******************************************************************************** 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/406/406.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10191 1.0000 500 11654 1.0000 500 11794 1.0000 500 11796 1.0000 500 11927 1.0000 500 12118 1.0000 500 2006 1.0000 500 20907 1.0000 500 20979 1.0000 500 21439 1.0000 500 21651 1.0000 500 21807 1.0000 500 23901 1.0000 500 24497 1.0000 500 24955 1.0000 500 25079 1.0000 500 25164 1.0000 500 25347 1.0000 500 25749 1.0000 500 263012 1.0000 500 263911 1.0000 500 264783 1.0000 500 268335 1.0000 500 2957 1.0000 500 3065 1.0000 500 3517 1.0000 500 36368 1.0000 500 4143 1.0000 500 4726 1.0000 500 4834 1.0000 500 5778 1.0000 500 9257 1.0000 500 988 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/406/406.seqs.fa -oc motifs/406 -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= 33 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= 16500 N= 33 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.225 G 0.243 T 0.272 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.225 G 0.243 T 0.272 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 33 llr = 277 E-value = 3.9e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::41::21:: pos.-specific C 1::::1::::12 probability G 6:2a3:743258 matrix T 2a8:4926574: bits 2.1 1.9 * 1.7 * * 1.5 * * Relative 1.3 * * * * Entropy 1.1 *** ** * (12.1 bits) 0.9 *** *** * 0.6 **** *** *** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GTTGATGTTTGG consensus T G T TGGGT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 5778 472 6.32e-07 GAGATGCTCT GTTGTTGTTTTG CAAATGATCA 2957 472 6.32e-07 GAGATGCTCT GTTGTTGTTTTG CAAATGATCA 21439 293 1.06e-06 GCTTGGTGTT GTTGTTGGTTTG GTTGTTTCGT 3065 50 1.39e-06 GCGTGTCGAT GTTGATGTGTTG TACTGTATCA 263012 395 1.39e-06 TCAACTATGT GTTGATGTGTTG GAAAAAACTG 3517 138 1.63e-06 GTTAGGTTGT GTTGTTGGGTGG GATGGAACAC 988 304 3.25e-06 TCGTCTCATG GTGGATGTTTTG TGATTGTTCG 263911 228 4.23e-06 TGATTTCAAG GTGGGTGTTTGG TGCTGGTCAT 11654 34 6.75e-06 TGTGGTGTGG GTTGATGTGGGG AGGTGTAGTG 9257 109 7.51e-06 GAGAGACGAG GTTGTTGTTTCG GCCGACGCCG 10191 202 7.51e-06 CCCAGCAGAC GTTGATTGTTTG TGCCCTTCCC 11794 306 1.16e-05 CTCGTTTGAG GTTGATGTGTGC GACGATGAGG 24497 37 1.40e-05 GGGTTGTGTG GTTGGTGGTTTC TTTCATTGAA 11796 256 1.71e-05 GAAGAGAGGT GTTGGTGTTAGG GGGCGTCCAA 25347 165 2.74e-05 GACGTTGTGA GTTGATTGATGG AGACAAACAT 36368 110 3.59e-05 GATGGTACAA CTTGTTGGTGGG ACGACGCTTC 25164 122 4.03e-05 TGTCGATCAT TTTGGTGGATTG CTGGTATAAA 25079 155 4.49e-05 TATGAGTTCA TTTGGTTTGTGG CGCCTGTTGA 4143 307 7.22e-05 TGACTGCAGT TTTGGTGTAGGG TGTAGGGCGG 4834 289 8.74e-05 CACTGGAGAA GTGGTTGGTGGC GATTGTGATG 21807 308 8.74e-05 ACCAACACGA