******************************************************************************** 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/408/408.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42569 1.0000 500 42578 1.0000 500 8996 1.0000 500 8963 1.0000 500 8678 1.0000 500 43027 1.0000 500 1859 1.0000 500 46795 1.0000 500 54703 1.0000 500 32539 1.0000 500 43354 1.0000 500 43467 1.0000 500 10100 1.0000 500 10122 1.0000 500 44873 1.0000 500 11368 1.0000 500 45084 1.0000 500 8239 1.0000 500 12309 1.0000 500 46010 1.0000 500 46063 1.0000 500 12752 1.0000 500 12740 1.0000 500 46273 1.0000 500 42510 1.0000 500 46306 1.0000 500 31888 1.0000 500 39483 1.0000 500 33776 1.0000 500 32455 1.0000 500 44461 1.0000 500 35095 1.0000 500 46497 1.0000 500 32883 1.0000 500 46601 1.0000 500 45091 1.0000 500 36063 1.0000 500 45436 1.0000 500 36058 1.0000 500 41298 1.0000 500 44316 1.0000 500 44677 1.0000 500 35461 1.0000 500 35181 1.0000 500 45439 1.0000 500 46138 1.0000 500 45045 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/408/408.seqs.fa -oc motifs/408 -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= 47 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= 23500 N= 47 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.238 G 0.234 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.238 G 0.234 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 20 llr = 231 E-value = 1.2e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::a:8:::96: pos.-specific C 3:7:9:::8::4 probability G 113:1:a:214: matrix T 791:12:a:::7 bits 2.1 * 1.9 * ** 1.7 * ** 1.5 * * ** * Relative 1.3 * ******* Entropy 1.0 * ********* (16.6 bits) 0.8 ************ 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTCACAGTCAAT consensus C G T G GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 33776 215 7.44e-08 AAAGATATGT TTCACAGTCAAT GGAACCCAAT 43027 183 7.44e-08 TGAGGCAGTG TTCACAGTCAAT TCAAAAATTC 45439 216 1.40e-07 GCCATCAAGA TTCACAGTCAGT TCCATTCCCA 12309 2 1.40e-07 C TTCACAGTCAGT AATTGCGGCA 42578 203 4.08e-07 ATGACGCTAG CTCACAGTCAAT CGCCGACTGT 45436 274 7.44e-07 AGGACTGGTC TTCACTGTCAAT TTTACACCGT 46138 277 1.11e-06 GGTGTAGAGA CTCACAGTCAGC CACCGGAATA 43354 328 1.65e-06 GGCTGCGCGA TTGACAGTGAAT TGACGACGAA 44316 251 1.83e-06 TTGGCACCAA CTGACAGTCAAC AACAACCACG 44677 140 2.27e-06 TGGTAGTTTT TTGACAGTGAGT AGTATCTCGA 41298 62 2.27e-06 GGTCGCAAAG TTGACTGTCAGT GCCCTGTCCC 46497 18 3.85e-06 CGATGCAGAA TTCAGAGTCAGC GCGTGACTTT 8678 225 3.85e-06 ATAGTTCGAG TGCACAGTCAGC GAAGGGAGCG 36063 452 4.71e-06 TTCGATCACA TTTACAGTCAAC GCAAAGAAGA 35461 12 5.97e-06 AATTTTGACA TTGACTGTGAAT GACCGGTCGC 32883 