******************************************************************************** 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/141/141.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31465 1.0000 500 9235 1.0000 500 36743 1.0000 500 37009 1.0000 500 47056 1.0000 500 47116 1.0000 500 54710 1.0000 500 14366 1.0000 500 21922 1.0000 500 47943 1.0000 500 14996 1.0000 500 48338 1.0000 500 48410 1.0000 500 15019 1.0000 500 5128 1.0000 500 39052 1.0000 500 8000 1.0000 500 15354 1.0000 500 39419 1.0000 500 41745 1.0000 500 43579 1.0000 500 43677 1.0000 500 15639 1.0000 500 39714 1.0000 500 55067 1.0000 500 30585 1.0000 500 16364 1.0000 500 50071 1.0000 500 50103 1.0000 500 51277 1.0000 500 16911 1.0000 500 18579 1.0000 500 44096 1.0000 500 51630 1.0000 500 44242 1.0000 500 17059 1.0000 500 17029 1.0000 500 44311 1.0000 500 11088 1.0000 500 45715 1.0000 500 20335 1.0000 500 46132 1.0000 500 47222 1.0000 500 44446 1.0000 500 37583 1.0000 500 48031 1.0000 500 34588 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/141/141.seqs.fa -oc motifs/141 -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 0.271 C 0.242 G 0.235 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.242 G 0.235 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 18 llr = 221 E-value = 4.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 41:a:81::7333144 pos.-specific C 2:a:a::29:4:353: probability G :1::::9:1324:431 matrix T 49:::218:::34::5 bits 2.1 * * 1.9 *** 1.7 *** * 1.5 **** * * Relative 1.3 **** *** Entropy 1.0 ********* (17.7 bits) 0.8 ********* 0.6 ********* * * 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel ATCACAGTCACGTCAT consensus T T GAAAGCA sequence GTC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 44096 255 5.31e-10 ACCAAAGCAG TTCACAGTCACGTCAT TTTCTCGTCC 41745 94 9.39e-08 CTGACTGTGA TTCACAGTCAGGTCGA TGATGTCATC 44446 303 1.12e-07 CAAGGTAATA TTCACAGTCAGATCAT ACAAAAATAT 45715 379 1.33e-07 CTCTCAAACG ATCACAGTCAGTCCAT TCATCAATTC 55067 197 1.33e-07 CAGTAACTAG TTCACAGTCACACGGT CCAGGCTACT 5128 110 1.54e-07 ATGGATTGCC ATCACAGTCGCGAGCT TTTGGAACTT 37583 196 3.77e-07 TGCGTGTCGT CTCACAGTCACTCCGA ATGAAAGAGG 17029 40 4.64e-07 TTCTAGTCCT TTCACAGTCAAGCAAT TTGTCGATCG 37009 135 5.12e-07 CTCTAGGTAG ATCACAGTCGATTGGA TTGTCGAACT 14996 167 1.52e-06 CCGTACCTGC CTCACTGTCAAATCGA TTCCAACCAT 20335 128 3.21e-06 CATCAGGATC ATCACTGTCAAATGAG ACAAGCTCGT 47116 451 3.21e-06 AACAAAGACC TTCACATTCGAGTCCT TGATTGCTGA 48338 157 3.43e-06 AATGGTGTCT CACACAGTCAAGAGAT TTCGTTTCTA 15354 136 3.67e-06 TCCGGGATAG ATCACAGCGACGACAA CGACTCTTTT 39714 163 3.93e-06 GCAACAACCA ATCACTGCCGCTACCA CACATTTTGG 9235 294 3.93e-06 AACCAAGACT ATCACTGTCAGTAACA AAGCTCACTG 14366 362 4.19e-06 AGTCCGAATC ATCACAACCACGCGAT GGAAGCGAAA 16364 131 5.06e-06 AGGGTATCTC TGCACAGTCGCAAGCA AAAATGGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44096 