TTGGTTGTTTTC TCAGGGTCAC 23901 184 9.43e-05 ACCTCCTTCG TTTGTTTTTTCG GTTCACCCTT 4726 133 1.33e-04 CATCTGTGCC GTTGTCTTGTGG TTTGGCTTGC 20907 47 1.41e-04 GGAGGAGGAA CTTGATTGTTGC TGCTGCTGCT 24955 367 1.52e-04 GTCCGTCCAC CTTGGTTGATGG CCTCGTTCCT 2006 395 1.52e-04 GCCGGACGAA TTGGGTGGGTGC TGTGCCATCT 21651 115 1.63e-04 TTTCTTTCTT GTTGAAGTTAGG AGAACCACTC 12118 310 1.86e-04 TTACTACTAC TTGGACGTTTTG TGCTCAATTG 268335 113 2.14e-04 GAGAAACAAC CTTGGTTGGGTG TCCGTAGAGG 264783 256 3.76e-04 GTCAGAATGT GTTGTAGTTCTG GACACAACAA 11927 290 4.48e-04 AAGAATATAA TTGGATGGAGCG AGGGCGCCTC 25749 176 6.98e-04 AGATCATCGA GTGGTTGTGAGA AGGCAGCAGC 20979 255 1.11e-03 TAGCAGATCA GATGATAGTGTG AAATTAGATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5778 6.3e-07 471_[+1]_17 2957 6.3e-07 471_[+1]_17 21439 1.1e-06 292_[+1]_196 3065 1.4e-06 49_[+1]_439 263012 1.4e-06 394_[+1]_94 3517 1.6e-06 137_[+1]_351 988 3.3e-06 303_[+1]_185 263911 4.2e-06 227_[+1]_261 11654 6.7e-06 33_[+1]_455 9257 7.5e-06 108_[+1]_380 10191 7.5e-06 201_[+1]_287 11794 1.2e-05 305_[+1]_183 24497 1.4e-05 36_[+1]_452 11796 1.7e-05 255_[+1]_233 25347 2.7e-05 164_[+1]_324 36368 3.6e-05 109_[+1]_379 25164 4e-05 121_[+1]_367 25079 4.5e-05 154_[+1]_334 4143 7.2e-05 306_[+1]_182 4834 8.7e-05 288_[+1]_200 21807 8.7e-05 307_[+1]_181 23901 9.4e-05 183_[+1]_305 4726 0.00013 132_[+1]_356 20907 0.00014 46_[+1]_442 24955 0.00015 366_[+1]_122 2006 0.00015 394_[+1]_94 21651 0.00016 114_[+1]_374 12118 0.00019 309_[+1]_179 268335 0.00021 112_[+1]_376 264783 0.00038 255_[+1]_233 11927 0.00045 289_[+1]_199 25749 0.0007 175_[+1]_313 20979 0.0011 254_[+1]_234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=33 5778 ( 472) GTTGTTGTTTTG 1 2957 ( 472) GTTGTTGTTTTG 1 21439 ( 293) GTTGTTGGTTTG 1 3065 ( 50) GTTGATGTGTTG 1 263012 ( 395) GTTGATGTGTTG 1 3517 ( 138) GTTGTTGGGTGG 1 988 ( 304) GTGGATGTTTTG 1 263911 ( 228) GTGGGTGTTTGG 1 11654 ( 34) GTTGATGTGGGG 1 9257 ( 109) GTTGTTGTTTCG 1 10191 ( 202) GTTGATTGTTTG 1 11794 ( 306) GTTGATGTGTGC 1 24497 ( 37) GTTGGTGGTTTC 1 11796 ( 256) GTTGGTGTTAGG 1 25347 ( 165) GTTGATTGATGG 1 36368 ( 110) CTTGTTGGTGGG 1 25164 ( 122) TTTGGTGGATTG 1 25079 ( 155) TTTGGTTTGTGG 1 4143 ( 307) TTTGGTGTAGGG 1 4834 ( 289) GTGGTTGGTGGC 1 21807 ( 308) TTGGTTGTTTTC 1 23901 ( 184) TTTGTTTTTTCG 1 4726 ( 133) GTTGTCTTGTGG 1 20907 ( 47) CTTGATTGTTGC 1 24955 ( 367) CTTGGTTGATGG 1 2006 ( 395) TTGGGTGGGTGC 1 21651 ( 115) GTTGAAGTTAGG 1 12118 ( 310) TTGGACGTTTTG 1 268335 ( 113) CTTGGTTGGGTG 1 264783 ( 256) GTTGTAGTTCTG 1 11927 ( 290) TTGGATGGAGCG 1 25749 ( 176) GTGGTTGTGAGA 1 20979 ( 255) GATGATAGTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 16137 bayes= 8.96621 E= 3.9e-005 -1169 -89 139 -17 -309 -1169 -1169 183 -1169 -1169 0 148 -1169 -1169 204 -1169 49 -1169 17 42 -210 -189 -1169 169 -309 -1169 158 -17 -1169 -1169 80 108 -78 -1169 32 100 -151 -289 -20 129 -1169 -131 100 64 -309 -31 170 -1169 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 33 E= 3.9e-005 0.000000 0.121212 0.636364 0.242424 0.030303 0.000000 0.000000 0.969697 0.000000 0.000000 0.242424 0.757576 0.000000 0.000000 1.000000 0.000000 0.363636 0.000000 0.272727 0.363636 0.060606 0.060606 0.000000 0.878788 0.030303 0.000000 0.727273 0.242424 0.000000 0.000000 0.424242 0.575758 0.151515 0.000000 0.303030 0.545455 0.090909 0.030303 0.212121 0.666667 0.000000 0.090909 0.484848 0.424242 0.030303 0.181818 0.787879 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT]T[TG]G[ATG]T[GT][TG][TG][TG][GT]G -------------------------------------------------------------------------------- Time 9.55 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 24 llr = 229 E-value = 1.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::1::1:::2:: pos.-specific C 5a148:478:93 probability G ::::::3:11:: matrix T 5:86294317:6 bits 2.1 * 1.9 * 1.7 * * 1.5 * * Relative 1.3 * * ** * Entropy 1.1 ****** ** * (13.7 bits) 0.9 ****** ** ** 0.6 ****** ***** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCTTCTCCCTCT consensus T CT TT A C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 4143 262 4.35e-08 AACTACCCTG CCTTCTCCCTCT CGCCCGGGAA 20907 16 1.49e-07 CTTCCCATGA TCTTCTCCCTCT ACGTCGTATG 4834 455 6.83e-07 CGATCTCCTT TCTCCTTCCTCT TGCATTACTG 3517 435 9.87e-07 AAGGATCTTC TCTCCTGCCTCT CTTCAGCTAC 263012 473 1.29e-06 GTCTGATCCA TCTTCTCTCTCT CCGTCACACA 20979 217 3.34e-06 TCTAACCATC TCTCCTTCCACT TTTCTTTGCG 24497 184 3.74e-06 GAAAGCGAGC TCATCTCCCTCT CCACAGTTCA 4726 258 5.27e-06 GATGCGAAGT TCTTCTGCCACC TCTCGTCGGC 988 480 7.23e-06 TTCCTTCCAC CCCCCTTCCTCT CATCCAACG 25079 458 7.90e-06 AACTAACACC CCTTCTTCTTCT AATCAACCAA 2006 78 1.07e-05 TTTAGAAAAA CCTTTTCTCTCC TTCACATGCA 264783 404 1.42e-05 CTGTCTCTTG CCATCTCTCTCC TCGGCCACGA 263911 258 2.05e-05 ATTTGTCATT TCTCTTGTCTCT GTTGATATCC 10191 234 2.26e-05 CATGCCAGCA TCTTCTTCCTTT ACATTTTCCC 12118 466 3.15e-05 GGAAGTTCTC CCTTCTGCCTGC GCTGCTCAAT 36368 290 3.97e-05 TTCAGCAATG CCTCCACCCGCC TACCGGTTCG 21651 405 4.61e-05 GTTCCTCGCT CCTCCTGCCACG GCTCCCGACG 24955 261 4.92e-05 TTGGTTGTCC CCTTTTTCTTCC CGTTCAATGT 11927 334 4.92e-05 GGTGGAGTCC CCCTTTCCCACT GTAAATCAGT 3065 115 6.13e-05 TACGTATTGA TCTTCTTCGGCC CTGTTTGACA 23901 145 6.59e-05 CTTCGTACGC TCACCTCTCGCT CTCGTCTCGA 25347 401 7.04e-05 GCGCGCTGCG CCTCCTTTGACT TAAAATACCT 25164 63 7.04e-05 TTGTATGGTA CCTTGATCCTCT TTGAGGTTCG 268335 467 8.58e-05 TTTCGCTCAC CCTTTAGTCTCC TCAACTTCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4143 