271 6.45e-06 AAAGAGTGGA CGCACAGTCAAC GCTATTTTAG 46601 460 8.83e-06 TATTCATCGA TTGACTGTGAAC ATGATGTGTT 8239 157 9.26e-06 ACGTGTACAT CTCATAGTCAGT TTCAAATTTT 45084 461 9.26e-06 TGTCACTGGA TTCAGAGTCGAT TGATTCATCT 43467 32 1.27e-05 TCTTCACGTG GTCACAGTCGAT GCCCCGAGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 33776 7.4e-08 214_[+1]_274 43027 7.4e-08 182_[+1]_306 45439 1.4e-07 215_[+1]_273 12309 1.4e-07 1_[+1]_487 42578 4.1e-07 202_[+1]_286 45436 7.4e-07 273_[+1]_215 46138 1.1e-06 276_[+1]_212 43354 1.7e-06 327_[+1]_161 44316 1.8e-06 250_[+1]_238 44677 2.3e-06 139_[+1]_349 41298 2.3e-06 61_[+1]_427 46497 3.8e-06 17_[+1]_471 8678 3.8e-06 224_[+1]_264 36063 4.7e-06 451_[+1]_37 35461 6e-06 11_[+1]_477 32883 6.4e-06 270_[+1]_218 46601 8.8e-06 459_[+1]_29 8239 9.3e-06 156_[+1]_332 45084 9.3e-06 460_[+1]_28 43467 1.3e-05 31_[+1]_457 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=20 33776 ( 215) TTCACAGTCAAT 1 43027 ( 183) TTCACAGTCAAT 1 45439 ( 216) TTCACAGTCAGT 1 12309 ( 2) TTCACAGTCAGT 1 42578 ( 203) CTCACAGTCAAT 1 45436 ( 274) TTCACTGTCAAT 1 46138 ( 277) CTCACAGTCAGC 1 43354 ( 328) TTGACAGTGAAT 1 44316 ( 251) CTGACAGTCAAC 1 44677 ( 140) TTGACAGTGAGT 1 41298 ( 62) TTGACTGTCAGT 1 46497 ( 18) TTCAGAGTCAGC 1 8678 ( 225) TGCACAGTCAGC 1 36063 ( 452) TTTACAGTCAAC 1 35461 ( 12) TTGACTGTGAAT 1 32883 ( 271) CGCACAGTCAAC 1 46601 ( 460) TTGACTGTGAAC 1 8239 ( 157) CTCATAGTCAGT 1 45084 ( 461) TTCAGAGTCGAT 1 43467 ( 32) GTCACAGTCGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 22983 bayes= 11.1091 E= 1.2e-010 -1097 7 -223 142 -1097 -1097 -123 178 -1097 145 36 -238 191 -1097 -1097 -1097 -1097 184 -123 -238 158 -1097 -1097 -38 -1097 -1097 209 -1097 -1097 -1097 -1097 194 -1097 175 -23 -1097 175 -1097 -123 -1097 117 -1097 77 -1097 -1097 56 -1097 132 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 20 E= 1.2e-010 0.000000 0.250000 0.050000 0.700000 0.000000 0.000000 0.100000 0.900000 0.000000 0.650000 0.300000 0.050000 1.000000 0.000000 0.000000 0.000000 0.000000 0.850000 0.100000 0.050000 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 0.900000 0.000000 0.100000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.350000 0.000000 0.650000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]T[CG]AC[AT]GT[CG]A[AG][TC] -------------------------------------------------------------------------------- Time 17.84 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 21 llr = 234 E-value = 5.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 7a318927a2274591 pos.