-08 40_[+3]_439 46097 2.7e-08 378_[+3]_101 48186 7.8e-08 432_[+3]_47 42749 1.2e-07 273_[+3]_206 44738 1.4e-07 315_[+3]_164 24119 1.4e-07 341_[+3]_138 8810 2.8e-07 199_[+3]_280 43280 3.1e-07 75_[+3]_404 37133 1.1e-06 391_[+3]_88 15627 1.1e-06 358_[+3]_121 43807 1.2e-06 70_[+3]_409 47254 1.9e-06 13_[+3]_466 34460 2.2e-06 477_[+3]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=16 49241 ( 477) ACACACACACAAAAAGACAGA 1 43317 ( 255) CAACAAACAACAAAACACACA 1 12732 ( 266) ACACACACACACACACACACA 1 43174 ( 41) AAAAAAAAAAAAAAAGAACAA 1 46097 ( 379) AAACACACAAAAAGAGAACGA 1 48186 ( 433) ATAAAAACACAAAACGAAAGA 1 42749 ( 274) AAAGAAAATCACAAAGGACGA 1 44738 ( 316) CCAGACAGATAGACAGACAGA 1 24119 ( 342) ATACACACATACACACACACA 1 8810 ( 200) CAAGAAAAAGAAAAGCAAAGG 1 43280 ( 76) AAAAACAGTAAACAAGACCAA 1 37133 ( 392) CCAGAAATAGAACAACACGCA 1 15627 ( 359) CAAGAAAATCTCCAAGGCACA 1 43807 ( 71) CCAAGCACATTAAAAGAAAGG 1 47254 ( 14) AAAGATAAAAACCAAAACCGG 1 34460 ( 478) CGAAAAAGAGCCAAAGCAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 30720 bayes= 11.6434 E= 1.8e+001 106 89 -1064 -1064 89 40 -187 -107 189 -1064 -1064 -1064 21 40 71 -1064 179 -1064 -187 -1064 89 89 -1064 -207 189 -1064 -1064 -1064 21 89 -29 -207 159 -1064 -1064 -49 21 40 -29 -49 147 -92 -1064 -107 106 66 -187 -1064 147 8 -1064 -1064 147 -34 -187 -1064 169 -192 -187 -1064 -211 40 144 -1064 159 -192 -88 -1064 69 125 -1064 -1064 121 40 -187 -1064 -111 40 129 -1064 159 -1064 -29 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 1.8e+001 0.562500 0.437500 0.000000 0.000000 0.500000 0.312500 0.062500 0.125000 1.000000 0.000000 0.000000 0.000000 0.312500 0.312500 0.375000 0.000000 0.937500 0.000000 0.062500 0.000000 0.500000 0.437500 0.000000 0.062500 1.000000 0.000000 0.000000 0.000000 0.312500 0.437500 0.187500 0.062500 0.812500 0.000000 0.000000 0.187500 0.312500 0.312500 0.187500 0.187500 0.750000 0.125000 0.000000 0.125000 0.562500 0.375000 0.062500 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.187500 0.062500 0.000000 0.875000 0.062500 0.062500 0.000000 0.062500 0.312500 0.625000 0.000000 0.812500 0.062500 0.125000 0.000000 0.437500 0.562500 0.000000 0.000000 0.625000 0.312500 0.062500 0.000000 0.125000 0.312500 0.562500 0.000000 0.812500 0.000000 0.187500 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AC][AC]A[GAC]A[AC]A[CA]A[AC]A[AC][AC]AA[GC]A[CA][AC][GC]A -------------------------------------------------------------------------------- Time 113.06 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42424 5.19e-02 500 42606 5.14e-01 500 42749 1.21e-04 273_[+3(1.15e-07)]_132_\ [+2(7.14e-05)]_58 