******************************************************************************** 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/148/148.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 17555 1.0000 500 24772 1.0000 500 43029 1.0000 500 32202 1.0000 500 43222 1.0000 500 42051 1.0000 500 13538 1.0000 500 46908 1.0000 500 47067 1.0000 500 13581 1.0000 500 47829 1.0000 500 2271 1.0000 500 48391 1.0000 500 22597 1.0000 500 48756 1.0000 500 22803 1.0000 500 43285 1.0000 500 25183 1.0000 500 32550 1.0000 500 18241 1.0000 500 4025 1.0000 500 49134 1.0000 500 23059 1.0000 500 40200 1.0000 500 49522 1.0000 500 49533 1.0000 500 30514 1.0000 500 23472 1.0000 500 49783 1.0000 500 50302 1.0000 500 3140 1.0000 500 18551 1.0000 500 33633 1.0000 500 24238 1.0000 500 45306 1.0000 500 7664 1.0000 500 43855 1.0000 500 46394 1.0000 500 50024 1.0000 500 47133 1.0000 500 49748 1.0000 500 43683 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/148/148.seqs.fa -oc motifs/148 -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= 42 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= 21000 N= 42 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.247 G 0.232 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.247 G 0.232 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 11 llr = 152 E-value = 6.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :75::::::::2:::: pos.-specific C ::259::971:57:5a probability G a3121a:::62:15:: matrix T ::33::a13383255: 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 GAACCGTCCGTCCGCC consensus GTT TT T TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 24772 318 3.20e-09 TGACAAGTTT GAATCGTCCGTCCGTC GCATCCCAAC 23059 375 3.27e-08 TAGTTTCGAA GGAGCGTCCGTCCTCC GTCCTCACAT 17555 177 3.67e-08 GCTATGCCGA GACCCGTCCTTCCTCC TCCAAGGCTA 43855 282 1.09e-07 ATAGACTTGT GAACCGTCTGTCTTTC AGCTGGTGGC 18241 329 1.66e-07 TGCTGGTGAC GAAGCGTCTGTACGTC GCTATTCCGG 43222 361 2.63e-07 TTACCCAATA GATTCGTCTGTACTCC TATCAGCTAC 49134 110 2.85e-07 GATAAGGTTC GAGCCGTCCTGCCGCC TGGCAGGAGT 47829 135 4.71e-07 CCTCGGACGC GGTCCGTCCGTTGGTC CGTCGGAATC 30514 136 5.06e-07 CGGTTGGTTG GAATCGTTCGGCCGCC ACTCTCCCAG 49533 15 7.73e-07 TTTGGTTGAC GGTCCGTCCTTTTTCC TTTTGGGTTC 4025 421 1.73e-06 TCCGGCCTCC GACCGGTCCCTTCGTC TCCTGGCACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24772 3.2e-09 317_[+1]_167 23059 3.3e-08 374_[+1]_110 17555 3.7e-08 176_[+1]_308 43855 1.1e-07 281_[+1]_203 18241 1.7e-07 328_[+1]_156 43222 2.6e-07 360_[+1]_124 49134 2.8e-07 109_[+1]_375 47829 4.7e-07 134_[+1]_350 30514 5.1e-07 135_[+1]_349 49533 7.7e-07 14_[+1]_470 4025 1.7e-06 