4.3e-08 261_[+2]_227 20907 1.5e-07 15_[+2]_473 4834 6.8e-07 454_[+2]_34 3517 9.9e-07 434_[+2]_54 263012 1.3e-06 472_[+2]_16 20979 3.3e-06 216_[+2]_272 24497 3.7e-06 183_[+2]_305 4726 5.3e-06 257_[+2]_231 988 7.2e-06 479_[+2]_9 25079 7.9e-06 457_[+2]_31 2006 1.1e-05 77_[+2]_411 264783 1.4e-05 403_[+2]_85 263911 2.1e-05 257_[+2]_231 10191 2.3e-05 233_[+2]_255 12118 3.1e-05 465_[+2]_23 36368 4e-05 289_[+2]_199 21651 4.6e-05 404_[+2]_84 24955 4.9e-05 260_[+2]_228 11927 4.9e-05 333_[+2]_155 3065 6.1e-05 114_[+2]_374 23901 6.6e-05 144_[+2]_344 25347 7e-05 400_[+2]_88 25164 7e-05 62_[+2]_426 268335 8.6e-05 466_[+2]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=24 4143 ( 262) CCTTCTCCCTCT 1 20907 ( 16) TCTTCTCCCTCT 1 4834 ( 455) TCTCCTTCCTCT 1 3517 ( 435) TCTCCTGCCTCT 1 263012 ( 473) TCTTCTCTCTCT 1 20979 ( 217) TCTCCTTCCACT 1 24497 ( 184) TCATCTCCCTCT 1 4726 ( 258) TCTTCTGCCACC 1 988 ( 480) CCCCCTTCCTCT 1 25079 ( 458) CCTTCTTCTTCT 1 2006 ( 78) CCTTTTCTCTCC 1 264783 ( 404) CCATCTCTCTCC 1 263911 ( 258) TCTCTTGTCTCT 1 10191 ( 234) TCTTCTTCCTTT 1 12118 ( 466) CCTTCTGCCTGC 1 36368 ( 290) CCTCCACCCGCC 1 21651 ( 405) CCTCCTGCCACG 1 24955 ( 261) CCTTTTTCTTCC 1 11927 ( 334) CCCTTTCCCACT 1 3065 ( 115) TCTTCTTCGGCC 1 23901 ( 145) TCACCTCTCGCT 1 25347 ( 401) CCTCCTTTGACT 1 25164 ( 63) CCTTGATCCTCT 1 268335 ( 467) CCTTTAGTCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 16137 bayes= 9.83901 E= 1.3e-002 -1123 126 -1123 75 -1123 215 -1123 -1123 -105 -143 -1123 154 -1123 73 -1123 120 -1123 173 -254 -38 -105 -1123 -1123 169 -1123 73 4 46 -1123 165 -1123 10 -1123 189 -154 -171 -32 -1123 -96 129 -1123 202 -254 -270 -1123 56 -254 120 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 24 E= 1.3e-002 0.000000 0.541667 0.000000 0.458333 0.000000 1.000000 0.000000 0.000000 0.125000 0.083333 0.000000 0.791667 0.000000 0.375000 0.000000 0.625000 0.000000 0.750000 0.041667 0.208333 0.125000 0.000000 0.000000 0.875000 0.000000 0.375000 0.250000 0.375000 0.000000 0.708333 0.000000 0.291667 0.000000 0.833333 0.083333 0.083333 0.208333 0.000000 0.125000 0.666667 0.000000 0.916667 0.041667 0.041667 0.000000 0.333333 0.041667 0.625000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]CT[TC][CT]T[CTG][CT]C[TA]C[TC] -------------------------------------------------------------------------------- Time 19.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 12 llr = 177 E-value = 1.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :37843255392644a385:9 pos.