******************************************************************************** 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/333/333.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11039 1.0000 500 11148 1.0000 500 11563 1.0000 500 14492 1.0000 500 1457 1.0000 500 18820 1.0000 500 20661 1.0000 500 20666 1.0000 500 20732 1.0000 500 24072 1.0000 500 24507 1.0000 500 24949 1.0000 500 25161 1.0000 500 25217 1.0000 500 25417 1.0000 500 262088 1.0000 500 268194 1.0000 500 268196 1.0000 500 269997 1.0000 500 30969 1.0000 500 36073 1.0000 500 36301 1.0000 500 37609 1.0000 500 5856 1.0000 500 5875 1.0000 500 9008 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/333/333.seqs.fa -oc motifs/333 -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= 26 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= 13000 N= 26 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.274 C 0.232 G 0.227 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.274 C 0.232 G 0.227 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 23 llr = 229 E-value = 6.2e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1421:1:2:::::::: pos.-specific C 643:734426571a:a probability G 2:1:13212::::::: matrix T 1149234364439:a: bits 2.1 * 1.9 *** 1.7 *** 1.5 **** Relative 1.3 * **** Entropy 1.1 * **** (14.4 bits) 0.9 ** ******* 0.6 ** ******* 0.4 ** ** * ******** 0.2 **************** 0.0 ---------------- Multilevel CATTCTCCTCCCTCTC consensus GCC GTT TTT sequence A CGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11148 181 6.98e-08 GGAAAGAAAG CCCTCCTCTCCTTCTC CAAATCTTCA 25217 481 1.83e-07 CATCAACACA CCCTCCCCCCTCTCTC CTTC 269997 371 3.60e-07 TTATCTCTCG CACTCTTTTTCTTCTC TTCTCGTCGT 24072 390 4.22e-07 TGTCTGAAGT CATTTGGCTCCCTCTC GGAGGGTGAG 25417 480 4.93e-07 ACCACTCTCT CTCTCCTCTTCCTCTC CCCAC 37609 215 1.01e-06 TTGCCAAGTC CAAACTTCTCCCTCTC GAAATCAATA 14492 229 2.76e-06 TTTCTTTACC CCCTCTGGTTCTTCTC CGAACGTCCG 20732 179 3.86e-06 AGAGAGCCAT CCTTCTCCGCCGTCTC GATGATGGAC 5856 459 4.31e-06 ACAACGCATC GCGTCCCCCCTCTCTC GGCACACATC 11563 209 6.53e-06 AGTGATATGT CTATCGCTGTTCTCTC GTATGATAAA 268194 192 7.20e-06 TCATCCTTGG AATTGTGCTCTCTCTC GAGCTGAGAG 262088 473 1.05e-05 ACTGATCAAA CAAACACATCCCTCTC TGAAATACCG 20666 371 1.05e-05 TGCGCAACGG TGCTCTCTTCCCTCTC CAACCCAAAG 20661 410 1.05e-05 GTCTGTCGCT CCTTCTTAGCTCCCTC CTGCGGACAC 1457 377 1.38e-05 CCTCATCTTG AATTGGCATCCTTCTC TACATGATTG 25161 228 2.10e-05 GAGCCGAACG CTTTTGTTCTTCTCTC CCCTCCGCCG 24949 36 2.27e-05 ATCCATATCG GAATTGGAGCCCTCTC