-specific C 3::3:14:::721512 probability G ::762:41:7::5::6 matrix T :::::::2:111:::: bits 2.1 1.9 * * 1.7 * * 1.5 * * Relative 1.3 * ** * * Entropy 1.0 ** ** * ** (16.1 bits) 0.8 *** ** *** ** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel AAGGAACAAGCAGCAG consensus C AC GT AA AA C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 46795 312 2.67e-09 CTGGCAACAA AAGCAACAAGCAGCAG GACGACGCAA 11368 459 7.16e-09 AATGAAGCCG CAGGAAGAAGCAGAAG GTGCTTCGTT 43354 469 1.10e-07 CTTTGAACAC AAAGAACAAACAAAAG GAGATAGAAA 39483 51 4.83e-07 ACTTTCAGAT AAGGAAAAAGACGAAG TCCGAGCCAA 1859 3 4.83e-07 GT AAGGAAGAAGCAACCC AGCTACAATC 10122 16 5.42e-07 CAGGCGGCTG AAAGAAGAAAAAGAAG AGAGCATCAT 42569 38 6.05e-07 AAGGCTGGCG CAGAAACAAGCCGAAG AATCACAGGA 46273 194 1.35e-06 ACTCGTTCGC AAAGGCCAAGCAAAAG GCATAATGCA 42578 459 1.35e-06 TCGAGATTCG CAAAAAGTAGCAGCAG TATACGACAC 46063 427 4.66e-06 ACTAACCTCC AAGCAACTAACTGCAC TGCTGTATTA 35181 356 5.07e-06 ACAATGCTGG CAAGAACAAGAAGCAT TTTGAGAAAC 44316 376 5.07e-06 TTGCTTTCGA AAGAAAAAAGAACAAG GTGGTTTTCG 8678 187 5.07e-06 ACTTCAAATT CAGGAACAATCTACAC CAAGTTATCG 45439 421 7.67e-06 TCGAGAAGAC AAGGGAGTAGTAAAAC ACCCTTTCTG 54703 27 7.67e-06 CGAATAATTT AAGCAACAAGCAAAGA TCTTTTATTA 35095 452 8.96e-06 AACTCACAAA AAGCACGTAACTGCAG GGCATTTACT 36058 174 1.04e-05 AGACGACGTG CAGGGAAGAGCCAAAG TGGAATTATG 10100 157 1.20e-05 GTTCCCGTGC AAACGAGGAGCACCAG GACTCTCTTG 46138 122 1.59e-05 ATATCATCGA GAGGAACAATCAACAA AGTAGTCCAC 44461 210 1.59e-05 TATAGCTTAA AAACACGTAAAAACAG TACTGTTTCG 46306 392 2.07e-05 AACCATGGCG AAGGAAAAAGTCGCCC AAGAAAGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46795 2.7e-09 311_[+2]_173 11368 7.2e-09 458_[+2]_26 43354 1.1e-07 468_[+2]_16 39483 4.8e-07 50_[+2]_434 1859 4.8e-07 2_[+2]_482 10122 5.4e-07 15_[+2]_469 42569 6.1e-07 37_[+2]_447 46273 1.4e-06 193_[+2]_291 42578 1.4e-06 458_[+2]_26 46063 4.7e-06 426_[+2]_58 35181 5.1e-06 355_[+2]_129 44316 5.1e-06 375_[+2]_109 8678 5.1e-06 186_[+2]_298 45439 7.7e-06 420_[+2]_64 54703 7.7e-06 26_[+2]_458 35095 9e-06 451_[+2]_33 36058 1e-05 173_[+2]_311 10100 1.2e-05 156_[+2]_328 46138 1.6e-05 121_[+2]_363 44461 1.6e-05 209_[+2]_275 46306 2.1e-05 391_[+2]_93 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=21 46795 ( 312) AAGCAACAAGCAGCAG 1 11368 ( 459) CAGGAAGAAGCAGAAG 1 43354 ( 469) AAAGAACAAACAAAAG 1 39483 ( 51) AAGGAAAAAGACGAAG 1 1859 ( 3) AAGGAAGAAGCAACCC 1 10122 ( 16) AAAGAAGAAAAAGAAG 1 42569 ( 38) CAGAAACAAGCCGAAG 1 46273 ( 194) AAAGGCCAAGCAAAAG 1 42578 ( 459) CAAAAAGTAGCAGCAG 1 46063 ( 427) AAGCAACTAACTGCAC 1 35181 ( 356) CAAGAACAAGAAGCAT 1 44316 ( 376) AAGAAAAAAGAACAAG 1 8678 ( 187) CAGGAACAATCTACAC 1 45439 ( 421) AAGGGAGTAGTAAAAC 1 54703 ( 27) AAGCAACAAGCAAAGA 1 35095 ( 