******************************************************************************** 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/325/325.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10223 1.0000 500 10398 1.0000 500 13308 1.0000 500 13326 1.0000 500 20696 1.0000 500 21311 1.0000 500 2137 1.0000 500 21670 1.0000 500 23441 1.0000 500 2375 1.0000 500 261002 1.0000 500 261614 1.0000 500 264034 1.0000 500 269953 1.0000 500 32827 1.0000 500 35740 1.0000 500 36477 1.0000 500 39592 1.0000 500 41246 1.0000 500 4136 1.0000 500 5706 1.0000 500 6217 1.0000 500 6295 1.0000 500 8698 1.0000 500 9866 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/325/325.seqs.fa -oc motifs/325 -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= 25 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= 12500 N= 25 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.239 G 0.234 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.239 G 0.234 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 20 llr = 239 E-value = 2.0e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :2519316812a255: pos.-specific C 673a:4a51a81661a probability G 2:1::1::2::::::: matrix T 322:23::::::2:41 bits 2.1 1.9 1.7 * * * * * 1.5 * * * * * Relative 1.3 ** * *** * Entropy 1.0 ** ** *** * * (17.3 bits) 0.8 * ** ****** * * 0.6 ** ** ********** 0.4 ** ** ********** 0.2 **************** 0.0 ---------------- Multilevel CCACACCAACCACCAC consensus TTC A C A AAT sequence T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 261614 448 3.31e-09 GACGCAACAA CCACACCCACCACAAC CGTTGGCTGT 9866 477 1.31e-07 ACCCTTCATC TCTCAACAACCACAAC CCTCGACG 8698 476 1.31e-07 AAGCGCCTTC CCTCACCAACCAAAAC CTTCTCCTG 21670 151 2.18e-07 CCCACGAACA GCACATCAACCATCAC GAGATTGAAA 13308 152 2.18e-07 CCCACGAACA GCACATCAACCATCAC GAGATTGAAA 21311 7 5.11e-07 CTTCTG CACCACCCACCAACTC CCTCAACAAC 36477 68 6.43e-07 CTTCGCAACG CCAAATCCACCACCTC CTGACTGCTT 269953 22 7.89e-07 TGGTGGGAAA CAACAACAACAACAAC AACATGGTGA 20696 421 8.61e-07 CTCCTTCCCT CCCCAGCCACAACCAC CTCCCCTCCC 6217 150 9.33e-07 GTGCACTGAA CTACATCACCCACATC GTACGAACGA 5706 366 1.01e-06 TTCTTGCCCC CCTCTCCCGCCACCTC TTCGTCAGTG 39592 446 1.50e-06 CCAGAACTAA CCGCAACCACAACATC ATGAGAGTGC 2375 418 1.50e-06 GACCCTCATG GTACACCACCCACCAC TCCTCATTTG 13326 189 1.50e-06 ATCACAGCAG CATCAACAACAACAAC GAGAGGGGAG 261002 130 1.79e-06 CTACTCATTT TCACATCAAACACAAC AGACTCACCT 10398 311 1.97e-06 GGGCGTCGCT TCCCTACCACCACCCC ACCCCTTCTT 32827 452 4.84e-06 CTCCGTCGTC TCCCACCCACCAACTT TGGCTCAGTA 264034 458 8.48e-06 AGCCAACTGG CCCCAACAACCCAACC ACCCGCCAGC 23441 409 1.09e-05 CAGTTCATAT TTACTTCAGCCATCTC CGTCGAGTCA 4136 465 1.48e-05 ACGCATTCAA