5.3e-10 254_[+1]_230 41745 9.4e-08 93_[+1]_391 44446 1.1e-07 302_[+1]_182 45715 1.3e-07 378_[+1]_106 55067 1.3e-07 196_[+1]_288 5128 1.5e-07 109_[+1]_375 37583 3.8e-07 195_[+1]_289 17029 4.6e-07 39_[+1]_445 37009 5.1e-07 134_[+1]_350 14996 1.5e-06 166_[+1]_318 20335 3.2e-06 127_[+1]_357 47116 3.2e-06 450_[+1]_34 48338 3.4e-06 156_[+1]_328 15354 3.7e-06 135_[+1]_349 39714 3.9e-06 162_[+1]_322 9235 3.9e-06 293_[+1]_191 14366 4.2e-06 361_[+1]_123 16364 5.1e-06 130_[+1]_354 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=18 44096 ( 255) TTCACAGTCACGTCAT 1 41745 ( 94) TTCACAGTCAGGTCGA 1 44446 ( 303) TTCACAGTCAGATCAT 1 45715 ( 379) ATCACAGTCAGTCCAT 1 55067 ( 197) TTCACAGTCACACGGT 1 5128 ( 110) ATCACAGTCGCGAGCT 1 37583 ( 196) CTCACAGTCACTCCGA 1 17029 ( 40) TTCACAGTCAAGCAAT 1 37009 ( 135) ATCACAGTCGATTGGA 1 14996 ( 167) CTCACTGTCAAATCGA 1 20335 ( 128) ATCACTGTCAAATGAG 1 47116 ( 451) TTCACATTCGAGTCCT 1 48338 ( 157) CACACAGTCAAGAGAT 1 15354 ( 136) ATCACAGCGACGACAA 1 39714 ( 163) ATCACTGCCGCTACCA 1 9235 ( 294) ATCACTGTCAGTAACA 1 14366 ( 362) ATCACAACCACGCGAT 1 16364 ( 131) TGCACAGTCGCAAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 22795 bayes= 11.1539 E= 4.6e-005 71 -54 -1081 62 -228 -1081 -208 181 -1081 205 -1081 -1081 188 -1081 -1081 -1081 -1081 205 -1081 -1081 152 -1081 -1081 -19 -228 -1081 192 -218 -1081 -54 -1081 172 -1081 197 -208 -1081 141 -1081 24 -1081 30 88 -8 -1081 4 -1081 92 14 30 20 -1081 62 -128 105 73 -1081 71 20 24 -1081 71 -1081 -208 98 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 18 E= 4.6e-005 0.444444 0.166667 0.000000 0.388889 0.055556 0.000000 0.055556 0.888889 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.222222 0.055556 0.000000 0.888889 0.055556 0.000000 0.166667 0.000000 0.833333 0.000000 0.944444 0.055556 0.000000 0.722222 0.000000 0.277778 0.000000 0.333333 0.444444 0.222222 0.000000 0.277778 0.000000 0.444444 0.277778 0.333333 0.277778 0.000000 0.388889 0.111111 0.500000 0.388889 0.000000 0.444444 0.277778 0.277778 0.000000 0.444444 0.000000 0.055556 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT]TCAC[AT]GTC[AG][CAG][GAT][TAC][CG][ACG][TA] -------------------------------------------------------------------------------- Time 20.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 16 llr = 186 E-value = 1.3e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 39:::a:6::1a pos.-specific C 613:::9::1:: probability G 11:18:::a:6: matrix T 1:893:14:93: bits 2.1 * 1.9 * * * 1.7 * ** ** * 1.5 * ** ** * Relative 1.3 ****** ** * Entropy 1.0 ********* * (16.8 bits) 0.8 *********** 0.6 *********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CATTGACAGTGA consensus A C T T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 44446 480 6.64e-08 TGAGACGACT CATTGACAGTGA ACAAGCACC 55067 474 4.76e-07 TCTTCACTGT CATTGACTGTTA TATTACATTA 47116 