452) AAGCACGTAACTGCAG 1 36058 ( 174) CAGGGAAGAGCCAAAG 1 10100 ( 157) AAACGAGGAGCACCAG 1 46138 ( 122) GAGGAACAATCAACAA 1 44461 ( 210) AAACACGTAAAAACAG 1 46306 ( 392) AAGGAAAAAGTCGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 22795 bayes= 10.3879 E= 5.1e+000 132 27 -230 -1104 191 -1104 -1104 -1104 32 -1104 151 -1104 -90 27 128 -1104 160 -1104 -30 -1104 168 -73 -1104 -1104 -48 85 70 -1104 132 -1104 -130 -13 191 -1104 -1104 -1104 -16 -1104 151 -145 -16 149 -1104 -145 132 -32 -1104 -87 68 -132 102 -1104 84 114 -1104 -1104 168 -132 -230 -1104 -148 0 140 -245 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 21 E= 5.1e+000 0.666667 0.285714 0.047619 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.142857 0.285714 0.571429 0.000000 0.809524 0.000000 0.190476 0.000000 0.857143 0.142857 0.000000 0.000000 0.190476 0.428571 0.380952 0.000000 0.666667 0.000000 0.095238 0.238095 1.000000 0.000000 0.000000 0.000000 0.238095 0.000000 0.666667 0.095238 0.238095 0.666667 0.000000 0.095238 0.666667 0.190476 0.000000 0.142857 0.428571 0.095238 0.476190 0.000000 0.476190 0.523810 0.000000 0.000000 0.857143 0.095238 0.047619 0.000000 0.095238 0.238095 0.619048 0.047619 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC]A[GA][GC]AA[CG][AT]A[GA][CA]A[GA][CA]A[GC] -------------------------------------------------------------------------------- Time 35.61 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 40 llr = 348 E-value = 2.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:::2:11:2::431: pos.-specific C :::2342:7:2534:4 probability G 2:273:2:2231325: matrix T 6a91266a26641156 bits 2.1 1.9 * 1.7 * * 1.5 * * Relative 1.3 ** * Entropy 1.0 ** * * (12.5 bits) 0.8 *** * ** ** 0.6 **** * ***** ** 0.4 **** ******* ** 0.2 **** *********** 0.0 ---------------- Multilevel TTTGCTTTCTTCACGT consensus G GCC TGGTCATC sequence A G GG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 43467 15 2.64e-10 TGTGTGAAAC TTTGCTTTCTTCACGT GGTCACAGTC 1859 482 7.09e-07 GGAGTCTCAC ATTGTTTTCTTTACTT TAG 45091 245 1.72e-06 GAGAGGAGGA TTTGCTCTCTTTCGTC GTTTCCAATC 32883 311 1.72e-06 TTTATTCGTA TTGGGTTTCTGCACTT TTAATAGTGA 12740 172 2.37e-06 TACCTTGTTG TTTGGCTTCGGTGCGT ACAGAAACGG 46010 116 4.35e-06 TCGCTCTGTC TTTGTTTTCTGGAGGC AACAAGAAGA 42510 45 5.79e-06 AATTGGTTGT TTTGCCTTCTTTGCAT TAGGAATGTA 32539 343 7.60e-06 TGCGTTGCCG TTTTGTTTCTTTCGTC TCCTGGTCTT 35461 116 8.67e-06 AGTGAGAAGA TTTGGTATCTTTAATC TCCCAGGATG 45436 90 8.67e-06 TTCACCTTAT TTTTGTTTGTTCAAGT ACCAATGATA 45045 102 9.86e-06 ATTTCGTGAA TTTGACTTTGTTCCTT GTACATTTCC 54703 238 9.86e-06 GTGGTTCTCA GTTGCCTTCACCACGT ATTGTTGTTA 46795 76 9.86e-06 