CTCCACACGCCATCTC TGGAAAAGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261614 3.3e-09 447_[+1]_37 9866 1.3e-07 476_[+1]_8 8698 1.3e-07 475_[+1]_9 21670 2.2e-07 150_[+1]_334 13308 2.2e-07 151_[+1]_333 21311 5.1e-07 6_[+1]_478 36477 6.4e-07 67_[+1]_417 269953 7.9e-07 21_[+1]_463 20696 8.6e-07 420_[+1]_64 6217 9.3e-07 149_[+1]_335 5706 1e-06 365_[+1]_119 39592 1.5e-06 445_[+1]_39 2375 1.5e-06 417_[+1]_67 13326 1.5e-06 188_[+1]_296 261002 1.8e-06 129_[+1]_355 10398 2e-06 310_[+1]_174 32827 4.8e-06 451_[+1]_33 264034 8.5e-06 457_[+1]_27 23441 1.1e-05 408_[+1]_76 4136 1.5e-05 464_[+1]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=20 261614 ( 448) CCACACCCACCACAAC 1 9866 ( 477) TCTCAACAACCACAAC 1 8698 ( 476) CCTCACCAACCAAAAC 1 21670 ( 151) GCACATCAACCATCAC 1 13308 ( 152) GCACATCAACCATCAC 1 21311 ( 7) CACCACCCACCAACTC 1 36477 ( 68) CCAAATCCACCACCTC 1 269953 ( 22) CAACAACAACAACAAC 1 20696 ( 421) CCCCAGCCACAACCAC 1 6217 ( 150) CTACATCACCCACATC 1 5706 ( 366) CCTCTCCCGCCACCTC 1 39592 ( 446) CCGCAACCACAACATC 1 2375 ( 418) GTACACCACCCACCAC 1 13326 ( 189) CATCAACAACAACAAC 1 261002 ( 130) TCACATCAAACACAAC 1 10398 ( 311) TCCCTACCACCACCCC 1 32827 ( 452) TCCCACCCACCAACTT 1 264034 ( 458) CCCCAACAACCCAACC 1 23441 ( 409) TTACTTCAGCCATCTC 1 4136 ( 465) CTCCACACGCCATCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 12125 bayes= 9.49331 E= 2.0e-014 -1097 133 -64 -5 -84 144 -1097 -37 75 33 -223 -37 -242 199 -1097 -1097 166 -1097 -1097 -78 16 55 -223 21 -242 199 -1097 -1097 104 91 -1097 -1097 148 -126 -64 -1097 -242 199 -1097 -1097 -42 174 -1097 -1097 182 -225 -1097 -1097 -42 133 -1097 -37 75 120 -1097 -1097 90 -126 -1097 63 -1097 199 -1097 -237 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 20 E= 2.0e-014 0.000000 0.600000 0.150000 0.250000 0.150000 0.650000 0.000000 0.200000 0.450000 0.300000 0.050000 0.200000 0.050000 0.950000 0.000000 0.000000 0.850000 0.000000 0.000000 0.150000 0.300000 0.350000 0.050000 0.300000 0.050000 0.950000 0.000000 0.000000 0.550000 0.450000 0.000000 0.000000 0.750000 0.100000 0.150000 0.000000 0.050000 0.950000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.950000 0.050000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.450000 0.550000 0.000000 0.000000 0.500000 0.100000 0.000000 0.400000 0.000000 0.950000 0.000000 0.050000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CT][ACT]CA[CAT]C[AC]AC[CA]A[CAT][CA][AT]C -------------------------------------------------------------------------------- Time 6.20 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 25 llr = 226 E-value = 7.6e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :5::3:21::23 pos.