9115 9.19e-01 500 8810 1.78e-04 199_[+3(2.82e-07)]_130_\ [+1(2.72e-05)]_138 9625 4.23e-01 500 32314 1.08e-02 94_[+1(1.84e-06)]_394 43164 2.59e-01 500 43174 2.16e-06 40_[+3(2.10e-08)]_64_[+1(2.39e-05)]_\ 363 43277 5.16e-01 500 13157 2.29e-02 159_[+2(1.30e-05)]_325 13261 5.82e-05 61_[+2(1.70e-06)]_82_[+1(1.40e-06)]_\ 329 46939 7.78e-04 37_[+2(4.84e-06)]_56_[+1(5.46e-05)]_\ 379 47117 6.00e-04 314_[+1(2.90e-05)]_37_\ [+2(1.87e-06)]_121 42123 3.88e-02 311_[+1(3.67e-06)]_177 47881 2.41e-01 500 48186 1.11e-06 408_[+2(2.05e-06)]_8_[+3(7.80e-08)]_\ 47 48187 3.79e-02 390_[+1(2.22e-05)]_98 38927 1.50e-02 451_[+2(9.36e-06)]_33 15125 6.65e-01 500 15239 5.90e-01 500 43280 3.89e-05 75_[+3(3.06e-07)]_313_\ [+1(3.32e-05)]_79 43317 7.21e-08 254_[+3(1.64e-08)]_22_\ [+2(1.73e-07)]_187 43435 2.35e-03 457_[+1(3.69e-07)]_31 43515 8.04e-03 150_[+1(1.02e-06)]_338 18197 3.23e-01 500 18323 1.40e-02 52_[+1(7.21e-06)]_436 18335 4.18e-04 187_[+2(6.04e-07)]_139_\ [+1(3.74e-05)]_146 33037 1.08e-01 282_[+2(9.50e-05)]_202 15627 7.76e-03 358_[+3(1.08e-06)]_121 23557 3.44e-02 500 50146 3.02e-03 64_[+2(3.79e-06)]_420 51271 1.55e-02 43_[+1(1.71e-05)]_445 43807 7.52e-03 70_[+3(1.16e-06)]_409 44222 3.20e-02 367_[+1(2.04e-05)]_121 24119 1.12e-05 54_[+2(3.49e-06)]_271_\ [+3(1.39e-07)]_138 17086 9.92e-03 163_[+2(3.49e-06)]_321 44333 7.45e-04 281_[+2(4.77e-07)]_203 18945 4.24e-03 68_[+1(1.03e-05)]_420 33921 2.30e-03 457_[+1(1.84e-06)]_31 44480 1.89e-05 17_[+1(1.84e-06)]_151_\ [+2(9.35e-07)]_304 44738 4.26e-07 175_[+2(2.94e-07)]_124_\ [+3(1.39e-07)]_164 44868 5.36e-01 500 44905 1.43e-01 500 12107 7.81e-01 500 45572 1.23e-02 299_[+1(1.02e-06)]_189 35643 1.75e-03 412_[+3(1.83e-05)]_67 12732 3.94e-06 188_[+2(1.66e-05)]_61_\ [+3(1.86e-08)]_214 46097 3.47e-10 218_[+1(1.40e-06)]_148_\ [+3(2.65e-08)]_28_[+2(1.98e-07)]_57 4413 3.14e-04 90_[+1(5.88e-06)]_87_[+2(2.69e-06)]_\ 295 36077 3.08e-01 500 48342 7.05e-02 392_[+1(1.55e-05)]_52_\ [+1(5.68e-05)]_32 42868 2.21e-02 86_[+1(3.02e-06)]_241_\ [+1(3.02e-06)]_78_[+1(5.26e-05)]_59 48661 3.93e-01 500 49241 4.60e-09 [+1(6.55e-06)]_464_[+3(3.54e-11)]_3 32315 3.97e-03 358_[+1(2.90e-05)]_3_[+1(2.65e-06)]_\ 115 47254 6.20e-04 13_[+3(1.92e-06)]_227_\ [+1(2.54e-05)]_227 45803 1.45e-05 157_[+2(1.15e-06)]_187_\ [+2(6.90e-05)]_2_[+1(6.89e-07)]_40_[+1(1.14e-05)]_58 34460 4.50e-06 391_[+2(8.55e-08)]_70_\ [+3(2.16e-06)]_2 37133 5.40e-03 363_[+3(8.13e-05)]_7_[+3(1.08e-06)]_\ 88 47112 2.70e-04 358_[+2(1.98e-07)]_126 48772 1.20e-01 500 33099 9.90e-03 50_[+1(5.68e-05)]_78_[+1(6.55e-06)]_\ 348 43861 5.79e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************