420_[+1]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=11 24772 ( 318) GAATCGTCCGTCCGTC 1 23059 ( 375) GGAGCGTCCGTCCTCC 1 17555 ( 177) GACCCGTCCTTCCTCC 1 43855 ( 282) GAACCGTCTGTCTTTC 1 18241 ( 329) GAAGCGTCTGTACGTC 1 43222 ( 361) GATTCGTCTGTACTCC 1 49134 ( 110) GAGCCGTCCTGCCGCC 1 47829 ( 135) GGTCCGTCCGTTGGTC 1 30514 ( 136) GAATCGTTCGGCCGCC 1 49533 ( 15) GGTCCGTCCTTTTTCC 1 4025 ( 421) GACCGGTCCCTTCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 20370 bayes= 10.4062 E= 6.8e-001 -1010 -1010 211 -1010 151 -1010 23 -1010 83 -44 -135 4 -1010 114 -35 4 -1010 188 -135 -1010 -1010 -1010 211 -1010 -1010 -1010 -1010 191 -1010 188 -1010 -155 -1010 156 -1010 4 -1010 -144 145 4 -1010 -1010 -35 162 -49 114 -1010 4 -1010 156 -135 -55 -1010 -1010 123 77 -1010 114 -1010 77 -1010 202 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 11 E= 6.8e-001 0.000000 0.000000 1.000000 0.000000 0.727273 0.000000 0.272727 0.000000 0.454545 0.181818 0.090909 0.272727 0.000000 0.545455 0.181818 0.272727 0.000000 0.909091 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.909091 0.000000 0.090909 0.000000 0.727273 0.000000 0.272727 0.000000 0.090909 0.636364 0.272727 0.000000 0.000000 0.181818 0.818182 0.181818 0.545455 0.000000 0.272727 0.000000 0.727273 0.090909 0.181818 0.000000 0.000000 0.545455 0.454545 0.000000 0.545455 0.000000 0.454545 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[AG][AT][CT]CGTC[CT][GT]T[CT]C[GT][CT]C -------------------------------------------------------------------------------- Time 16.60 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 40 llr = 339 E-value = 2.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 4756233a61265674 pos.-specific C 5131:57::654::21 probability G 133:4:1:::3:54:1 matrix T :::342::54::::14 bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 * Entropy 1.1 ** * * (12.2 bits) 0.8 * *** *** 0.6 ** * **** **** 0.4 *************** 0.2 **************** 0.0 ---------------- Multilevel CAAAGCCAACCAGAAA consensus AGCTTAA TTGCAGCT sequence G T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 50302 44 6.05e-07 TACGAGGGAA CAAATCCAACGAAAAC TATCACAGTC 47133 461 7.63e-07 CCAGGTTTAT AAGATCCAACGAGGAA AAATCTGCCG 40200 282 1.18e-06 CCTTGCAGTC CACAGCCATCCAGGCA CGCCTTATAT 24772 269 1.46e-06 TTGTATTTGA AAGATCCAACGCAAAT GTTGTCTATT 42051 299 1.78e-06 AGCTAACTGT AAAAGCAAACGCAAAT ACCAATAAGA 13581 91 2.61e-06 CGTGGCCAGA CGAATCAAACAAGAAA GCGCCCAAGG 43285 312 3.73e-06 TCTCCAACTC GAGATCCATCCAAAAT GAATACCGGT 4025 86 4.42e-06 GGCATTACCG CAGATACATCACGAAT CTCATGATGG 24238 118 8.32e-06 CATTCGGTCG CACTTTCATCCAGGAA GTTGGGTGTC 48391 324 8.32e-06 ATTCACAGGC