374 6.74e-07 TTGTGGCAAA CACTGACTGTGA AACCACAACA 20335 331 1.02e-06 CAGTGATATT TATTGACTGTGA AACGAGTTTC 50103 114 1.10e-06 GCTTCCAAAG CATTTACAGTTA TTGTTTTTTG 48410 253 1.10e-06 TGTGCCTACG CATTTACAGTTA GGTAGGTATG 47056 198 1.32e-06 TTGTAGTTAG AATTTACAGTGA GAATGTGAAA 41745 82 1.59e-06 TTGACATGTG AACTGACTGTGA TTCACAGTCA 46132 264 1.80e-06 ACTTACAAAA CATTGACAGTAA AATCATGCAA 18579 409 2.19e-06 CGAGCATCCA CATTGACAGCGA TTAAACCAGA 51277 388 2.82e-06 TGCTCGGTTC GATTGACAGTTA GAGTTACTTG 54710 448 3.00e-06 CCTCGGTTTG CCTTGACTGTGA AAACACCCAT 48031 117 4.73e-06 GCGCTCCGTA TATTTACAGTTA GTGAAACGTG 14996 136 5.05e-06 CGGAAACACG CACGGACAGTGA CTGGAATATC 14366 388 5.05e-06 GGAAGCGAAA AATTGATAGTGA GATTGATCGG 45715 159 1.23e-05 GTGATGTCCA AGCTGACTGTGA AGCTGTTGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44446 6.6e-08 479_[+2]_9 55067 4.8e-07 473_[+2]_15 47116 6.7e-07 373_[+2]_115 20335 1e-06 330_[+2]_158 50103 1.1e-06 113_[+2]_375 48410 1.1e-06 252_[+2]_236 47056 1.3e-06 197_[+2]_291 41745 1.6e-06 81_[+2]_407 46132 1.8e-06 263_[+2]_225 18579 2.2e-06 408_[+2]_80 51277 2.8e-06 387_[+2]_101 54710 3e-06 447_[+2]_41 48031 4.7e-06 116_[+2]_372 14996 5.1e-06 135_[+2]_353 14366 5.1e-06 387_[+2]_101 45715 1.2e-05 158_[+2]_330 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=16 44446 ( 480) CATTGACAGTGA 1 55067 ( 474) CATTGACTGTTA 1 47116 ( 374) CACTGACTGTGA 1 20335 ( 331) TATTGACTGTGA 1 50103 ( 114) CATTTACAGTTA 1 48410 ( 253) CATTTACAGTTA 1 47056 ( 198) AATTTACAGTGA 1 41745 ( 82) AACTGACTGTGA 1 46132 ( 264) CATTGACAGTAA 1 18579 ( 409) CATTGACAGCGA 1 51277 ( 388) GATTGACAGTTA 1 54710 ( 448) CCTTGACTGTGA 1 48031 ( 117) TATTTACAGTTA 1 14996 ( 136) CACGGACAGTGA 1 14366 ( 388) AATTGATAGTGA 1 45715 ( 159) AGCTGACTGTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 22983 bayes= 10.4873 E= 1.3e-004 -12 122 -191 -101 169 -195 -191 -1064 -1064 5 -1064 157 -1064 -1064 -191 189 -1064 -1064 168 -2 188 -1064 -1064 -1064 -1064 195 -1064 -201 121 -1064 -1064 57 -1064 -1064 209 -1064 -1064 -195 -1064 189 -211 -1064 141 31 188 -1064 -1064 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 16 E= 1.3e-004 0.250000 0.562500 0.062500 0.125000 0.875000 0.062500 0.062500 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.062500 0.937500 0.000000 0.000000 0.750000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 0.937500 0.000000 0.062500 0.625000 0.000000 0.000000 0.375000 0.000000 0.000000 1.000000 0.000000 0.000000 0.062500 0.000000 0.937500 0.062500 0.000000 0.625000 0.312500 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA]A[TC]T[GT]AC[AT]GT[GT]A -------------------------------------------------------------------------------- Time 41.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 39 llr = 351 E-value = 1.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 13627864478635a7 pos.