******************************************************************************** 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/329/329.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11025 1.0000 500 14096 1.0000 500 1477 1.0000 500 1692 1.0000 500 19158 1.0000 500 21598 1.0000 500 21602 1.0000 500 2178 1.0000 500 2217 1.0000 500 2219 1.0000 500 23751 1.0000 500 23837 1.0000 500 23906 1.0000 500 24993 1.0000 500 2523 1.0000 500 25652 1.0000 500 2605 1.0000 500 261802 1.0000 500 264633 1.0000 500 268574 1.0000 500 269210 1.0000 500 269400 1.0000 500 27852 1.0000 500 2885 1.0000 500 3132 1.0000 500 36650 1.0000 500 38361 1.0000 500 38735 1.0000 500 38770 1.0000 500 4012 1.0000 500 4061 1.0000 500 6020 1.0000 500 9604 1.0000 500 bd1875 1.0000 500 bd1877 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/329/329.seqs.fa -oc motifs/329 -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= 35 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= 17500 N= 35 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.229 G 0.245 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.256 C 0.229 G 0.245 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 34 llr = 317 E-value = 4.0e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :21::::121321:32 pos.-specific C 2:111:::2:33:::: probability G 32:8::9319423817 matrix T 56819a1651136161 bits 2.1 1.9 * 1.7 ** 1.5 ** Relative 1.3 *** * Entropy 1.1 ***** * * (13.4 bits) 0.9 ***** * * * 0.6 ******* * **** 0.4 ******** * **** 0.2 *********** **** 0.0 ---------------- Multilevel TTTGTTGTTGGCTGTG consensus GG GA ATG A sequence C C CA G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 23751 185 6.64e-08 TAGGCGTGAT CTTGTTGTTGGATGAG GAAGATGCAC 1477 114 1.43e-07 AGGCTTGAGG TGTGTTGTTGGTGGTG TGACCGCTAT 38735 105 1.96e-07 GGCAATGGTG TATGTTGTTGCCTGAG CTGGCGTTAA 36650 105 1.96e-07 GGCAATGGTG TATGTTGTTGCCTGAG CTGGCGTTAA 23906 21 1.96e-07 GCCGTGATGT TTTGTTGGAGCTTGTG GCTTGGTTGG 4012 185 2.32e-07 TATTTGAGGC GTTGTTGGTGGCTGGG AGGTCGGCGT 24993 354 3.68e-07 CGTTCGAGGC GTTGTTGGTGGATGGG GGGTCGGCTT bd1875 193 9.89e-07 GGGACGGACG TTTGTTGGAGGAGGAG AGGCCATGGT 23837 348 2.66e-06 CTGTAAGTTG TTTTTTGTTGGAAGTG ATTGGAAGTG 19158 338 2.66e-06 CTGTAAGTTG TTTTTTGTTGGAAGTG ATTGGAAGTG 268574 300 3.36e-06 CGCCTGCTGG TTCGTTGTTGGATGGG AACGAAAGTA 2523 434 4.20e-06 GCGTTTGACT GTTGTTGTCGAGTGAT TACCTGTCGT 269210 28 9.75e-06 CGTTTCAATA CTTCTTGTTAGCTGTG AGGTGTTGCA 261802 389 1.19e-05 CGTAGCGGTT TGTGTTGGTGTTGGTA GTTTGGGCGA 11025 351 1.19e-05 