CCCTACTTAT TTTGCCGTGTGCAAGT GTGTAAATTT 31888 320 1.26e-05 ATAGATCCGT TTTCCTTTCTCTGATC AAATTCATTT 36063 53 1.42e-05 ATAATTTAAT TTTGCCTTGTTGCCTC ACGGGTGACG 46601 394 1.60e-05 TAGGTAGGAG GTTGTCGTCGTCCAGT CATATCAGCG 8239 290 1.60e-05 GCATCCACCG TTTGATGTCATCGGGC AGCCATCCTC 45439 462 2.24e-05 TGCTGCTGGA TTTGTTCTTTGTCAGC TCCTTCTCGG 12752 245 2.24e-05 CGCCTTCCGC GTTGTCCTCGTCGCGC AAGCGGAAAT 42569 457 2.24e-05 TGCTGGCGTA TTTCCTTTTTCTGCTT GTGCTGCTGG 33776 10 2.50e-05 TTTGGAATT GTGGGTGTCTTTCATT TCAAAGGACA 44873 207 2.50e-05 TAGTATTGTT TTTGTCGTTTGTCCGC TGTCAGAAGC 32455 210 2.79e-05 GTGAATACGG GTTGCTCTGGTCAAGT GAGGTAGAGA 45084 153 3.80e-05 GGCCGCGGAG TTTGGCTTCGTGTCGT TCTGGGATGG 35181 159 5.07e-05 GCAACTCTAT GTTGACCTCTTGGGGC CCTACTCAAA 10122 336 5.57e-05 TGTGGTTTGT TTTCCCTTGATCAGTT ACAGTCGACA 8996 466 6.10e-05 CGTTCGAACG ATGGATTTCATCAGGT TGCTCCGACA 12309 451 6.67e-05 ATTGACCTTA GTTGTCATCTCCAATT GGGAACTGCC 43027 392 7.93e-05 TGCTCGCACG ATTGATTTTTGCATTT AGTGTTTATC 36058 359 9.38e-05 TCTAATAAAA GTTCGTTTCGTTTCTT TGTCTATATT 35095 160 1.02e-04 TTTTCCCGCA ATTCTCCTCTCCACGC CTCTGCCATG 41298 138 1.19e-04 AGGCACGGTT TTTTCTCACTTTCCGT ATGAGCGGTG 46138 333 1.50e-04 AAACGTCACT TTTTATTTCCTCGAGC AAGTCGGCTC 44677 122 1.73e-04 CAATTTTGAT ATTGATGTTGGTAGTT TTTTGACAGT 44461 177 1.99e-04 AATCGTATGG TTTCGTCTTTGTGTTT CTATTTTTAT 46273 369 2.27e-04 CCAAATTTTG TTGTGCGTCTCCGGTT TGGAACAGGA 8963 144 2.27e-04 CGTATGGTGT TTTGCTTTCAGCCTAC CGCCAACAAC 46063 171 2.93e-04 GTACGAATTC TTGCATTTTTCGAATT TACGACTGGA 42578 16 3.12e-04 AGCAATAGAA ATTGTTGTGTTCAAGG TTGAAGCTGC 8678 60 3.72e-04 GAAGTTGATC GTGGATTACATCCAGT CGCAGTACGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43467 2.6e-10 14_[+3]_470 1859 7.1e-07 481_[+3]_3 45091 1.7e-06 244_[+3]_240 32883 1.7e-06 310_[+3]_174 12740 2.4e-06 171_[+3]_313 46010 4.3e-06 115_[+3]_369 42510 5.8e-06 44_[+3]_440 32539 7.6e-06 342_[+3]_142 35461 8.7e-06 115_[+3]_369 45436 8.7e-06 89_[+3]_395 45045 9.9e-06 101_[+3]_383 54703 9.9e-06 237_[+3]_247 46795 9.9e-06 75_[+3]_409 31888 1.3e-05 319_[+3]_165 36063 1.4e-05 52_[+3]_432 46601 1.6e-05 393_[+3]_91 8239 1.6e-05 289_[+3]_195 45439 2.2e-05 461_[+3]_23 12752 2.2e-05 244_[+3]_240 42569 2.2e-05 456_[+3]_28 33776 2.5e-05 9_[+3]_475 44873 2.5e-05 206_[+3]_278 32455 2.8e-05 209_[+3]_275 45084 3.8e-05 152_[+3]_332 35181 5.1e-05 158_[+3]_326 10122 5.6e-05 335_[+3]_149 8996 6.1e-05 465_[+3]_19 12309 6.7e-05 450_[+3]_34 43027 7.9e-05 391_[+3]_93 36058 9.4e-05 358_[+3]_126 35095 0.0001 159_[+3]_325 41298 0.00012 137_[+3]_347 46138 0.00015 332_[+3]_152 44677 0.00017 121_[+3]_363 44461 0.0002 176_[+3]_308 46273 0.00023 368_[+3]_116 