-specific C :::1:212:::: probability G a2:87255:a54 matrix T :3a::623a:22 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 GATGGTGGTGGG consensus T AGAT AA sequence G T TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 13326 237 8.98e-08 GGGTTCGAGA GATGGTGGTGGA TCTAATTATC 269953 7 1.67e-07 TGTTTT GTTGGTGGTGGG AAACAACAAC 21311 217 2.09e-06 CTCATGCTTG GTTGGTTGTGGG GAGAGCGGGT 6217 350 4.21e-06 GGAAATTGGT GATGGTGATGGG TGTTTTAAGT 32827 128 4.21e-06 TGGTCATCGT GATGGTGTTGTA CTGTTATTGG 10398 117 4.21e-06 CGGTTGTGTT GGTGGGGTTGGG TGCTCGCGTA 261614 8 4.95e-06 AATGATT GATGATTGTGGG AAGCCGATGC 23441 258 6.83e-06 GTGCATTTCT GGTGGTTGTGGT GCGATTGTTG 5706 178 1.05e-05 GCAAGGACTG GTTGGTGCTGTG AAATACGAGA 261002 102 1.93e-05 AGGGGGGGGT GATGATAGTGTG TCATTGCTAC 21670 13 1.93e-05 GTAGGTTGTA GATGGTCTTGGA GGTGCAGGAG 13308 14 1.93e-05 GTAGGTTGTA GATGGTCTTGGA GGTGCAGGAG 20696 85 2.46e-05 AATGATCTCC GTTGATGTTGAG TTGATGGCAC 9866 134 3.03e-05 TAATAGAAGC GTTGGCGCTGGA GTGGGAGGGA 36477 315 3.31e-05 GGCGTCAGCT GGTGGTACTGGT AGAAAAGCTT 35740 243 3.31e-05 CAGTGAAGGC GGTGGCTGTGGT GGCGATCAAG 39592 127 4.39e-05 CTTCATGGTT GATGACGGTGTT TGTTGTAGTG 6295 85 5.23e-05 CGACCTTAGA GTTCGGGGTGGT ACGCTTGAAA 4136 165 6.57e-05 GGGAGCCAAA GGTGACGGTGAA GGAGGGATTG 10223 108 9.34e-05 ACAAGCACTA GATCGTATTGAG GATGTGAGCA 264034 234 1.28e-04 GGTATTGTAT GGTGGTGGCGAA AGCGAAAGCA 2137 143 1.28e-04 GTCGTTTCCG GTTGAGGATGTG CTTGTGAGCG 2375 168 1.51e-04 ACTTCATCGA GATCGGATTGAG ATGTAGCGGA 8698 181 1.59e-04 CATACTTTAC GATGAGTCTGAT GTACTCTATC 41246 98 2.46e-04 GCGAAGAGAG GATAGGAGTGTA TCATTTGCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13326 9e-08 236_[+2]_252 269953 1.7e-07 6_[+2]_482 21311 2.1e-06 216_[+2]_272 6217 4.2e-06 349_[+2]_139 32827 4.2e-06 127_[+2]_361 10398 4.2e-06 116_[+2]_372 261614 5e-06 7_[+2]_481 23441 6.8e-06 257_[+2]_231 5706 1.1e-05 177_[+2]_311 261002 1.9e-05 101_[+2]_387 21670 1.9e-05 12_[+2]_476 13308 1.9e-05 13_[+2]_475 20696 2.5e-05 84_[+2]_404 9866 3e-05 133_[+2]_355 36477 3.3e-05 314_[+2]_174 35740 3.3e-05 242_[+2]_246 39592 4.4e-05 126_[+2]_362 6295 5.2e-05 84_[+2]_404 4136 6.6e-05 164_[+2]_324 10223 9.3e-05 107_[+2]_381 264034 0.00013 233_[+2]_255 2137 0.00013 142_[+2]_346 2375 0.00015 167_[+2]_321 8698 0.00016 180_[+2]_308 41246 0.00025 97_[+2]_391 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=25 13326 ( 237) GATGGTGGTGGA 1 269953 ( 7) GTTGGTGGTGGG 1 21311 ( 217) GTTGGTTGTGGG 1 6217 ( 350) GATGGTGATGGG 1 32827 ( 128) GATGGTGTTGTA 1 10398 ( 117) GGTGGGGTTGGG 1 261614 ( 8) GATGATTGTGGG 1 23441 ( 258) GGTGGTTGTGGT 1 5706 ( 178) GTTGGTGCTGTG 1 261002 ( 102) GATGATAGTGTG 1 21670 ( 13) GATGGTCTTGGA 1 13308 ( 