AACAAACATCCAGGAT AGAGGGACCA 49533 58 9.63e-06 GTCTTTCCAC AGCTGCCAATCAAAAA TTTAAAATTA 22803 210 9.63e-06 TAGTGCAGCG CAACGCAATCGAGAAT ACGGCGCTTT 25183 454 1.11e-05 ATTCCGTCGT AACATCCATTCCGACT CGACGGGAGG 3140 293 1.46e-05 CCGTCACGGA AAGTGTCATCCAGGAA ATTGTGCAAG 50024 150 2.14e-05 TTTTTCACGG AAGATCAAACGAGGCT GTCTATCCAA 2271 242 3.06e-05 AGAACGGCAT CACATCCATACAAACA GAAGCAGCCG 43029 391 3.06e-05 GGCAAACACG CGCATCCATTCCAGAG CGGACCTGAC 47067 210 3.42e-05 GGAAGAGTGC CAACGTCATCCAAACA CGAACCATCT 49134 292 3.81e-05 CCCTCACTCT CACATCCATCACAACC GCTCCGTGTC 49522 407 4.24e-05 CCTGGCCTAC CAAAATCAATCAAATT CATTCGTTGA 32550 10 4.24e-05 TTTCCTCCA AACTACCATTGCGAAT TGCCTTACAC 32202 415 4.24e-05 ATAAATGGAA CCAAGAAAACCCAGAA TGTGTCTAAA 49783 341 5.21e-05 AATACCACCA CAAATGAAATCAAAAT GCCGTGTTTT 23059 223 5.75e-05 ATGGTGGTAC AACATCAAATGCAGCA ATAGTGGCGT 47829 74 5.75e-05 TGTGCCTGTC GAAAAACAATCAAAAG CTGAATAGGG 17555 392 6.34e-05 ATAAAGTTGG AGAAAAAAATAAGAAA CAGAGTTCGT 7664 389 6.96e-05 GTGTCCTTTC CGGTGACAATACGGAT TGGCGTGGAA 30514 24 7.64e-05 AAAGTGTATT CAGTGACAATCAGGCC GAACGTTGGA 22597 331 7.64e-05 TTGGCCAATT CACGGTCAACGAAAAA GTGGCTGTGG 18551 461 9.12e-05 GAGGTGATTT GACTGCAAATACGAAA AGCGAGCACA 49748 272 9.93e-05 TGGTCTAGAG AGGAGCAAACACAGAC CCGTATTGGG 23472 370 1.17e-04 TTACGAACCG AGATAAAATCCAAGAT TTGGGCGCTT 43683 386 1.84e-04 CCGAATCTGC GAAATACATCGCGATG GTGTGAGTTG 18241 355 2.25e-04 GCTATTCCGG AGACGACATCGAGGTA AAAGTTAAGG 45306 166 2.56e-04 GTAATTTGTC CGATGTGAATCCGGAT ATCCGGAATA 46908 6 2.89e-04 GAATC CGATGCCAATCCCAAC GTTCCGGTCT 48756 450 3.06e-04 GGAAGAAGGC CAACTCCAAAAAGACG ACGCCTTGCC 33633 353 4.90e-04 ACGACGATCC GGAAATGATCGAGGAA GAAGAGTTCA 46394 21 5.13e-04 CTACTTAGTA CCAAGACATAAAAATT CTGGAAAGTT 43222 431 5.61e-04 ATTCTCCTCT CCGAGTAAATCCGATG CCAGTGTTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50302 6e-07 43_[+2]_441 47133 7.6e-07 460_[+2]_24 40200 1.2e-06 281_[+2]_203 24772 1.5e-06 268_[+2]_216 42051 1.8e-06 298_[+2]_186 13581 2.6e-06 90_[+2]_394 43285 3.7e-06 311_[+2]_173 4025 4.4e-06 85_[+2]_399 24238 8.3e-06 117_[+2]_367 48391 8.3e-06 323_[+2]_161 49533 9.6e-06 57_[+2]_427 22803 9.6e-06 209_[+2]_275 25183 1.1e-05 453_[+2]_31 3140 1.5e-05 292_[+2]_192 50024 2.1e-05 149_[+2]_335 2271 3.1e-05 241_[+2]_243 43029 3.1e-05 390_[+2]_94 47067 3.4e-05 209_[+2]_275 49134 3.8e-05 291_[+2]_193 49522 4.2e-05 406_[+2]_78 32550 4.2e-05 9_[+2]_475 32202 4.2e-05 414_[+2]_70 49783 5.2e-05 340_[+2]_144 23059 5.8e-05 222_[+2]_262 47829 5.8e-05 73_[+2]_411 17555 6.3e-05 391_[+2]_93 7664 7e-05 388_[+2]_96 30514 7.6e-05 23_[+2]_461 22597 7.6e-05 330_[+2]_154 18551 9.1e-05 460_[+2]_24 49748 9.9e-05 271_[+2]_213 