8963 0.00023 143_[+3]_341 46063 0.00029 170_[+3]_314 42578 0.00031 15_[+3]_469 8678 0.00037 59_[+3]_425 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=40 43467 ( 15) TTTGCTTTCTTCACGT 1 1859 ( 482) ATTGTTTTCTTTACTT 1 45091 ( 245) TTTGCTCTCTTTCGTC 1 32883 ( 311) TTGGGTTTCTGCACTT 1 12740 ( 172) TTTGGCTTCGGTGCGT 1 46010 ( 116) TTTGTTTTCTGGAGGC 1 42510 ( 45) TTTGCCTTCTTTGCAT 1 32539 ( 343) TTTTGTTTCTTTCGTC 1 35461 ( 116) TTTGGTATCTTTAATC 1 45436 ( 90) TTTTGTTTGTTCAAGT 1 45045 ( 102) TTTGACTTTGTTCCTT 1 54703 ( 238) GTTGCCTTCACCACGT 1 46795 ( 76) TTTGCCGTGTGCAAGT 1 31888 ( 320) TTTCCTTTCTCTGATC 1 36063 ( 53) TTTGCCTTGTTGCCTC 1 46601 ( 394) GTTGTCGTCGTCCAGT 1 8239 ( 290) TTTGATGTCATCGGGC 1 45439 ( 462) TTTGTTCTTTGTCAGC 1 12752 ( 245) GTTGTCCTCGTCGCGC 1 42569 ( 457) TTTCCTTTTTCTGCTT 1 33776 ( 10) GTGGGTGTCTTTCATT 1 44873 ( 207) TTTGTCGTTTGTCCGC 1 32455 ( 210) GTTGCTCTGGTCAAGT 1 45084 ( 153) TTTGGCTTCGTGTCGT 1 35181 ( 159) GTTGACCTCTTGGGGC 1 10122 ( 336) TTTCCCTTGATCAGTT 1 8996 ( 466) ATGGATTTCATCAGGT 1 12309 ( 451) GTTGTCATCTCCAATT 1 43027 ( 392) ATTGATTTTTGCATTT 1 36058 ( 359) GTTCGTTTCGTTTCTT 1 35095 ( 160) ATTCTCCTCTCCACGC 1 41298 ( 138) TTTTCTCACTTTCCGT 1 46138 ( 333) TTTTATTTCCTCGAGC 1 44677 ( 122) ATTGATGTTGGTAGTT 1 44461 ( 177) TTTCGTCTTTGTGTTT 1 46273 ( 369) TTGTGCGTCTCCGGTT 1 8963 ( 144) TTTGCTTTCAGCCTAC 1 46063 ( 171) TTGCATTTTTCGAATT 1 42578 ( 16) ATTGTTGTGTTCAAGG 1 8678 ( 60) GTGGATTACATCCAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 22795 bayes= 9.40391 E= 2.5e+000 -83 -1197 -6 126 -1197 -1197 -1197 194 -1197 -1197 -64 170 -1197 -44 158 -106 -24 34 9 -21 -1197 66 -1197 126 -241 -25 -23 107 -241 -1197 -1197 186 -1197 145 -64 -38 -83 -325 -23 126 -1197 -44 9 114 -1197 100 -91 62 67 21 9 -238 29 66 -6 -180 -241 -1197 109 78 -1197 56 -323 126 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 40 E= 2.5e+000 0.150000 0.000000 0.225000 0.625000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.150000 0.850000 0.000000 0.175000 0.700000 0.125000 0.225000 0.300000 0.250000 0.225000 0.000000 0.375000 0.000000 0.625000 0.050000 0.200000 0.200000 0.550000 0.050000 0.000000 0.000000 0.950000 0.000000 0.650000 0.150000 0.200000 0.150000 0.025000 0.200000 0.625000 0.000000 0.175000 0.250000 0.575000 0.000000 0.475000 0.125000 0.400000 0.425000 0.275000 0.250000 0.050000 0.325000 0.375000 0.225000 0.075000 0.050000 0.000000 0.500000 0.450000 0.000000 0.350000 0.025000 0.625000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TG]TTG[CGAT][TC][TCG]T[CT][TG][TG][CT][ACG][CAG][GT][TC] -------------------------------------------------------------------------------- Time 