14) GATGGTCTTGGA 1 20696 ( 85) GTTGATGTTGAG 1 9866 ( 134) GTTGGCGCTGGA 1 36477 ( 315) GGTGGTACTGGT 1 35740 ( 243) GGTGGCTGTGGT 1 39592 ( 127) GATGACGGTGTT 1 6295 ( 85) GTTCGGGGTGGT 1 4136 ( 165) GGTGACGGTGAA 1 10223 ( 108) GATCGTATTGAG 1 264034 ( 234) GGTGGTGGCGAA 1 2137 ( 143) GTTGAGGATGTG 1 2375 ( 168) GATCGGATTGAG 1 8698 ( 181) GATGAGTCTGAT 1 41246 ( 98) GATAGGAGTGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 12225 bayes= 10.0652 E= 7.6e-008 -1129 -1129 209 -1129 84 -1129 3 11 -1129 -1129 -1129 195 -274 -99 184 -1129 6 -1129 162 -1129 -1129 -58 3 121 -42 -158 115 -37 -174 -58 103 11 -1129 -258 -1129 189 -1129 -1129 209 -1129 -16 -1129 115 -11 25 -1129 91 -11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 25 E= 7.6e-008 0.000000 0.000000 1.000000 0.000000 0.480000 0.000000 0.240000 0.280000 0.000000 0.000000 0.000000 1.000000 0.040000 0.120000 0.840000 0.000000 0.280000 0.000000 0.720000 0.000000 0.000000 0.160000 0.240000 0.600000 0.200000 0.080000 0.520000 0.200000 0.080000 0.160000 0.480000 0.280000 0.000000 0.040000 0.000000 0.960000 0.000000 0.000000 1.000000 0.000000 0.240000 0.000000 0.520000 0.240000 0.320000 0.000000 0.440000 0.240000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[ATG]TG[GA][TG][GAT][GT]TG[GAT][GAT] -------------------------------------------------------------------------------- Time 11.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 25 llr = 235 E-value = 1.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :12::1::321::211 pos.-specific C 27445337:592:625 probability G 1:1::::1:::1:::: matrix T 7246467273:8a284 bits 2.1 1.9 * 1.7 * 1.5 * * Relative 1.3 * * Entropy 1.0 * *** * (13.5 bits) 0.8 ** *** *** * 0.6 ** ************* 0.4 ** ************* 0.2 **************** 0.0 ---------------- Multilevel TCCTCTTCTCCTTCTC consensus CTTCTCCTAT T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 6217 440 2.37e-07 CCACGGCAGC TCTTCCTCTTCTTTTT GACCATTGGT 269953 228 2.76e-07 GGTACACTAC TCCCCTCCTCCTTCCC TTTCTAACCA 20696 404 3.22e-07 CTCCTGTCCC TCTCCTCCTCCTTCCC TCCCCAGCCA 2375 66 1.46e-06 TTCCCACTAC GCTTTCTCTTCTTCTT CGTAGGCCCA 23441 450 1.46e-06 GACACACACA TCATCATCACCTTCTC CGCACCAATC 41246 297 2.37e-06 AGCATTCATC TTACCTTCTCCTTCTA TAATTTTATC 21670 220 2.37e-06 ACGCTTTGAG TCCTTTTTATCTTATC GGTAGAGAAT 13308 221 2.37e-06 ACGCTTTGAG TCCTTTTTATCTTATC GGTAGAGAAT 36477 418 2.99e-06 TCACACATCC TCCCTTCCTCCCTCCC TCCCTCCCTG 6295 465 4.66e-06 AAATGGAAGA GCCCTTTCACCTTTTT GCCCCGACAG 21311 264 5.79e-06 AAAAGGTTGT TTTTATTCTTCTTCTT TCGAACTTCG 5706 17 1.43e-05 AAAGAAGTCA CACTCCTTTTCTTCTT GGAGACCTTT 4136 435 1.43e-05 CGGAGTTGTG TCGTCTCCTACTTTTA GGAGACGCAT 261002 396 