GCTCAGCAGT GTTGTTGTTTTGTGAG GGCTTCTTTC 4061 213 1.44e-05 TTGATGTGTT TTTGTTGTTGAGATGG CATATTGAAT 25652 152 1.44e-05 GGCCTTTGCT GATGTTGTCGACGTTG ACTACGAAAT 6020 60 1.58e-05 GAGTGAGGTA CTTGTTGTCGTGTGAT GTCTACTGTT 2605 98 1.90e-05 AATTGAAGGC CAAGTTGGAGGCTGTG GGAGGACAGA 264633 333 2.08e-05 TAATATTAGC GTAGTTGGCGCTTGTA TGCCACTACG 3132 312 2.72e-05 GGTCGCTGTG GGTCTTGTTGACGTTG GATTTTGTTC 21598 245 2.97e-05 TGTTGGGCGT TGGGTTGGAGGTTGTG CTGGTTTGCT 2217 377 3.24e-05 TTGTTCAAAT GTTTCTGTTGCCAGTG TCGTCGTACT 1692 38 3.53e-05 TGAAACTCTA TTTGCTGTATATTGTG GATAGTTTCG 2219 187 3.84e-05 AGAATTGCAC TATGTTGTGGACGTTG CTTGACGGTG 2178 199 4.53e-05 ATCGAAAGGA CGAGTTGTGGCGTGTG CCAATGCTGA 38770 364 6.75e-05 GTACCAAGGA CTTCTTTTCGTCTGTG AGGTCGTGTC 2885 192 6.75e-05 GGCTGCAGAG CGTCTTGTAGAGGGTA TATGCATTGT 14096 425 9.15e-05 CCACCCTCTC TGTGTTTTCGGTGGAA ACCTCTTCAT 269400 344 1.22e-04 TCATACATCA TTTGTTGGTGAGTCGT TGCATCGTCG 38361 136 2.91e-04 CGAACAAACA GTCGTTGCCGATTGAA TTGGCTGCCG 21602 314 3.09e-04 GTCGGACCGA TTTGCTGAAGCAAGTT CTAGCTTAAA 9604 135 4.17e-04 GATATTTCAG GATGATGATGCTTGAA AAAAGAAATG bd1877 154 4.95e-04 GCGTTGATCC GTTCTTGGTACAGATG AGGGAGACTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23751 6.6e-08 184_[+1]_300 1477 1.4e-07 113_[+1]_371 38735 2e-07 104_[+1]_380 36650 2e-07 104_[+1]_380 23906 2e-07 20_[+1]_464 4012 2.3e-07 184_[+1]_300 24993 3.7e-07 353_[+1]_131 bd1875 9.9e-07 192_[+1]_292 23837 2.7e-06 347_[+1]_137 19158 2.7e-06 337_[+1]_147 268574 3.4e-06 299_[+1]_185 2523 4.2e-06 433_[+1]_51 269210 9.7e-06 27_[+1]_457 261802 1.2e-05 388_[+1]_96 11025 1.2e-05 350_[+1]_134 4061 1.4e-05 212_[+1]_272 25652 1.4e-05 151_[+1]_333 6020 1.6e-05 59_[+1]_425 2605 1.9e-05 97_[+1]_387 264633 2.1e-05 332_[+1]_152 3132 2.7e-05 311_[+1]_173 21598 3e-05 244_[+1]_240 2217 3.2e-05 376_[+1]_108 1692 3.5e-05 37_[+1]_447 2219 3.8e-05 186_[+1]_298 2178 4.5e-05 198_[+1]_286 38770 6.8e-05 363_[+1]_121 2885 6.8e-05 191_[+1]_293 14096 9.2e-05 424_[+1]_60 269400 0.00012 343_[+1]_141 38361 0.00029 135_[+1]_349 21602 0.00031 313_[+1]_171 9604 0.00042 134_[+1]_350 bd1877 0.0005 153_[+1]_331 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=34 23751 ( 185) CTTGTTGTTGGATGAG 1 1477 ( 114) TGTGTTGTTGGTGGTG 1 38735 ( 105) TATGTTGTTGCCTGAG 1 36650 ( 105) TATGTTGTTGCCTGAG 1 23906 ( 21) TTTGTTGGAGCTTGTG 1 4012 ( 185) GTTGTTGGTGGCTGGG 1 24993 ( 354) GTTGTTGGTGGATGGG 1 bd1875 ( 193) TTTGTTGGAGGAGGAG 1 23837 ( 348) TTTTTTGTTGGAAGTG 1 19158 ( 338) TTTTTTGTTGGAAGTG 1 268574 ( 300) TTCGTTGTTGGATGGG 1 2523 ( 