TTAAGGTTTA 36301 115 3.09e-05 TCGGCAAGTT CCTACGCCTATTTCTC AAACACTGAT 24507 184 3.57e-05 AACTTTTACG AAGTTTTTTTTCTCTC AAAGATGACC 36073 485 5.06e-05 TATGTTGTTT GATTCCGTATTTTCTC 9008 175 7.42e-05 ATGTAGAACG TCTTGCTTTCACTCTC CACACCTGAG 268196 231 9.94e-05 AGATTGAGAA GAATCGTGCTTCCCTC GAGCTTATGG 18820 412 9.94e-05 TGGAATTCCC GCCTCACATTCTTCTG TACACTTAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11148 7e-08 180_[+1]_304 25217 1.8e-07 480_[+1]_4 269997 3.6e-07 370_[+1]_114 24072 4.2e-07 389_[+1]_95 25417 4.9e-07 479_[+1]_5 37609 1e-06 214_[+1]_270 14492 2.8e-06 228_[+1]_256 20732 3.9e-06 178_[+1]_306 5856 4.3e-06 458_[+1]_26 11563 6.5e-06 208_[+1]_276 268194 7.2e-06 191_[+1]_293 262088 1.1e-05 472_[+1]_12 20666 1.1e-05 370_[+1]_114 20661 1.1e-05 409_[+1]_75 1457 1.4e-05 376_[+1]_108 25161 2.1e-05 227_[+1]_257 24949 2.3e-05 35_[+1]_449 36301 3.1e-05 114_[+1]_370 24507 3.6e-05 183_[+1]_301 36073 5.1e-05 484_[+1] 9008 7.4e-05 174_[+1]_310 268196 9.9e-05 230_[+1]_254 18820 9.9e-05 411_[+1]_73 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=23 11148 ( 181) CCCTCCTCTCCTTCTC 1 25217 ( 481) CCCTCCCCCCTCTCTC 1 269997 ( 371) CACTCTTTTTCTTCTC 1 24072 ( 390) CATTTGGCTCCCTCTC 1 25417 ( 480) CTCTCCTCTTCCTCTC 1 37609 ( 215) CAAACTTCTCCCTCTC 1 14492 ( 229) CCCTCTGGTTCTTCTC 1 20732 ( 179) CCTTCTCCGCCGTCTC 1 5856 ( 459) GCGTCCCCCCTCTCTC 1 11563 ( 209) CTATCGCTGTTCTCTC 1 268194 ( 192) AATTGTGCTCTCTCTC 1 262088 ( 473) CAAACACATCCCTCTC 1 20666 ( 371) TGCTCTCTTCCCTCTC 1 20661 ( 410) CCTTCTTAGCTCCCTC 1 1457 ( 377) AATTGGCATCCTTCTC 1 25161 ( 228) CTTTTGTTCTTCTCTC 1 24949 ( 36) GAATTGGAGCCCTCTC 1 36301 ( 115) CCTACGCCTATTTCTC 1 24507 ( 184) AAGTTTTTTTTCTCTC 1 36073 ( 485) GATTCCGTATTTTCTC 1 9008 ( 175) TCTTGCTTTCACTCTC 1 268196 ( 231) GAATCGTGCTTCCCTC 1 18820 ( 412) GCCTCACATTCTTCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 12610 bayes= 9.49927 E= 6.2e-004 -107 128 -6 -161 67 75 -238 -103 -33 39 -139 55 -107 -1117 -1117 171 -1117 158 -80 -62 -165 17 42 38 -1117 75 -6 55 -33 75 -139 19 -265 -42 -39 119 -265 128 -1117 55 -265 117 -1117 71 -1117 149 -238 19 -1117 -142 -1117 178 -1117 211 -1117 -1117 -1117 -1117 -1117 191 -1117 204 -238 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 23 E= 6.2e-004 0.130435 0.565217 0.217391 0.086957 0.434783 0.391304 0.043478 0.130435 0.217391 0.304348 0.086957 0.391304 0.130435 0.000000 0.000000 0.869565 0.000000 0.695652 0.130435 0.173913 0.086957 0.260870 0.304348 0.347826 0.000000 0.391304 0.217391 0.391304 