-specific C 8623187347:23:3:8::a: probability G 312:1::11:17223::1::1 matrix T ::::4:21:::::4:::25:: bits 2.1 * 1.9 * * 1.7 * * 1.5 * * ** Relative 1.3 * * * * ** ** Entropy 1.1 * * * ** ** ** (21.3 bits) 0.9 ** * ** *** ****** 0.6 **** ** ***** ****** 0.4 **** **************** 0.2 ********************* 0.0 --------------------- Multilevel CCAAACCAACAGAAAACAACA consensus GA CTA CCA CTC A T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5778 206 1.19e-11 GAAAATTCAT CCAATCCACCAGATGACAACA GCACCATCGC 2957 206 1.19e-11 GAAAATTCAT CCAATCCACCAGATGACAACA GCACCATCGC 9257 467 6.47e-09 CTACCAAGAA CAACACCACAAGGACACATCA GAGTAGTAGC 24497 232 3.33e-08 AGCCAAGAAG CAAAAACAACAGCAAACAACG CCACTGCACC 21807 363 6.46e-08 CGTGCCCCCC CCGAACAGCCAGAGCACAACA ACATGCCAGA 11796 274 8.42e-08 TAGGGGGCGT CCAAACCAAAGAAAAAAATCA TAGTAGTCAT 25749 457 9.19e-08 CAGCTGACAT CCAAGACCGCAGCTGACATCA TTCACGACAT 23901 210 1.76e-07 ACCCTTCAAA GAACTCTCAAAGGAAACAACA CGCGTTTATA 3517 461 2.94e-07 AGCTACCTCT GCCATCTTCCACATCACATCA CACCCATCAA 4143 395 3.39e-07 AGGAGTCGGA CGAACCCCACACCTCACTACA CCCGCACGTT 36368 358 7.24e-07 AATACAGGGA GAGCTCCAAAAGAAAAAGTCA ATTTCCCATT 3065 202 1.45e-06 GGGAGAGGCA CCCAAAACACAAAGAAATTCA CTGTTGAGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5778 1.2e-11 205_[+3]_274 2957 1.2e-11 205_[+3]_274 9257 6.5e-09 466_[+3]_13 24497 3.3e-08 231_[+3]_248 21807 6.5e-08 362_[+3]_117 11796 8.4e-08 273_[+3]_206 25749 9.2e-08 456_[+3]_23 23901 1.8e-07 209_[+3]_270 3517 2.9e-07 460_[+3]_19 4143 3.4e-07 394_[+3]_85 36368 7.2e-07 357_[+3]_122 3065 1.4e-06 201_[+3]_278 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=12 5778 ( 206) CCAATCCACCAGATGACAACA 1 2957 ( 206) CCAATCCACCAGATGACAACA 1 9257 ( 467) CAACACCACAAGGACACATCA 1 24497 ( 232) CAAAAACAACAGCAAACAACG 1 21807 ( 363) CCGAACAGCCAGAGCACAACA 1 11796 ( 274) CCAAACCAAAGAAAAAAATCA 1 25749 ( 457) CCAAGACCGCAGCTGACATCA 1 23901 ( 210) GAACTCTCAAAGGAAACAACA 1 3517 ( 461) GCCATCTTCCACATCACATCA 1 4143 ( 395) CGAACCCCACACCTCACTACA 1 36368 ( 358) GAGCTCCAAAAGAAAAAGTCA 1 3065 ( 202) CCCAAAACACAAAGAAATTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15840 bayes= 10.813 E= 1.3e-001 -1023 173 4 -1023 36 137 -154 -1023 136 -44 -54 -1023 153 15 -1023 -1023 68 -143 -154 61 -5 173 -1023 -1023 -64 156 -1023 -71 95 56 -154 -170 95 89 -154 -1023 36 156 -1023 -1023 182 -1023 -154 -1023 -64 -44 145 -1023 117 15 -54 -1023 68 -1023 -54 61 68 56 4 -1023 195 -1023 -1023 -1023 -5 173 -1023 -1023 153 -1023 -154 -71 95 -1023 -1023 88 -1023 215 -1023 -1023 182 -1023 -154 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 12 E= 1.3e-001 0.000000 0.750000 0.250000 0.000000 0.333333 0.583333 0.083333 0.000000 0.666667 0.166667 0.166667 0.000000 0.750000 0.250000 0.000000 0.000000 0.416667 0.083333 0.083333 0.416667 0.250000 0.750000 0.000000 0.000000 0.166667 0.666667 0.000000 0.166667 0.500000 