23472 0.00012 369_[+2]_115 43683 0.00018 385_[+2]_99 18241 0.00023 354_[+2]_130 45306 0.00026 165_[+2]_319 46908 0.00029 5_[+2]_479 48756 0.00031 449_[+2]_35 33633 0.00049 352_[+2]_132 46394 0.00051 20_[+2]_464 43222 0.00056 430_[+2]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=40 50302 ( 44) CAAATCCAACGAAAAC 1 47133 ( 461) AAGATCCAACGAGGAA 1 40200 ( 282) CACAGCCATCCAGGCA 1 24772 ( 269) AAGATCCAACGCAAAT 1 42051 ( 299) AAAAGCAAACGCAAAT 1 13581 ( 91) CGAATCAAACAAGAAA 1 43285 ( 312) GAGATCCATCCAAAAT 1 4025 ( 86) CAGATACATCACGAAT 1 24238 ( 118) CACTTTCATCCAGGAA 1 48391 ( 324) AACAAACATCCAGGAT 1 49533 ( 58) AGCTGCCAATCAAAAA 1 22803 ( 210) CAACGCAATCGAGAAT 1 25183 ( 454) AACATCCATTCCGACT 1 3140 ( 293) AAGTGTCATCCAGGAA 1 50024 ( 150) AAGATCAAACGAGGCT 1 2271 ( 242) CACATCCATACAAACA 1 43029 ( 391) CGCATCCATTCCAGAG 1 47067 ( 210) CAACGTCATCCAAACA 1 49134 ( 292) CACATCCATCACAACC 1 49522 ( 407) CAAAATCAATCAAATT 1 32550 ( 10) AACTACCATTGCGAAT 1 32202 ( 415) CCAAGAAAACCCAGAA 1 49783 ( 341) CAAATGAAATCAAAAT 1 23059 ( 223) AACATCAAATGCAGCA 1 47829 ( 74) GAAAAACAATCAAAAG 1 17555 ( 392) AGAAAAAAATAAGAAA 1 7664 ( 389) CGGTGACAATACGGAT 1 30514 ( 24) CAGTGACAATCAGGCC 1 22597 ( 331) CACGGTCAACGAAAAA 1 18551 ( 461) GACTGCAAATACGAAA 1 49748 ( 272) AGGAGCAAACACAGAC 1 23472 ( 370) AGATAAAATCCAAGAT 1 43683 ( 386) GAAATACATCGCGATG 1 18241 ( 355) AGACGACATCGAGGTA 1 45306 ( 166) CGATGTGAATCCGGAT 1 46908 ( 6) CGATGCCAATCCCAAC 1 48756 ( 450) CAACTCCAAAAAGACG 1 33633 ( 353) GGAAATGATCGAGGAA 1 46394 ( 21) CCAAGACATAAAAATT 1 43222 ( 431) CCGAGTAAATCCGATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 20370 bayes= 9.24139 E= 2.6e+001 46 109 -89 -1197 135 -172 24 -1197 82 28 11 -1197 129 -130 -321 -9 -54 -1197 87 59 11 102 -321 -41 23 140 -221 -1197 197 -1197 -1197 -1197 111 -1197 -1197 76 -177 116 -1197 50 -18 95 37 -1197 123 70 -1197 -1197 82 -330 118 -1197 123 -1197 78 -1197 135 -13 -1197 -109 55 -98 -89 50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 40 E= 2.6e+001 0.350000 0.525000 0.125000 0.000000 0.650000 0.075000 0.275000 0.000000 0.450000 0.300000 0.250000 0.000000 0.625000 0.100000 0.025000 0.250000 0.175000 0.000000 0.425000 0.400000 0.275000 0.500000 0.025000 0.200000 0.300000 0.650000 0.050000 0.000000 1.000000 0.000000 0.000000 0.000000 0.550000 0.000000 0.000000 0.450000 0.075000 0.550000 0.000000 0.375000 0.225000 0.475000 0.300000 0.000000 0.600000 0.400000 0.000000 0.000000 0.450000 0.025000 0.525000 0.000000 0.600000 0.000000 0.400000 0.000000 0.650000 0.225000 0.000000 0.125000 0.375000 0.125000 0.125000 0.375000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA][AG][ACG][AT][GT][CAT][CA]A[AT][CT][CGA][AC][GA][AG][AC][AT] -------------------------------------------------------------------------------- Time 33.24 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 11 llr = 143 E-value = 3.