0.217391 0.391304 0.086957 0.304348 0.043478 0.173913 0.173913 0.608696 0.043478 0.565217 0.000000 0.391304 0.043478 0.521739 0.000000 0.434783 0.000000 0.652174 0.043478 0.304348 0.000000 0.086957 0.000000 0.913043 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.956522 0.043478 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][AC][TCA]TC[TGC][CTG][CTA]T[CT][CT][CT]TCTC -------------------------------------------------------------------------------- Time 6.16 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 13 llr = 157 E-value = 4.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:::3:22:1:2:21: pos.-specific C :5:2:12:1:::::32 probability G 75137:359:a11664 matrix T 2:95:944:9:792:5 bits 2.1 * 1.9 * 1.7 * * 1.5 * * *** * Relative 1.3 * * *** * Entropy 1.1 ** ** *** * (17.4 bits) 0.9 *** ** ***** * 0.6 ****** ********* 0.4 ****** ********* 0.2 **************** 0.0 ---------------- Multilevel GCTTGTTGGTGTTGGT consensus TG GA GT A ACG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 30969 259 2.24e-09 GGTTGACTTT GCTTGTGTGTGTTGGT GTCGTACGAT 20732 384 7.00e-09 TGGTTGAACT GCTTGTTGGTGTTGGC TGTGAAGAAA 14492 2 1.71e-08 C GGTTATGGGTGTTGGG GTGACGGCTG 5856 294 4.51e-07 AGTGAAGAAG GGTTATCTGTGTTAGT GCCAGCCTTG 18820 343 6.29e-07 AGCTACAAGG GCTCGTGTGTGTTTCT GTTATATATC 268194 163 7.65e-07 CAGAGTCGCC GCTGGTTGGTGAGGGT GTTTCATCCT 1457 257 1.07e-06 CAGATGCTGA GGTGGTGAGTGTTGAG AAGAGAAGGC 24072 290 3.07e-06 ACAGGTAATG TCTGATCGGTGTTACG ATGTACCTCC 37609 400 5.03e-06 CGCTCTTTAT TGTCGTAAGTGATGGT GTCAATCTGT 9008 200 5.41e-06 CCACACCTGA GGTTGCTTGAGTTGCG TTCAGGTACA 24949 413 5.77e-06 CACTTAGCCT TCGTGTTGCTGTTGGG CACGCTCCAT 20661 445 6.16e-06 CGAACACGAC GCTGGTAGGTGGTACC ACACGTCGCA 24507 263 7.78e-06 TATGTCATTT AGTTATTTGTGATTGT CACATCGATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 30969 2.2e-09 258_[+2]_226 20732 7e-09 383_[+2]_101 14492 1.7e-08 1_[+2]_483 5856 4.5e-07 293_[+2]_191 18820 6.3e-07 342_[+2]_142 268194 7.6e-07 162_[+2]_322 1457 1.1e-06 256_[+2]_228 24072 3.1e-06 289_[+2]_195 37609 5e-06 399_[+2]_85 9008 5.4e-06 199_[+2]_285 24949 5.8e-06 412_[+2]_72 20661 6.2e-06 444_[+2]_40 24507 7.8e-06 262_[+2]_222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=13 30969 ( 259) GCTTGTGTGTGTTGGT 1 20732 ( 384) GCTTGTTGGTGTTGGC 1 14492 ( 2) GGTTATGGGTGTTGGG 1 5856 ( 294) GGTTATCTGTGTTAGT 1 18820 ( 343) GCTCGTGTGTGTTTCT 1 268194 ( 163) GCTGGTTGGTGAGGGT 1 1457 ( 257) GGTGGTGAGTGTTGAG 1 24072 ( 290) TCTGATCGGTGTTACG 1 37609 ( 400) TGTCGTAAGTGATGGT 