0.333333 0.083333 0.083333 0.500000 0.416667 0.083333 0.000000 0.333333 0.666667 0.000000 0.000000 0.916667 0.000000 0.083333 0.000000 0.166667 0.166667 0.666667 0.000000 0.583333 0.250000 0.166667 0.000000 0.416667 0.000000 0.166667 0.416667 0.416667 0.333333 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.750000 0.000000 0.083333 0.166667 0.500000 0.000000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.916667 0.000000 0.083333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][CA]A[AC][AT][CA]C[AC][AC][CA]AG[AC][AT][ACG]A[CA]A[AT]CA -------------------------------------------------------------------------------- Time 28.16 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10191 1.26e-04 201_[+1(7.51e-06)]_20_\ [+2(2.26e-05)]_255 11654 7.56e-02 33_[+1(6.75e-06)]_53_[+1(7.86e-05)]_\ 390 11794 3.42e-02 305_[+1(1.16e-05)]_183 11796 4.04e-05 255_[+1(1.71e-05)]_6_[+3(8.42e-08)]_\ 206 11927 6.74e-02 333_[+2(4.92e-05)]_155 12118 9.32e-03 465_[+2(3.15e-05)]_23 2006 7.71e-03 41_[+2(8.05e-05)]_24_[+2(1.07e-05)]_\ 240_[+2(7.55e-05)]_159 20907 2.69e-04 15_[+2(1.49e-07)]_473 20979 5.17e-03 216_[+2(3.34e-06)]_272 21439 9.54e-03 292_[+1(1.06e-06)]_196 21651 1.24e-02 404_[+2(4.61e-05)]_84 21807 5.62e-05 307_[+1(8.74e-05)]_43_\ [+3(6.46e-08)]_117 23901 1.74e-05 144_[+2(6.59e-05)]_27_\ [+1(9.43e-05)]_14_[+3(1.76e-07)]_270 24497 5.43e-08 36_[+1(1.40e-05)]_135_\ [+2(3.74e-06)]_36_[+3(3.33e-08)]_110_[+2(1.89e-05)]_126 24955 1.16e-02 260_[+2(4.92e-05)]_228 25079 3.86e-03 154_[+1(4.49e-05)]_291_\ [+2(7.90e-06)]_31 25164 7.74e-03 62_[+2(7.04e-05)]_47_[+1(4.03e-05)]_\ 367 25347 6.98e-03 164_[+1(2.74e-05)]_224_\ [+2(7.04e-05)]_88 25749 6.38e-04 456_[+3(9.19e-08)]_23 263012 3.51e-05 394_[+1(1.39e-06)]_48_\ [+2(9.67e-06)]_6_[+2(1.29e-06)]_16 263911 1.11e-03 73_[+1(2.74e-05)]_142_\ [+1(4.23e-06)]_18_[+2(2.05e-05)]_231 264783 1.34e-02 65_[+2(9.76e-05)]_326_\ [+2(1.42e-05)]_85 268335 7.19e-02 466_[+2(8.58e-05)]_22 2957 4.94e-10 205_[+3(1.19e-11)]_245_\ [+1(6.32e-07)]_17 3065 2.55e-06 49_[+1(1.39e-06)]_53_[+2(6.13e-05)]_\ 75_[+3(1.45e-06)]_278 3517 1.65e-08 137_[+1(1.63e-06)]_285_\ [+2(9.87e-07)]_14_[+3(2.94e-07)]_19 36368 1.68e-05 109_[+1(3.59e-05)]_168_\ [+2(3.97e-05)]_56_[+3(7.24e-07)]_122 4143 3.42e-08 261_[+2(4.35e-08)]_33_\ [+1(7.22e-05)]_76_[+3(3.39e-07)]_85 4726 2.26e-03 257_[+2(5.27e-06)]_231 4834 3.42e-04 190_[+2(4.92e-05)]_86_\ [+1(8.74e-05)]_154_[+2(6.83e-07)]_34 5778 6.01e-10 205_[+3(1.19e-11)]_245_\ [+1(6.32e-07)]_17 9257 9.59e-07 30_[+3(7.59e-05)]_57_[+1(7.51e-06)]_\ 346_[+3(6.47e-09)]_13 988 1.57e-04 303_[+1(3.25e-06)]_150_\ [+2(5.73e-05)]_2_[+2(7.23e-06)]_9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************