-specific C 812412:151:131:1 probability G 16:42:44121:34:: matrix T ::2::::1::141::2 bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 * * Entropy 1.0 * ** * * (13.0 bits) 0.8 ** *** ** ** 0.6 *** *** **** *** 0.4 ************ *** 0.2 ************ *** 0.0 ---------------- Multilevel CGAGAAAACAAACAAA consensus ATC CGGA TAG T sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 21922 377 4.94e-08 ATATACGCGC CGAGAAGGAAAAGAAA TTGACGGCGG 17029 374 3.51e-07 ACAACGAAGG CGACGAAACAAAAGAA TTCACAGGTA 47116 51 5.76e-07 TAACGAAGTC CGAAAAGGAAATCGAA AGCTTCGTTT 9235 259 6.81e-07 GGTCGTCTGC CACGAAAACAAAAAAA AACATCGACA 51630 234 9.54e-07 GTTTTGATCG CGACAAACCAAATAAA ACGTTTTTCA 20335 352 1.76e-06 AAACGAGTTT CGTCAAGCCAATCAAA TATTTTGTCG 41745 53 2.02e-06 AGATTTGATG CGACACAACAAACGAT CGTTTGACAT 8000 79 2.65e-06 AGCCGCCTAA GGAAAAAGCAAACAAA TTTTTTTTCA 54710 354 2.65e-06 CGGTCGGTCG CGAGAAGGAAAACGAC GCCCAAAAAC 39714 209 3.04e-06 TTTCGTTCGG CGTGAAAGCCATCAAA CTTCTCGTTC 50071 367 6.57e-06 TGAGTGCTCG CGCGGAACCAAAAAAA CAGAAACGTG 30585 22 6.57e-06 GTATTGATTT CAAGACGACAAAGAAT TTTCCGGATT 43677 73 6.57e-06 CAAAAGCTCA AGAAAAAGCAATAGAA TCCGCTAGTA 15354 431 6.57e-06 ATTCGAGTGA AGACGAAGCAAACGAA GATGAGTTGC 48410 33 7.39e-06 ACTTTTTGGC CAAGAAACAAATTAAA TAGAGCATCG 46132 389 9.32e-06 TATTTCTCAT CGTCCAAGCAAATGAA TTTTCGGTTT 44242 331 9.32e-06 ATTACCCTGG CATCCAAGCAAAAAAA AAGCTTGTCG 50103 445 1.62e-05 CCAACACCTA CCACAAAAAAATCCAA ACCCTCACAT 48031 19 1.80e-05 AACCAGGATA AGAGAAGGAGAAGAAA AAGAGAAACG 16364 323 2.94e-05 GCCGTAGGTT CGACAAGGAAGAAGAT TGCGGCACAA 14366 416 3.56e-05 TCGGACGAAG CAACAAGGGCATAGAA TGCCTGCCAT 51277 169 4.29e-05 CAATCAAAGG CGTAAAAACATAAGAT TATAGACTTG 39419 320 4.70e-05 AACCCTCGAG AGCCACAAAAAAGGAA TTGGCGCACC 18579 89 5.12e-05 CAGGGAGGGA CGTCAAGTCCATCAAA AGTCATATAT 55067 362 6.06e-05 ATCCCAAAAT CGAGACGTAAATACAA TCAAGCGACA 48338 52 6.06e-05 TCGTAACGAT CGTGGAAAAGATCAAT TGCATTAGGG 47056 391 7.75e-05 GTGACCTCAC CAAGACGACGACCAAA GGTTGTCTTG 44446 280 8.40e-05 GTCTGTCCTG CAAGCCGAAAAAACAA GGTAATATTC 15639 413 9.10e-05 CAATCGACGC CATCAAAACCATTCAA CAGTATCACC 15019 367 9.10e-05 CACGAAATCG CGCAAAGGGAACGAAA GCCGGAGGCT 47222 450 9.84e-05 TCTCAACAGC GGAGAAAAAAATCCAC GCAAGGCAGA 31465 478 9.84e-05 TTCTTGTTCG CACGGAAAGGAAGAAA CGGTGTG 16911 276 1.15e-04 CTTTGCGTAC CGTCAAGAAATTGAAC TCGTTATTGA 14996 244 1.15e-04 CTGCAGCATC CCCGACACCAAATGAA CGTTTTATCT 17059 260 1.23e-04 CCTTTCCTGC CCAGAAAAGGAAGGAT CGCGCATCGC 39052 431 1.32e-04 TATATTGGTC CACACAGGCGATGGAA AGCATTCTAG 5128 3 1.52e-04 AT CAAAGAAGCAGAGGAT ATCAAGAAAA 47943 338 2.14e-04 TCGTTCGGAA GGAAGAGGAATTGAAA AAAAGGAATC 43579 465 2.43e-04 CATACTGCCT GAAGACAACATAAGAT ACAAGAAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21922 4.9e-08 376_[+3]_108 17029 3.5e-07 373_[+3]_111 47116 5.8e-07 50_[+3]_434 9235 6.8e-07 258_[+3]_226 51630 9.5e-07 233_[+3]_251 20335 1.8e-06 351_[+3]_133 41745 2e-06 52_[+3]_432 