1 9008 ( 200) GGTTGCTTGAGTTGCG 1 24949 ( 413) TCGTGTTGCTGTTGGG 1 20661 ( 445) GCTGGTAGGTGGTACC 1 24507 ( 263) AGTTATTTGTGATTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 12610 bayes= 11.0856 E= 4.0e+000 -183 -1035 161 -21 -1035 121 102 -1035 -1035 -1035 -156 179 -1035 -59 44 101 17 -1035 161 -1035 -1035 -159 -1035 179 -83 -59 44 53 -83 -1035 102 53 -1035 -159 202 -1035 -183 -1035 -1035 179 -1035 -1035 214 -1035 -25 -1035 -156 138 -1035 -1035 -156 179 -25 -1035 144 -79 -183 41 144 -1035 -1035 -59 76 79 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 13 E= 4.0e+000 0.076923 0.000000 0.692308 0.230769 0.000000 0.538462 0.461538 0.000000 0.000000 0.000000 0.076923 0.923077 0.000000 0.153846 0.307692 0.538462 0.307692 0.000000 0.692308 0.000000 0.000000 0.076923 0.000000 0.923077 0.153846 0.153846 0.307692 0.384615 0.153846 0.000000 0.461538 0.384615 0.000000 0.076923 0.923077 0.000000 0.076923 0.000000 0.000000 0.923077 0.000000 0.000000 1.000000 0.000000 0.230769 0.000000 0.076923 0.692308 0.000000 0.000000 0.076923 0.923077 0.230769 0.000000 0.615385 0.153846 0.076923 0.307692 0.615385 0.000000 0.000000 0.153846 0.384615 0.461538 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][CG]T[TG][GA]T[TG][GT]GTG[TA]T[GA][GC][TG] -------------------------------------------------------------------------------- Time 12.63 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 26 llr = 214 E-value = 1.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:42:2::::25 pos.-specific C :8::92111:61 probability G 32:4:52::a:1 matrix T 5:5511798:24 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * * Relative 1.3 * * *** Entropy 1.1 * * *** (11.9 bits) 0.9 * * **** 0.6 *** * ***** 0.4 ***** ***** 0.2 ************ 0.0 ------------ Multilevel TCTTCGTTTGCA consensus G AG AT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 9008 322 6.58e-07 GATTTGTTCT TCAGCGTTTGCT GGACGTGGAT 36073 178 1.18e-06 CGTACTTCCA TCTGCGTTTGAA AAGGTTCTAT 14492 354 1.98e-06 CTTGCAGTTA GCTTCCTTTGCA GTTCTCTTGC 269997 163 2.84e-06 GTTTAAAATC TCTTCGTTTGTT TATTGTCGTC 5875 259 4.46e-06 CATCTCGTTC GCTTCGTTTGAT CAGCCACCGA 36301 327 4.46e-06 GTGTCTCGAC GCATCCTTTGCA TCCCAGCAAC 37609 87 7.52e-06 TACGTTGGAT GCAACGTTTGCT TGTTTGACTG 24072 210 8.57e-06 ACAGTGGTAA GCTTCTTTTGCA GGTGAAGATG 268196 59 1.62e-05 TGATGTGGTC TCAGCGTCTGCA CCAGCCAATA 25217 457 2.59e-05 TCCACACCAA TCTGCCTTCGCA GCCATCAACA 1457 54 3.47e-05 ACTTCCAACG ACATCATTTGCA AATCTATTAT 18820 134 4.65e-05 GGACATCAGT