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 8611::a2:346::: pos.-specific C :2:4a:::a6::588 probability G ::1::a:4:16::2: matrix T 2285:::5:::45:2 bits 2.1 ** * 1.9 *** * 1.7 *** * 1.5 *** * Relative 1.3 * *** * ** Entropy 1.1 * * *** * ***** (18.8 bits) 0.8 * * *** ******* 0.6 ******* ******* 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel AATTCGATCCGATCC consensus C G AATC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 13581 48 1.05e-09 ACCGTAGAAT AATTCGATCCGATCC ATTTTTTTCG 49533 391 4.75e-09 AGCTGGATCC AATCCGATCCGATCC GATCCGATCT 47133 293 1.56e-07 TCCTGCTGAA ATTTCGATCAGATCC GGAGCAGCAT 22597 441 1.56e-07 TCAAGAGACA ACTTCGAACCGACCC GCATATTTGA 50302 280 7.50e-07 ATTTACATGA TATCCGAGCAAACCC GCAACTATCT 47829 383 8.16e-07 ATCCGATGTG ATTTCGAACCATCCC CCAGGGATTC 40200 377 1.40e-06 GGTCGATTGG AAGTCGATCCAACGC TGGACTGGTC 43285 474 1.40e-06 CCATTTTGCA AATACGAGCAGATCT CTTGTCGTAA 48391 31 1.49e-06 CGGTTCTTCT TATCCGAGCCGTCCT CCAAATTCAT 48756 196 1.60e-06 GACGCCCTCG AATCCGAGCGGTTGC GCCGTTACCT 25183 434 2.11e-06 CTCTCGTGCA ACATCGATCCATTCC GTCGTAACAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13581 1e-09 47_[+3]_438 49533 4.8e-09 390_[+3]_95 47133 1.6e-07 292_[+3]_193 22597 1.6e-07 440_[+3]_45 50302 7.5e-07 279_[+3]_206 47829 8.2e-07 382_[+3]_103 40200 1.4e-06 376_[+3]_109 43285 1.4e-06 473_[+3]_12 48391 1.5e-06 30_[+3]_455 48756 1.6e-06 195_[+3]_290 25183 2.1e-06 433_[+3]_52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=11 13581 ( 48) AATTCGATCCGATCC 1 49533 ( 391) AATCCGATCCGATCC 1 47133 ( 293) ATTTCGATCAGATCC 1 22597 ( 441) ACTTCGAACCGACCC 1 50302 ( 280) TATCCGAGCAAACCC 1 47829 ( 383) ATTTCGAACCATCCC 1 40200 ( 377) AAGTCGATCCAACGC 1 43285 ( 474) AATACGAGCAGATCT 1 48391 ( 31) TATCCGAGCCGTCCT 1 48756 ( 196) AATCCGAGCGGTTGC 1 25183 ( 434) ACATCGATCCATTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 20412 bayes= 11.2122 E= 3.7e+002 168 -1010 -1010 -55 132 -44 -1010 -55 -149 -1010 -135 162 -149 56 -1010 104 -1010 202 -1010 -1010 -1010 -1010 211 -1010 197 -1010 -1010 -1010 -49 -1010 65 77 -1010 202 -1010 -1010 10 137 -135 -1010 51 -1010 145 -1010 132 -1010 -1010 45 -1010 88 -1010 104 -1010 173 -35 -1010 -1010 173 -1010 -55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 11 E= 3.7e+002 0.818182 0.000000 0.000000 0.181818 0.636364 0.181818 0.000000 0.181818 0.090909 0.000000 0.090909 0.818182 0.090909 