8000 2.6e-06 78_[+3]_406 54710 2.6e-06 353_[+3]_131 39714 3e-06 208_[+3]_276 50071 6.6e-06 366_[+3]_118 30585 6.6e-06 21_[+3]_463 43677 6.6e-06 72_[+3]_412 15354 6.6e-06 430_[+3]_54 48410 7.4e-06 32_[+3]_452 46132 9.3e-06 388_[+3]_96 44242 9.3e-06 330_[+3]_154 50103 1.6e-05 444_[+3]_40 48031 1.8e-05 18_[+3]_466 16364 2.9e-05 322_[+3]_162 14366 3.6e-05 415_[+3]_69 51277 4.3e-05 168_[+3]_316 39419 4.7e-05 319_[+3]_165 18579 5.1e-05 88_[+3]_396 55067 6.1e-05 361_[+3]_123 48338 6.1e-05 51_[+3]_433 47056 7.8e-05 390_[+3]_94 44446 8.4e-05 279_[+3]_205 15639 9.1e-05 412_[+3]_72 15019 9.1e-05 366_[+3]_118 47222 9.8e-05 449_[+3]_35 31465 9.8e-05 477_[+3]_7 16911 0.00011 275_[+3]_209 14996 0.00011 243_[+3]_241 17059 0.00012 259_[+3]_225 39052 0.00013 430_[+3]_54 5128 0.00015 2_[+3]_482 47943 0.00021 337_[+3]_147 43579 0.00024 464_[+3]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=39 21922 ( 377) CGAGAAGGAAAAGAAA 1 17029 ( 374) CGACGAAACAAAAGAA 1 47116 ( 51) CGAAAAGGAAATCGAA 1 9235 ( 259) CACGAAAACAAAAAAA 1 51630 ( 234) CGACAAACCAAATAAA 1 20335 ( 352) CGTCAAGCCAATCAAA 1 41745 ( 53) CGACACAACAAACGAT 1 8000 ( 79) GGAAAAAGCAAACAAA 1 54710 ( 354) CGAGAAGGAAAACGAC 1 39714 ( 209) CGTGAAAGCCATCAAA 1 50071 ( 367) CGCGGAACCAAAAAAA 1 30585 ( 22) CAAGACGACAAAGAAT 1 43677 ( 73) AGAAAAAGCAATAGAA 1 15354 ( 431) AGACGAAGCAAACGAA 1 48410 ( 33) CAAGAAACAAATTAAA 1 46132 ( 389) CGTCCAAGCAAATGAA 1 44242 ( 331) CATCCAAGCAAAAAAA 1 50103 ( 445) CCACAAAAAAATCCAA 1 48031 ( 19) AGAGAAGGAGAAGAAA 1 16364 ( 323) CGACAAGGAAGAAGAT 1 14366 ( 416) CAACAAGGGCATAGAA 1 51277 ( 169) CGTAAAAACATAAGAT 1 39419 ( 320) AGCCACAAAAAAGGAA 1 18579 ( 89) CGTCAAGTCCATCAAA 1 55067 ( 362) CGAGACGTAAATACAA 1 48338 ( 52) CGTGGAAAAGATCAAT 1 47056 ( 391) CAAGACGACGACCAAA 1 44446 ( 280) CAAGCCGAAAAAACAA 1 15639 ( 413) CATCAAAACCATTCAA 1 15019 ( 367) CGCAAAGGGAACGAAA 1 47222 ( 450) GGAGAAAAAAATCCAC 1 31465 ( 478) CACGGAAAGGAAGAAA 1 16911 ( 276) CGTCAAGAAATTGAAC 1 14996 ( 244) CCCGACACCAAATGAA 1 17059 ( 260) CCAGAAAAGGAAGGAT 1 39052 ( 431) CACACAGGCGATGGAA 1 5128 ( 3) CAAAGAAGCAGAGGAT 1 47943 ( 338) GGAAGAGGAATTGAAA 1 43579 ( 465) GAAGACAACATAAGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 22795 bayes= 9.41254 E= 1.6e-002 -140 172 -119 -1193 18 -165 139 -1193 112 -43 -1193 -13 -40 57 89 -1193 141 -124 -39 -1193 155 -24 -1193 -1193 112 -1193 81 -1193 60 -91 81 -230 41 115 -119 -1193 146 -124 -61 -1193 164 -1193 -219 -130 106 -224 -1193 61 6 35 27 -98 77 -91 81 -1193 188 -1193 -1193 -1193 141 -165 -1193 -30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 39 E= 1.6e-002 0.102564 0.794872 0.102564 0.000000 0.307692 0.076923 0.615385 0.000000 0.589744 0.179487 0.000000 0.230769 0.205128 0.358974 0.435897 0.000000 0.717949 0.102564 0.179487 0.000000 0.794872 0.205128 0.000000 0.000000 0.589744 0.000000 0.410256 0.000000 0.410256 0.128205 