53.31 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42569 8.25e-05 37_[+2(6.05e-07)]_403_\ [+3(2.24e-05)]_28 42578 3.25e-06 202_[+1(4.08e-07)]_244_\ [+2(1.35e-06)]_26 8996 8.96e-02 465_[+3(6.10e-05)]_19 8963 3.20e-01 500 8678 8.71e-05 186_[+2(5.07e-06)]_22_\ [+1(3.85e-06)]_264 43027 6.08e-05 182_[+1(7.44e-08)]_197_\ [+3(7.93e-05)]_93 1859 9.32e-06 2_[+2(4.83e-07)]_463_[+3(7.09e-07)]_\ 3 46795 4.40e-07 75_[+3(9.86e-06)]_220_\ [+2(2.67e-09)]_173 54703 7.10e-04 26_[+2(7.67e-06)]_195_\ [+3(9.86e-06)]_247 32539 3.42e-02 342_[+3(7.60e-06)]_142 43354 6.73e-06 327_[+1(1.65e-06)]_129_\ [+2(1.10e-07)]_16 43467 1.58e-07 14_[+3(2.64e-10)]_1_[+1(1.27e-05)]_\ 457 10100 6.31e-02 156_[+2(1.20e-05)]_328 10122 2.40e-05 15_[+2(5.42e-07)]_317_\ [+1(5.16e-05)]_140 44873 8.21e-02 206_[+3(2.50e-05)]_278 11368 9.32e-05 458_[+2(7.16e-09)]_26 45084 1.98e-03 152_[+3(3.80e-05)]_292_\ [+1(9.26e-06)]_28 8239 1.94e-03 156_[+1(9.26e-06)]_121_\ [+3(1.60e-05)]_195 12309 1.60e-05 1_[+1(1.40e-07)]_308_[+1(8.37e-05)]_\ 21_[+1(2.02e-06)]_84_[+3(6.67e-05)]_34 46010 5.69e-03 115_[+3(4.35e-06)]_369 46063 9.94e-03 426_[+2(4.66e-06)]_58 12752 4.64e-02 244_[+3(2.24e-05)]_240 12740 1.84e-02 171_[+3(2.37e-06)]_313 46273 1.49e-03 193_[+2(1.35e-06)]_291 42510 2.73e-02 44_[+3(5.79e-06)]_440 46306 6.14e-02 391_[+2(2.07e-05)]_93 31888 4.51e-02 319_[+3(1.26e-05)]_165 39483 7.41e-03 50_[+2(4.83e-07)]_139_\ [+2(2.64e-05)]_279 33776 1.23e-05 9_[+3(2.50e-05)]_189_[+1(7.44e-08)]_\ 274 32455 1.00e-01 209_[+3(2.79e-05)]_275 44461 2.38e-02 209_[+2(1.59e-05)]_275 35095 4.92e-03 451_[+2(8.96e-06)]_33 46497 2.59e-02 17_[+1(3.85e-06)]_471 32883 3.37e-05 270_[+1(6.45e-06)]_28_\ [+3(1.72e-06)]_174 46601 2.10e-03 129_[+1(9.93e-05)]_164_\ [+1(1.15e-05)]_76_[+3(1.60e-05)]_50_[+1(8.83e-06)]_29 45091 1.47e-02 244_[+3(1.72e-06)]_240 36063 1.35e-04 52_[+3(1.42e-05)]_148_\ [+1(1.88e-05)]_36_[+1(7.98e-05)]_175_[+1(4.71e-06)]_37 45436 1.28e-05 89_[+3(8.67e-06)]_168_\ [+1(7.44e-07)]_215 36058 7.26e-03 173_[+2(1.04e-05)]_169_\ [+3(9.38e-05)]_126 41298 9.33e-04 61_[+1(2.27e-06)]_427 44316 7.31e-05 250_[+1(1.83e-06)]_113_\ [+2(5.07e-06)]_109 44677 4.40e-03 139_[+1(2.27e-06)]_349 35461 9.27e-04 11_[+1(5.97e-06)]_92_[+3(8.67e-06)]_\ 77_[+1(1.35e-05)]_280 35181 2.52e-03 98_[+2(6.38e-05)]_44_[+3(5.07e-05)]_\ 181_[+2(5.07e-06)]_129 45439 5.90e-07 215_[+1(1.40e-07)]_73_\ [+1(3.41e-06)]_108_[+2(7.67e-06)]_25_[+3(2.24e-05)]_23 46138 3.79e-05 121_[+2(1.59e-05)]_139_\ [+1(1.11e-06)]_212 45045 7.80e-03 101_[+3(9.86e-06)]_48_\ [+3(4.19e-05)]_319 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************