434) GTTGTTGTCGAGTGAT 1 269210 ( 28) CTTCTTGTTAGCTGTG 1 261802 ( 389) TGTGTTGGTGTTGGTA 1 11025 ( 351) GTTGTTGTTTTGTGAG 1 4061 ( 213) TTTGTTGTTGAGATGG 1 25652 ( 152) GATGTTGTCGACGTTG 1 6020 ( 60) CTTGTTGTCGTGTGAT 1 2605 ( 98) CAAGTTGGAGGCTGTG 1 264633 ( 333) GTAGTTGGCGCTTGTA 1 3132 ( 312) GGTCTTGTTGACGTTG 1 21598 ( 245) TGGGTTGGAGGTTGTG 1 2217 ( 377) GTTTCTGTTGCCAGTG 1 1692 ( 38) TTTGCTGTATATTGTG 1 2219 ( 187) TATGTTGTGGACGTTG 1 2178 ( 199) CGAGTTGTGGCGTGTG 1 38770 ( 364) CTTCTTTTCGTCTGTG 1 2885 ( 192) CGTCTTGTAGAGGGTA 1 14096 ( 425) TGTGTTTTCGGTGGAA 1 269400 ( 344) TTTGTTGGTGAGTCGT 1 38361 ( 136) GTCGTTGCCGATTGAA 1 21602 ( 314) TTTGCTGAAGCAAGTT 1 9604 ( 135) GATGATGATGCTTGAA 1 bd1877 ( 154) GTTCTTGGTACAGATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16975 bayes= 9.03045 E= 4.0e-010 -1173 -15 40 80 -54 -1173 -25 119 -154 -196 -305 161 -1173 -64 164 -161 -312 -138 -1173 171 -1173 -1173 -1173 189 -1173 -1173 194 -220 -212 -296 27 119 -32 -15 -205 97 -212 -1173 185 -220 5 21 53 -120 -12 36 -25 -3 -80 -1173 11 112 -312 -296 175 -120 20 -1173 -73 105 -54 -1173 153 -120 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 34 E= 4.0e-010 0.000000 0.205882 0.323529 0.470588 0.176471 0.000000 0.205882 0.617647 0.088235 0.058824 0.029412 0.823529 0.000000 0.147059 0.764706 0.088235 0.029412 0.088235 0.000000 0.882353 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.941176 0.058824 0.058824 0.029412 0.294118 0.617647 0.205882 0.205882 0.058824 0.529412 0.058824 0.000000 0.882353 0.058824 0.264706 0.264706 0.352941 0.117647 0.235294 0.294118 0.205882 0.264706 0.147059 0.000000 0.264706 0.588235 0.029412 0.029412 0.823529 0.117647 0.294118 0.000000 0.147059 0.558824 0.176471 0.000000 0.705882 0.117647 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TGC][TG]TGTTG[TG][TAC]G[GAC][CTAG][TG]G[TA]G -------------------------------------------------------------------------------- Time 11.11 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 10 llr = 173 E-value = 3.4e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :42::::3:24:1::::41:2 pos.-specific C 918:8:a15833:a:884:15 probability G 1:::2::51::7::22:1123 matrix T :5:a:a:14:3:9:8:2187: bits 2.1 * * 1.9 * ** * 1.7 * * ** * 1.5 * **** ** * Relative 1.3 * ***** * ****** Entropy 1.1 * ***** * ****** * (25.0 bits) 0.9 * ***** * ****** ** 0.6 ******* ** ****** *** 0.4 ***************** *** 0.2 ********************* 0.0 --------------------- Multilevel CTCTCTCGCCAGTCTCCATTC consensus AA G ATACC GGTC GG sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 38361 48 5.65e-12 GAGAGCTACC CACTCTCGTCCGTCTCCATTC TTTCTCAGTC 38735 457 1.55e-10 CGAGCTTGCT CACTCTCGCCAGTCGCCCTTA GCTGCTAGAA 36650 457 1.55e-10 CGAGCTTGCT CACTCTCGCCAGTCGCCCTTA GCTGCTAGAA 23837 166 2.08e-09 CAACAGCTCG CTCTCTCACCTCTCTGCATGC GATCAATGGG 19158 156 2.08e-09 CAACAGCTCG CTCTCTCACCTCTCTGCATGC GATCAATGGG 4012 237 6.35e-09 TTATCACGTG CACTGTCGCACGTCTCCAATC TACCCCCTCC bd1875 459 1.22e-08 CGCTCCACTT CCATCTCATCAGTCTCTCTTG ACAACAAGTA 2217 315 3.10e-08 TATTGTGTAG CTATCTCCTACGTCTCCGTTG TCGCACATTG 25652 459 7.99e-08 TGCGTCCGTC GTCTGTCGTCTCTCTCTCTCC TCCTATCGTT 1692 470 1.51e-07 ACCTCTCTCT CTCTCTCTGCAGACTCCTGTG TACAGCTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38361 5.7e-12 47_[+2]_432 38735 1.6e-10 456_[+2]_23 36650 1.6e-10 456_[+2]_23 23837 2.1e-09 165_[+2]_314 19158 2.1e-09 155_[+2]_324 4012 6.4e-09 236_[+2]_243 bd1875 1.2e-08 458_[+2]_21 2217 3.1e-08 314_[+2]_165 25652 8e-08 458_[+2]_21 1692 1.5e-07 469_[+2]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=10 38361 ( 48) CACTCTCGTCCGTCTCCATTC 1 38735 ( 457) CACTCTCGCCAGTCGCCCTTA 1 36650 ( 457) CACTCTCGCCAGTCGCCCTTA 1 23837 ( 166) CTCTCTCACCTCTCTGCATGC 1 19158 ( 156) CTCTCTCACCTCTCTGCATGC 1 4012 ( 237) CACTGTCGCACGTCTCCAATC 1 bd1875 ( 459) CCATCTCATCAGTCTCTCTTG 1 2217 ( 315) CTATCTCCTACGTCTCCGTTG 1 25652 ( 459) GTCTGTCGTCTCTCTCTCTCC 1 1692 ( 470) CTCTCTCTGCAGACTCCTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16800 bayes= 11.6572 E= 3.4e-007 -997 197 -129 -997 64 -119 -997 89 -36 180 -997 -997 -997 -997 -997 189 -997 180 -29 -997 -997 -997 -997 189 -997 212 -997 -997 23 -119 103 -143 -997 113 -129 57 -36 180 -997 -997 64 39 -997 15 -997 39 152 -997 -136 -997 -997 174 -997 212 -997 -997 -997 -997 -29 157 -997 180 -29 -997 -997 180 -997 -43 64 80 -129 -143 -136 -997 -129 157 -997 -119 -29 137 -36 113 29 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 10 E= 3.4e-007 0.000000 0.900000 0.100000 0.000000 0.400000 0.100000 0.000000 0.500000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.300000 0.100000 0.500000 0.100000 0.000000 0.500000 0.100000 0.400000 0.200000 0.800000 0.000000 0.000000 0.400000 0.300000 0.000000 0.300000 0.000000 0.300000 0.700000 0.000000 0.100000 0.000000 0.000000 0.900000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.800000 0.000000 0.200000 0.400000 0.400000 0.100000 0.100000 0.100000 0.000000 0.100000 0.800000 0.000000 0.100000 0.200000 0.700000 0.200000 0.500000 0.300000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TA][CA]T[CG]TC[GA][CT][CA][ACT][GC]TC[TG][CG][CT][AC]T[TG][CGA] -------------------------------------------------------------------------------- Time 21.