0.410256 0.051282 0.358974 0.538462 0.102564 0.000000 0.743590 0.102564 0.153846 0.000000 0.846154 0.000000 0.051282 0.102564 0.564103 0.051282 0.000000 0.384615 0.282051 0.307692 0.282051 0.128205 0.461538 0.128205 0.410256 0.000000 1.000000 0.000000 0.000000 0.000000 0.717949 0.076923 0.000000 0.205128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[GA][AT][GCA]A[AC][AG][AG][CA]AA[AT][CAG][AG]A[AT] -------------------------------------------------------------------------------- Time 61.71 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31465 1.90e-01 477_[+3(9.84e-05)]_7 9235 9.92e-06 258_[+3(6.81e-07)]_19_\ [+1(3.93e-06)]_191 36743 5.30e-01 500 37009 3.04e-03 134_[+1(5.12e-07)]_350 47056 9.26e-04 197_[+2(1.32e-06)]_181_\ [+3(7.75e-05)]_94 47116 4.02e-08 50_[+3(5.76e-07)]_307_\ [+2(6.74e-07)]_65_[+1(3.21e-06)]_34 54710 1.30e-04 353_[+3(2.65e-06)]_78_\ [+2(3.00e-06)]_41 14366 1.28e-05 361_[+1(4.19e-06)]_10_\ [+2(5.05e-06)]_16_[+3(3.56e-05)]_69 21922 9.02e-04 376_[+3(4.94e-08)]_108 47943 2.50e-02 500 14996 1.45e-05 135_[+2(5.05e-06)]_19_\ [+1(1.52e-06)]_318 48338 1.05e-03 51_[+3(6.06e-05)]_89_[+1(3.43e-06)]_\ 328 48410 5.02e-05 32_[+3(7.39e-06)]_204_\ [+2(1.10e-06)]_236 15019 3.81e-01 366_[+3(9.10e-05)]_118 5128 2.77e-04 109_[+1(1.54e-07)]_375 39052 1.70e-01 500 8000 2.15e-02 78_[+3(2.65e-06)]_406 15354 3.98e-04 135_[+1(3.67e-06)]_279_\ [+3(6.57e-06)]_54 39419 6.46e-02 319_[+3(4.70e-05)]_165 41745 1.10e-08 52_[+3(2.02e-06)]_13_[+2(1.59e-06)]_\ [+1(9.39e-08)]_391 43579 1.35e-01 500 43677 6.27e-03 72_[+3(6.57e-06)]_286_\ [+3(8.40e-05)]_110 15639 2.86e-01 412_[+3(9.10e-05)]_72 39714 1.28e-04 162_[+1(3.93e-06)]_30_\ [+3(3.04e-06)]_276 55067 1.11e-07 196_[+1(1.33e-07)]_149_\ [+3(6.06e-05)]_96_[+2(4.76e-07)]_15 30585 1.77e-03 21_[+3(6.57e-06)]_248_\ [+1(2.97e-05)]_82_[+3(8.40e-05)]_101 16364 1.87e-03 130_[+1(5.06e-06)]_176_\ [+3(2.94e-05)]_162 50071 2.64e-02 366_[+3(6.57e-06)]_118 50103 8.06e-05 113_[+2(1.10e-06)]_319_\ [+3(1.62e-05)]_40 51277 1.64e-03 168_[+3(4.29e-05)]_203_\ [+2(2.82e-06)]_101 16911 5.85e-02 500 18579 1.39e-03 88_[+3(5.12e-05)]_304_\ [+2(2.19e-06)]_80 44096 4.41e-06 254_[+1(5.31e-10)]_230 51630 1.73e-03 233_[+3(9.54e-07)]_251 44242 1.08e-02 330_[+3(9.32e-06)]_154 17059 2.41e-01 500 17029 3.99e-06 39_[+1(4.64e-07)]_318_\ [+3(3.51e-07)]_111 44311 3.98e-01 500 11088 1.70e-01 500 45715 4.25e-05 129_[+1(5.38e-05)]_13_\ [+2(1.23e-05)]_208_[+1(1.33e-07)]_106 20335 1.63e-07 127_[+1(3.21e-06)]_187_\ [+2(1.02e-06)]_9_[+3(1.76e-06)]_133 46132 4.98e-05 263_[+2(1.80e-06)]_113_\ [+3(9.32e-06)]_96 47222 4.61e-02 449_[+3(9.84e-05)]_35 44446 2.10e-08 279_[+3(8.40e-05)]_7_[+1(1.12e-07)]_\ 161_[+2(6.64e-08)]_9 37583 4.57e-03 195_[+1(3.77e-07)]_289 48031 1.47e-04 18_[+3(1.80e-05)]_82_[+2(4.73e-06)]_\ 372 34588 7.04e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************