0.363636 0.000000 0.545455 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.363636 0.454545 0.000000 1.000000 0.000000 0.000000 0.272727 0.636364 0.090909 0.000000 0.363636 0.000000 0.636364 0.000000 0.636364 0.000000 0.000000 0.363636 0.000000 0.454545 0.000000 0.545455 0.000000 0.818182 0.181818 0.000000 0.000000 0.818182 0.000000 0.181818 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AAT[TC]CGA[TG]C[CA][GA][AT][TC]CC -------------------------------------------------------------------------------- Time 49.56 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17555 5.28e-05 176_[+1(3.67e-08)]_199_\ [+2(6.34e-05)]_93 24772 1.64e-07 268_[+2(1.46e-06)]_33_\ [+1(3.20e-09)]_167 43029 4.54e-02 390_[+2(3.06e-05)]_94 32202 8.18e-02 414_[+2(4.24e-05)]_70 43222 1.09e-04 360_[+1(2.63e-07)]_51_\ [+3(6.83e-05)]_58 42051 8.66e-03 298_[+2(1.78e-06)]_186 13538 3.51e-01 80_[+1(8.03e-05)]_404 46908 3.45e-01 500 47067 1.54e-02 209_[+2(3.42e-05)]_275 13581 8.42e-08 47_[+3(1.05e-09)]_28_[+2(2.61e-06)]_\ 394 47829 5.41e-07 73_[+2(5.75e-05)]_45_[+1(4.71e-07)]_\ 232_[+3(8.16e-07)]_103 2271 5.56e-03 241_[+2(3.06e-05)]_228_\ [+3(4.34e-05)] 48391 3.21e-05 30_[+3(1.49e-06)]_278_\ [+2(8.32e-06)]_161 22597 6.35e-05 330_[+2(7.64e-05)]_94_\ [+3(1.56e-07)]_45 48756 3.42e-04 50_[+1(7.55e-05)]_10_[+1(7.31e-05)]_\ 103_[+3(1.60e-06)]_290 22803 1.85e-02 209_[+2(9.63e-06)]_112_\ [+2(9.12e-05)]_147 43285 2.83e-05 311_[+2(3.73e-06)]_146_\ [+3(1.40e-06)]_12 25183 1.51e-04 433_[+3(2.11e-06)]_5_[+2(1.11e-05)]_\ 31 32550 1.95e-01 9_[+2(4.24e-05)]_475 18241 3.47e-04 328_[+1(1.66e-07)]_156 4025 4.78e-05 85_[+2(4.42e-06)]_319_\ [+1(1.73e-06)]_64 49134 4.75e-05 109_[+1(2.85e-07)]_166_\ [+2(3.81e-05)]_193 23059 4.92e-05 222_[+2(5.75e-05)]_136_\ [+1(3.27e-08)]_110 40200 3.49e-05 281_[+2(1.18e-06)]_79_\ [+3(1.40e-06)]_109 49522 6.56e-03 293_[+1(5.55e-05)]_97_\ [+2(4.24e-05)]_78 49533 1.50e-09 14_[+1(7.73e-07)]_27_[+2(9.63e-06)]_\ 317_[+3(4.75e-09)]_95 30514 4.41e-04 23_[+2(7.64e-05)]_96_[+1(5.06e-07)]_\ 349 23472 2.01e-01 500 49783 1.41e-01 340_[+2(5.21e-05)]_144 50302 4.54e-06 43_[+2(6.05e-07)]_220_\ [+3(7.50e-07)]_206 3140 2.75e-03 292_[+2(1.46e-05)]_19_\ [+2(8.35e-05)]_157 18551 9.31e-02 460_[+2(9.12e-05)]_24 33633 6.20e-01 500 24238 3.96e-02 117_[+2(8.32e-06)]_367 45306 1.96e-01 500 7664 1.55e-01 388_[+2(6.96e-05)]_96 43855 2.29e-03 281_[+1(1.09e-07)]_203 46394 2.80e-01 500 50024 2.21e-02 149_[+2(2.14e-05)]_335 47133 1.43e-06 117_[+3(4.97e-05)]_160_\ [+3(1.56e-07)]_153_[+2(7.63e-07)]_24 49748 9.50e-02 271_[+2(9.93e-05)]_213 43683 1.48e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************