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 34 llr = 287 E-value = 2.3e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 216141155::a pos.-specific C 69:8:683:8a: probability G 1:::21:1:::: matrix T 1131421:52:: bits 2.1 1.9 ** 1.7 ** 1.5 ** Relative 1.3 * * ** Entropy 1.1 * * * *** (12.2 bits) 0.9 *** * **** 0.6 *** * **** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCACTCCATCCA consensus A T AT CAT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 21598 5 1.89e-07 TCTC CCACTCCCTCCA CATGGCGGCA 2219 395 3.08e-06 CAAGAAGCGT CCTCTCCGACCA AAAGGCAAGG 264633 20 3.71e-06 TCCTTGTGGT CCTCTTCCTCCA GCAACAAAGG 23837 485 5.75e-06 TCATACCTCC CCACTCTCTCCA ACTC 19158 475 5.75e-06 TCATACCTCC CCACTCTCTCCA ACTCAACAAA 269210 488 6.37e-06 GGAAGGCCGC ACACACCGACCA C 11025 82 7.17e-06 ACACAGACGA CCAAACCAACCA CCTTGTTTCA bd1877 393 1.01e-05 TCACAATTTG ACACACCAATCA GTCCAGTCGA 9604 184 1.44e-05 TCACCTGCGG CCTCATCGTCCA ATTTTATCTA 268574 178 1.44e-05 ATCCATCATG TCACGCCCACCA AACTCGCATT 27852 344 1.59e-05 CTTCTACAAA ACACACAATCCA GAGAAGTTAT 25652 1 1.59e-05 . ACACAGCCACCA TCACATCCAC 21602 466 1.59e-05 ACAACACCCA CCCCACCAACCA ACAACGACCA 1477 238 1.78e-05 GTAGTAGTCG CCTCGGCCTCCA CGTCTGTCGC 24993 243 1.98e-05 GTCGGTGATA ACACTCTCTCCA CCCATCTACG 23751 43 2.17e-05 GTACCTCCCA TCACTTCCACCA CCATGTCAAT 3132 485 2.65e-05 GACTGCACAG CATCACCATCCA GTCA 38770 288 2.92e-05 ATCTCTTGCA CCTCAGCGACCA ATCCGCTGTT 38361 470 3.25e-05 ACCACCGACA CCATTCCATTCA ACTGCTCGAC 261802 49 3.94e-05 TCCGCCGCCC ACAAGCCAACCA TCATCGTTCG 2217 76 4.74e-05 CGTTGCCACT CCTCACCATGCA ACTAGTACAA 14096 392 5.20e-05 TCAGCTCTCA GCTCTCCAATCA TCGCAACTCG 38735 24 6.25e-05 CAACAAGCGT CTACGTCATCCA TTTCAACGAG 36650 24 6.25e-05 CAACAAGCGT CTACGTCATCCA TTTCAACGAG 2178 275 6.25e-05 ATGAGAAGAT ACATTTCAACCA GCATTTCAGA 2885 456 8.88e-05 CACAAATCAG CCACTCATACCA AATCAAACTA 269400 233 8.88e-05 CGGACTCATT CGACTCCATTCA TACTACTCGT 23906 484 8.88e-05 CAAAGTCAAA CAACAACAACCA CGACC 4012 114 1.13e-04 GCCCACGCGA CCACTATGACCA TAAGAAGCCT 1692 429 2.77e-04 CCCTCTCGTG CCACGACCTCGA GCTCCAGCGT 6020 480 3.19e-04 CTCCACCAGC TCTCACAATTCA CCACCAACC 4061 445 3.89e-04 AAAACTTAAA GCTAGTCAACCA CTTCCTTGTC 2523 479 4.15e-04 GAGTCGTTGT GCATTTCATTCA AAGGGGTGCC 2605 434 5.01e-04 ACAAATAATC ACTCTGACTTCA GGATCCGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21598 1.9e-07 4_[+3]_484 