GCAGTGTTTGCT ACGGTACTTG 11148 120 6.09e-05 TGGAGTACGT TCTTCGCTCGCT CGGAAGCAGA 11039 40 7.15e-05 TGTCATATCT TCTTCCTTTGTC TGTTTTTATC 262088 40 9.75e-05 AGAGACTTTG TGTTCGGTTGTT TCGCTGTATT 25417 264 9.75e-05 GATGGTGGCA TGTTCGTTTGTG GTGGAGGCTC 25161 90 9.75e-05 TCGGCATCAT TGTGCATTTGCG AGAGAAGTTC 20666 443 1.08e-04 GGCTTCAGCT GCTTCACTTGAA GGCCAAACTT 30969 135 1.18e-04 GTAGACGCCT GCTTCGTTGGAA CACTGTGTAC 24949 236 1.31e-04 TTCTGTGGCG GGAACGTTTGTT ACGTAATTGT 20732 424 1.42e-04 CCAAATTTTT TCAGCAGTTGCC AGCCCACGCC 268194 54 1.88e-04 TACGGAGAAA AGAGCTTTTGCA AATGCAAGTC 5856 334 2.59e-04 TATCATGCAT TCAGTATTTGAT ATTGGGGTAC 11563 466 2.77e-04 GGGTGTATCT TCTACTGTTGAT TTGGAGAGAA 20661 40 5.67e-04 ACAACAACAC ACAGCCGCTGCA AGAGCACTTA 24507 319 7.77e-04 AATCCCACTA TCGACGCTCGCA CAAAGCCCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9008 6.6e-07 321_[+3]_167 36073 1.2e-06 177_[+3]_311 14492 2e-06 353_[+3]_135 269997 2.8e-06 162_[+3]_326 5875 4.5e-06 258_[+3]_230 36301 4.5e-06 326_[+3]_162 37609 7.5e-06 86_[+3]_402 24072 8.6e-06 209_[+3]_279 268196 1.6e-05 58_[+3]_430 25217 2.6e-05 456_[+3]_32 1457 3.5e-05 53_[+3]_435 18820 4.6e-05 133_[+3]_355 11148 6.1e-05 119_[+3]_369 11039 7.2e-05 39_[+3]_449 262088 9.8e-05 39_[+3]_449 25417 9.8e-05 263_[+3]_225 25161 9.8e-05 89_[+3]_399 20666 0.00011 442_[+3]_46 30969 0.00012 134_[+3]_354 24949 0.00013 235_[+3]_253 20732 0.00014 423_[+3]_65 268194 0.00019 53_[+3]_435 5856 0.00026 333_[+3]_155 11563 0.00028 465_[+3]_23 20661 0.00057 39_[+3]_449 24507 0.00078 318_[+3]_170 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=26 9008 ( 322) TCAGCGTTTGCT 1 36073 ( 178) TCTGCGTTTGAA 1 14492 ( 354) GCTTCCTTTGCA 1 269997 ( 163) TCTTCGTTTGTT 1 5875 ( 259) GCTTCGTTTGAT 1 36301 ( 327) GCATCCTTTGCA 1 37609 ( 87) GCAACGTTTGCT 1 24072 ( 210) GCTTCTTTTGCA 1 268196 ( 59) TCAGCGTCTGCA 1 25217 ( 457) TCTGCCTTCGCA 1 1457 ( 54) ACATCATTTGCA 1 18820 ( 134) GCAGTGTTTGCT 1 11148 ( 120) TCTTCGCTCGCT 1 11039 ( 40) TCTTCCTTTGTC 1 262088 ( 40) TGTTCGGTTGTT 1 25417 ( 264) TGTTCGTTTGTG 1 25161 ( 90) TGTGCATTTGCG 1 20666 ( 443) GCTTCACTTGAA 1 30969 ( 135) GCTTCGTTGGAA 1 24949 ( 236) GGAACGTTTGTT 1 20732 ( 424) TCAGCAGTTGCC 1 268194 ( 54) AGAGCTTTTGCA 1 5856 ( 334) TCAGTATTTGAT 1 11563 ( 466) TCTACTGTTGAT 1 20661 ( 40) ACAGCCGCTGCA 1 24507 ( 319) TCGACGCTCGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 12714 bayes= 8.93074 E= 1.7e+001 -125 -1134 61 101 -1134 180 -24 -1134 63 -1134 -256 101 -83 -1134 76 79 -1134 199 -1134 -179 -51 -27 114 -121 -1134 -101 -56 146 -1134 -159 -1134 179 -1134 -101 -256 167 -1134 -1134 214 -1134 -25 131 -1134 -47 75 -159 -156 53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 26 E= 1.7e+001 0.115385 0.000000 0.346154 0.538462 0.000000 0.807692 0.192308 0.000000 0.423077 0.000000 0.038462 0.538462 0.153846 0.000000 0.384615 0.461538 0.000000 0.923077 0.000000 0.076923 0.192308 0.192308 0.500000 0.115385 0.000000 0.115385 0.153846 0.730769 0.000000 0.076923 0.000000 0.923077 0.000000 0.115385 0.038462 0.846154 0.000000 0.000000 1.000000 0.000000 0.230769 0.576923 0.000000 0.192308 0.461538 0.076923 0.076923 0.384615 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TG]C[TA][TG]CGTTTG[CA][AT] -------------------------------------------------------------------------------- Time 18.96 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11039 1.62e-01 39_[+3(7.15e-05)]_449 11148 1.09e-04 119_[+3(6.09e-05)]_49_\ [+1(6.98e-08)]_304 11563 6.07e-03 208_[+1(6.53e-06)]_276 14492 3.70e-09 1_[+2(1.71e-08)]_211_[+1(2.76e-06)]_\ 93_[+3(1.85e-05)]_4_[+3(1.98e-06)]_135 1457 9.13e-06 53_[+3(3.47e-05)]_191_\ [+2(1.07e-06)]_104_[+1(1.38e-05)]_108 18820 4.12e-05 133_[+3(4.65e-05)]_197_\ [+2(6.29e-07)]_53_[+1(9.94e-05)]_73 20661 3.38e-04 409_[+1(1.05e-05)]_19_\ [+2(6.16e-06)]_40 20666 2.42e-03 370_[+1(1.05e-05)]_114 20732 1.08e-07 178_[+1(3.86e-06)]_189_\ [+2(7.00e-09)]_101 24072 2.95e-07 209_[+3(8.57e-06)]_68_\ [+2(3.07e-06)]_84_[+1(4.22e-07)]_95 24507 1.43e-03 183_[+1(3.57e-05)]_63_\ [+2(7.78e-06)]_222 24949 1.92e-04 35_[+1(2.27e-05)]_361_\ [+2(5.77e-06)]_72 25161 1.76e-02 89_[+3(9.75e-05)]_126_\ [+1(2.10e-05)]_257 25217 8.25e-05 456_[+3(2.59e-05)]_12_\ [+1(1.83e-07)]_4 25417 1.64e-04 263_[+3(9.75e-05)]_204_\ [+1(4.93e-07)]_5 262088 9.13e-03 39_[+3(9.75e-05)]_311_\ [+1(5.06e-05)]_94_[+1(1.05e-05)]_12 268194 1.64e-05 162_[+2(7.65e-07)]_13_\ [+1(7.20e-06)]_293 268196 8.28e-03 58_[+3(1.62e-05)]_160_\ [+1(9.94e-05)]_254 269997 1.39e-05 162_[+3(2.84e-06)]_196_\ [+1(3.60e-07)]_114 30969 5.33e-06 258_[+2(2.24e-09)]_226 36073 2.45e-04 177_[+3(1.18e-06)]_295_\ [+1(5.06e-05)] 36301 1.24e-03 114_[+1(3.09e-05)]_196_\ [+3(4.46e-06)]_162 37609 9.01e-07 86_[+3(7.52e-06)]_116_\ [+1(1.01e-06)]_169_[+2(5.03e-06)]_85 5856 8.58e-06 293_[+2(4.51e-07)]_149_\ [+1(4.31e-06)]_26 5875 2.16e-02 258_[+3(4.46e-06)]_230 9008 5.02e-06 33_[+3(1.85e-05)]_62_[+2(9.82e-05)]_\ 51_[+1(7.42e-05)]_9_[+2(5.41e-06)]_106_[+3(6.58e-07)]_167 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************