1.43e-05 CGGATCGCCT TCTTTTGGTTCTTCTC GTTTCTTGTG 261614 195 1.89e-05 ATGATCTTAG TCCTTCTTTCCTTAAT CTATGTCATA 8698 304 2.07e-05 GTCGTACCAT TCCTCCCCTCTCTCTC GTCATTGCAC 2137 26 2.07e-05 GGATAGCACG CATTCTTCTTCGTCTT GTTGTGTATG 35740 384 4.82e-05 GGTACCGTCG TCATTTTGTACTTTTA TTTAAAGACG 10398 341 5.65e-05 CTTCTTCGGA TTGCCACCTCCCTCTC TGCCACCGTC 10223 338 6.58e-05 GACCAGAAAT TCTCCCTTTCATTCAT ATTCCTTTAT 13326 367 8.24e-05 ATTTTGTATC CTATTTTCACCGTTTC TAAGTATTGT 9866 29 1.02e-04 GGGAATGCCA CCTCTTCTACCCTCCT CTGGATCGGT 39592 308 1.35e-04 CAATCAGATT CACCGTTCAACTTCTT TCGCATTGCT 32827 255 1.64e-04 GACGACTGTT TCTGTGTCAACTTTTC CACGTAGGAA 264034 312 3.40e-04 GGGGGCTAGT TTGACCTCTCATTATC CCTTAGTTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6217 2.4e-07 439_[+3]_45 269953 2.8e-07 227_[+3]_257 20696 3.2e-07 403_[+3]_81 2375 1.5e-06 65_[+3]_419 23441 1.5e-06 449_[+3]_35 41246 2.4e-06 296_[+3]_188 21670 2.4e-06 219_[+3]_265 13308 2.4e-06 220_[+3]_264 36477 3e-06 417_[+3]_67 6295 4.7e-06 464_[+3]_20 21311 5.8e-06 263_[+3]_221 5706 1.4e-05 16_[+3]_468 4136 1.4e-05 434_[+3]_50 261002 1.4e-05 395_[+3]_89 261614 1.9e-05 194_[+3]_290 8698 2.1e-05 303_[+3]_181 2137 2.1e-05 25_[+3]_459 35740 4.8e-05 383_[+3]_101 10398 5.6e-05 340_[+3]_144 10223 6.6e-05 337_[+3]_147 13326 8.2e-05 366_[+3]_118 9866 0.0001 28_[+3]_456 39592 0.00013 307_[+3]_177 32827 0.00016 254_[+3]_230 264034 0.00034 311_[+3]_173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=25 6217 ( 440) TCTTCCTCTTCTTTTT 1 269953 ( 228) TCCCCTCCTCCTTCCC 1 20696 ( 404) TCTCCTCCTCCTTCCC 1 2375 ( 66) GCTTTCTCTTCTTCTT 1 23441 ( 450) TCATCATCACCTTCTC 1 41246 ( 297) TTACCTTCTCCTTCTA 1 21670 ( 220) TCCTTTTTATCTTATC 1 13308 ( 221) TCCTTTTTATCTTATC 1 36477 ( 418) TCCCTTCCTCCCTCCC 1 6295 ( 465) GCCCTTTCACCTTTTT 1 21311 ( 264) TTTTATTCTTCTTCTT 1 5706 ( 17) CACTCCTTTTCTTCTT 1 4136 ( 435) TCGTCTCCTACTTTTA 1 261002 ( 396) TCTTTTGGTTCTTCTC 1 261614 ( 195) TCCTTCTTTCCTTAAT 1 8698 ( 304) TCCTCCCCTCTCTCTC 1 2137 ( 26) CATTCTTCTTCGTCTT 1 35740 ( 384) TCATTTTGTACTTTTA 1 10398 ( 341) TTGCCACCTCCCTCTC 1 10223 ( 338) TCTCCCTTTCATTCAT 1 13326 ( 367) CTATTTTCACCGTTTC 1 9866 ( 29) CCTCTTCTACCCTCCT 1 39592 ( 308) CACCGTTCAACTTCTT 1 32827 ( 255) TCTGTGTCAACTTTTC 1 264034 ( 312) TTGACCTCTCATTATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 12125 bayes= 8.91886 E= 1.7e-001 -1129 -26 -155 148 -116 151 -1129 -37 -74 59 -96 48 -274 59 -255 111 -274 101 -255 77 -174 23 -255 121 -1129 23 -255 139 -1129 151 -155 -11 25 -1129 -1129 139 -74 112 -1129 31 -174 188 -1129 -269 -1129 -58 -155 156 -1129 -1129 -1129 195 -74 133 -1129 -11 -174 -58 -1129 156 -116 101 -1129 63 