2219 3.1e-06 394_[+3]_94 264633 3.7e-06 19_[+3]_469 23837 5.7e-06 484_[+3]_4 19158 5.7e-06 474_[+3]_14 269210 6.4e-06 487_[+3]_1 11025 7.2e-06 81_[+3]_407 bd1877 1e-05 392_[+3]_96 9604 1.4e-05 183_[+3]_305 268574 1.4e-05 177_[+3]_311 27852 1.6e-05 343_[+3]_145 25652 1.6e-05 [+3]_488 21602 1.6e-05 465_[+3]_23 1477 1.8e-05 237_[+3]_251 24993 2e-05 242_[+3]_246 23751 2.2e-05 42_[+3]_446 3132 2.7e-05 484_[+3]_4 38770 2.9e-05 287_[+3]_201 38361 3.2e-05 469_[+3]_19 261802 3.9e-05 48_[+3]_440 2217 4.7e-05 75_[+3]_413 14096 5.2e-05 391_[+3]_97 38735 6.3e-05 23_[+3]_465 36650 6.3e-05 23_[+3]_465 2178 6.3e-05 274_[+3]_214 2885 8.9e-05 455_[+3]_33 269400 8.9e-05 232_[+3]_256 23906 8.9e-05 483_[+3]_5 4012 0.00011 113_[+3]_375 1692 0.00028 428_[+3]_60 6020 0.00032 479_[+3]_9 4061 0.00039 444_[+3]_44 2523 0.00042 478_[+3]_10 2605 0.0005 433_[+3]_55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=34 21598 ( 5) CCACTCCCTCCA 1 2219 ( 395) CCTCTCCGACCA 1 264633 ( 20) CCTCTTCCTCCA 1 23837 ( 485) CCACTCTCTCCA 1 19158 ( 475) CCACTCTCTCCA 1 269210 ( 488) ACACACCGACCA 1 11025 ( 82) CCAAACCAACCA 1 bd1877 ( 393) ACACACCAATCA 1 9604 ( 184) CCTCATCGTCCA 1 268574 ( 178) TCACGCCCACCA 1 27852 ( 344) ACACACAATCCA 1 25652 ( 1) ACACAGCCACCA 1 21602 ( 466) CCCCACCAACCA 1 1477 ( 238) CCTCGGCCTCCA 1 24993 ( 243) ACACTCTCTCCA 1 23751 ( 43) TCACTTCCACCA 1 3132 ( 485) CATCACCATCCA 1 38770 ( 288) CCTCAGCGACCA 1 38361 ( 470) CCATTCCATTCA 1 261802 ( 49) ACAAGCCAACCA 1 2217 ( 76) CCTCACCATGCA 1 14096 ( 392) GCTCTCCAATCA 1 38735 ( 24) CTACGTCATCCA 1 36650 ( 24) CTACGTCATCCA 1 2178 ( 275) ACATTTCAACCA 1 2885 ( 456) CCACTCATACCA 1 269400 ( 233) CGACTCCATTCA 1 23906 ( 484) CAACAACAACCA 1 4012 ( 114) CCACTATGACCA 1 1692 ( 429) CCACGACCTCGA 1 6020 ( 480) TCTCACAATTCA 1 4061 ( 445) GCTAGTCAACCA 1 2523 ( 479) GCATTTCATTCA 1 2605 ( 434) ACTCTGACTTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 17115 bayes= 9.04232 E= 2.3e-005 -12 136 -147 -161 -212 190 -305 -220 134 -296 -1173 26 -154 185 -1173 -161 46 -1173 -25 71 -154 129 -106 -20 -112 174 -1173 -120 96 50 -73 -320 88 -1173 -1173 97 -1173 174 -305 -39 -1173 208 -305 -1173 196 -1173 -1173 -1173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 34 E= 2.3e-005 0.235294 0.588235 0.088235 0.088235 0.058824 0.852941 0.029412 0.058824 0.647059 0.029412 0.000000 0.323529 0.088235 0.823529 0.000000 0.088235 0.352941 0.000000 0.205882 0.441176 0.088235 0.558824 0.117647 0.235294 0.117647 0.764706 0.000000 0.117647 0.500000 0.323529 0.147059 