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 25 E= 1.7e-001 0.000000 0.200000 0.080000 0.720000 0.120000 0.680000 0.000000 0.200000 0.160000 0.360000 0.120000 0.360000 0.040000 0.360000 0.040000 0.560000 0.040000 0.480000 0.040000 0.440000 0.080000 0.280000 0.040000 0.600000 0.000000 0.280000 0.040000 0.680000 0.000000 0.680000 0.080000 0.240000 0.320000 0.000000 0.000000 0.680000 0.160000 0.520000 0.000000 0.320000 0.080000 0.880000 0.000000 0.040000 0.000000 0.160000 0.080000 0.760000 0.000000 0.000000 0.000000 1.000000 0.160000 0.600000 0.000000 0.240000 0.080000 0.160000 0.000000 0.760000 0.120000 0.480000 0.000000 0.400000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC][CT][CT][TC][CT][TC][TC][CT][TA][CT]CTT[CT]T[CT] -------------------------------------------------------------------------------- Time 16.98 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10223 1.92e-02 107_[+2(9.34e-05)]_218_\ [+3(6.58e-05)]_147 10398 8.38e-06 116_[+2(4.21e-06)]_182_\ [+1(1.97e-06)]_14_[+3(5.65e-05)]_106_[+1(2.60e-05)]_22 13308 2.66e-07 13_[+2(1.93e-05)]_126_\ [+1(2.18e-07)]_53_[+3(2.37e-06)]_264 13326 2.89e-07 188_[+1(1.50e-06)]_32_\ [+2(8.98e-08)]_118_[+3(8.24e-05)]_118 20696 1.89e-07 84_[+2(2.46e-05)]_307_\ [+3(3.22e-07)]_1_[+1(8.61e-07)]_64 21311 1.74e-07 6_[+1(5.11e-07)]_194_[+2(2.09e-06)]_\ 35_[+3(5.79e-06)]_221 2137 5.85e-03 25_[+3(2.07e-05)]_459 21670 2.66e-07 12_[+2(1.93e-05)]_126_\ [+1(2.18e-07)]_53_[+3(2.37e-06)]_265 23441 2.30e-06 257_[+2(6.83e-06)]_139_\ [+1(1.09e-05)]_25_[+3(1.46e-06)]_35 2375 6.01e-06 65_[+3(1.46e-06)]_263_\ [+3(4.82e-05)]_57_[+1(1.50e-06)]_67 261002 8.84e-06 101_[+2(1.93e-05)]_16_\ [+1(1.79e-06)]_250_[+3(1.43e-05)]_89 261614 1.11e-08 7_[+2(4.95e-06)]_175_[+3(1.89e-05)]_\ 237_[+1(3.31e-09)]_37 264034 2.38e-03 457_[+1(8.48e-06)]_27 269953 1.55e-09 6_[+2(1.67e-07)]_3_[+1(7.89e-07)]_\ 190_[+3(2.76e-07)]_79_[+3(5.65e-05)]_162 32827 4.64e-05 127_[+2(4.21e-06)]_312_\ [+1(4.84e-06)]_33 35740 1.81e-03 242_[+2(3.31e-05)]_129_\ [+3(4.82e-05)]_101 36477 1.42e-06 67_[+1(6.43e-07)]_231_\ [+2(3.31e-05)]_91_[+3(2.99e-06)]_67 39592 1.08e-04 126_[+2(4.39e-05)]_307_\ [+1(1.50e-06)]_39 41246 4.40e-03 296_[+3(2.37e-06)]_188 4136 1.62e-04 164_[+2(6.57e-05)]_258_\ [+3(1.43e-05)]_14_[+1(1.48e-05)]_20 5706 3.10e-06 16_[+3(1.43e-05)]_70_[+2(3.98e-05)]_\ 63_[+2(1.05e-05)]_176_[+1(1.01e-06)]_119 6217 3.08e-08 149_[+1(9.33e-07)]_184_\ [+2(4.21e-06)]_78_[+3(2.37e-07)]_45 6295 3.28e-03 84_[+2(5.23e-05)]_368_\ [+3(4.66e-06)]_20 8698 7.57e-06 303_[+3(2.07e-05)]_156_\ [+1(1.31e-07)]_9 9866 7.26e-06 133_[+2(3.03e-05)]_331_\ [+1(1.31e-07)]_8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************