0.029412 0.470588 0.000000 0.000000 0.529412 0.000000 0.764706 0.029412 0.205882 0.000000 0.970588 0.029412 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CA]C[AT]C[TAG][CT]C[AC][TA][CT]CA -------------------------------------------------------------------------------- Time 32.47 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11025 4.68e-04 81_[+3(7.17e-06)]_257_\ [+1(1.19e-05)]_134 14096 9.13e-03 391_[+3(5.20e-05)]_21_\ [+1(9.15e-05)]_60 1477 5.06e-05 113_[+1(1.43e-07)]_108_\ [+3(1.78e-05)]_47_[+1(7.87e-05)]_188 1692 2.17e-05 37_[+1(3.53e-05)]_365_\ [+2(5.62e-05)]_30_[+2(1.51e-07)]_10 19158 1.35e-09 155_[+2(2.08e-09)]_161_\ [+1(2.66e-06)]_121_[+3(5.75e-06)]_14 21598 2.22e-05 4_[+3(1.89e-07)]_228_[+1(2.97e-05)]_\ 211_[+3(2.66e-06)]_17 21602 1.62e-02 465_[+3(1.59e-05)]_23 2178 1.77e-02 198_[+1(4.53e-05)]_60_\ [+3(6.25e-05)]_214 2217 1.07e-06 75_[+3(4.74e-05)]_227_\ [+2(3.10e-08)]_41_[+1(3.24e-05)]_108 2219 1.28e-03 186_[+1(3.84e-05)]_158_\ [+3(1.44e-05)]_22_[+3(3.08e-06)]_94 23751 6.56e-06 42_[+3(2.17e-05)]_130_\ [+1(6.64e-08)]_300 23837 1.35e-09 165_[+2(2.08e-09)]_161_\ [+1(2.66e-06)]_121_[+3(5.75e-06)]_4 23906 2.90e-05 20_[+1(1.96e-07)]_447_\ [+3(8.88e-05)]_5 24993 2.17e-05 242_[+3(1.98e-05)]_99_\ [+1(3.68e-07)]_54_[+3(7.48e-05)]_65 2523 1.33e-02 433_[+1(4.20e-06)]_51 25652 4.56e-07 [+3(1.59e-05)]_139_[+1(1.44e-05)]_\ 291_[+2(7.99e-08)]_21 2605 1.62e-02 97_[+1(1.90e-05)]_387 261802 3.38e-03 48_[+3(3.94e-05)]_328_\ [+1(1.19e-05)]_96 264633 1.30e-03 19_[+3(3.71e-06)]_301_\ [+1(2.08e-05)]_152 268574 5.69e-04 177_[+3(1.44e-05)]_110_\ [+1(3.36e-06)]_185 269210 5.87e-04 27_[+1(9.75e-06)]_444_\ [+3(6.37e-06)]_1 269400 3.11e-02 232_[+3(8.88e-05)]_256 27852 1.19e-01 343_[+3(1.59e-05)]_145 2885 3.04e-02 191_[+1(6.75e-05)]_248_\ [+3(8.88e-05)]_33 3132 4.13e-03 311_[+1(2.72e-05)]_157_\ [+3(2.65e-05)]_4 36650 9.72e-11 23_[+3(6.25e-05)]_69_[+1(1.96e-07)]_\ 336_[+2(1.55e-10)]_23 38361 2.04e-09 47_[+2(5.65e-12)]_401_\ [+3(3.25e-05)]_19 38735 9.72e-11 23_[+3(6.25e-05)]_69_[+1(1.96e-07)]_\ 336_[+2(1.55e-10)]_23 38770 6.31e-03 287_[+3(2.92e-05)]_64_\ [+1(6.75e-05)]_121 4012 6.13e-09 184_[+1(2.32e-07)]_36_\ [+2(6.35e-09)]_177_[+2(1.58e-05)]_45 4061 2.08e-02 103_[+1(4.53e-05)]_93_\ [+1(1.44e-05)]_272 6020 2.92e-02 59_[+1(1.58e-05)]_425 9604 3.55e-02 183_[+3(1.44e-05)]_305 bd1875 5.19e-07 44_[+1(7.29e-05)]_132_\ [+1(9.89e-07)]_131_[+2(1.88e-05)]_98_[+2(1.22e-08)]_21 bd1877 3.62e-03 392_[+3(1.01e-05)]_96 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************