******************************************************************************** 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/48/48.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1109 1.0000 500 12070 1.0000 500 12097 1.0000 500 1326 1.0000 500 18796 1.0000 500 1888 1.0000 500 1889 1.0000 500 21939 1.0000 500 22579 1.0000 500 23228 1.0000 500 24247 1.0000 500 25249 1.0000 500 261637 1.0000 500 263700 1.0000 500 269148 1.0000 500 269759 1.0000 500 270372 1.0000 500 28425 1.0000 500 33008 1.0000 500 3461 1.0000 500 3588 1.0000 500 3691 1.0000 500 3741 1.0000 500 37450 1.0000 500 40107 1.0000 500 41778 1.0000 500 8546 1.0000 500 9511 1.0000 500 9943 1.0000 500 bd1069 1.0000 500 bd1221 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/48/48.seqs.fa -oc motifs/48 -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= 31 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= 15500 N= 31 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.254 C 0.229 G 0.253 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.254 C 0.229 G 0.253 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 24 llr = 303 E-value = 4.8e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :86:7373848417841523: pos.-specific C a13a:726:523811563536 probability G ::::2::11:::1:1221::1 matrix T :11:1:2:::13:2::12343 bits 2.1 1.9 * * 1.7 * * 1.5 * * Relative 1.3 * * Entropy 1.1 ** * * * * (18.2 bits) 0.9 ** *** **** *** * 0.6 *********** ***** * * 0.4 *********** ***** *** 0.2 ********************* 0.0 --------------------- Multilevel CAACACACACAACAACCACTC consensus C A A A C A CTCT sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 1888 462 3.04e-10 TCAATCTTAT CACCAAACAAACCAAACCCCC CACACCAGCA 21939 409 2.86e-09 GTAGCGGTGT CACCACACAAACCAAGCATTT TTTATCTGCT 41778 382 3.30e-09 TTCATCCCTT CAACTCCCACAACAACCATCC GTAATAATTT 261637 419 1.28e-08 CTGCCAAGCA CACCACTCAAAACAAACCCAG CTCCAGGCTG 23228 441 6.10e-08 CCTCTTCAGT CACCACAAGCAACACGCACCC ACCTCCACCC 25249 291 6.82e-08 GCCTAACAAA CCACAAACAAATCAACCTCCT CGTGGCACCA 269759 232 1.05e-07 CCACGTGGAC CTACACAAACAACAACAACAT CCTCGTCATC 269148 441 1.78e-07 CCGCACGCAC CAACAAAGACATCAACGCCCG CCTCCACCCA 37450 455 3.55e-07 CGCCACCCAA CAACGCCCAAATAAAACGCTC ATCTACCTCC 33008 425 3.55e-07 AGCCAAACTA CAACACACACCTCTCACCTTT CATTACCATC 270372 426 3.55e-07 AGCCAAACTA CAACACACACCTCTCACCTTT CATTACCATC 22579 478 6.22e-07 CGGTCTCACG GACCACACAATCCAAACAAAC GC 9511 426 6.81e-07 GTGTCATAAA CAACACTCACACACACCGACC AGACACCTGA 263700 325 8.14e-07 CTGATAGTAC CAATACAAGCAACAACCATTG CAACGAAGAG 40107 263 1.06e-06 CGAACGAAGT CAACACTCAAATGTAACTCTT CTGTTAGATT 1326 422 1.15e-06 TACTCTCTTG CACCACTCACAGGAAGCTCTC CCTCGCCGTA 12097 362 1.15e-06 CACATCATCA CACCGCCAGCACCCAGCACCC GGCCAGCACA 3461 89 1.26e-06 ATACCGTCTC CTACTCAAAAACCAACAAACC TGTCCAATGA 3588 434 1.75e-06 CTTGATTGTT CATCAAACTCACCAACGCAAC ACTGCAGACA bd1221 478 2.06e-06 GCAGCAGCAT CAACAAACAACAAAGCGTCTC AA 9943 352 3.30e-06 CTCTCCGTCG CATCGAACAACACCAATACAC CTTCCTAAAC 18796 455 6.86e-06 TTCAACACTT CAACAAAAATTACAGAGACAC AACGCCCACT bd1069 408 1.03e-05 AATGATACTG CCACGTAGACAACAACTATAC CCATACCATC 24247 73 1.35e-05 CGTTGGGGAG CACCTCCACCACCTACTCTTC CACCGCCGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1888 3e-10 461_[+1]_18 21939 2.9e-09 408_[+1]_71 41778 3.3e-09 381_[+1]_98 261637 1.3e-08 418_[+1]_61 23228 6.1e-08 440_[+1]_39 25249 6.8e-08 290_[+1]_189 269759 1.1e-07 231_[+1]_248 269148 1.8e-07 440_[+1]_39 37450 3.6e-07 454_[+1]_25 33008 3.6e-07 424_[+1]_55 270372 3.6e-07 425_[+1]_54 22579 6.2e-07 477_[+1]_2 9511 6.8e-07 425_[+1]_54 263700 8.1e-07 324_[+1]_155 40107 1.1e-06 262_[+1]_217 1326 1.2e-06 421_[+1]_58 12097 1.2e-06 361_[+1]_118 3461 1.3e-06 88_[+1]_391 3588 1.8e-06 433_[+1]_46 bd1221 2.1e-06 477_[+1]_2 9943 3.3e-06 351_[+1]_128 18796 6.9e-06 454_[+1]_25 bd1069 1e-05 407_[+1]_72 24247 1.3e-05 72_[+1]_407 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=24 1888 ( 462) CACCAAACAAACCAAACCCCC 1 21939 ( 409) CACCACACAAACCAAGCATTT 1 41778 ( 382) CAACTCCCACAACAACCATCC 1 261637 ( 419) CACCACTCAAAACAAACCCAG 1 23228 ( 441) CACCACAAGCAACACGCACCC 1 25249 ( 291) CCACAAACAAATCAACCTCCT 1 269759 ( 232) CTACACAAACAACAACAACAT 1 269148 ( 441) CAACAAAGACATCAACGCCCG 1 37450 ( 455) CAACGCCCAAATAAAACGCTC 1 33008 ( 425) CAACACACACCTCTCACCTTT 1 270372 ( 426) CAACACACACCTCTCACCTTT 1 22579 ( 478) GACCACACAATCCAAACAAAC 1 9511 ( 426) CAACACTCACACACACCGACC 1 263700 ( 325) CAATACAAGCAACAACCATTG 1 40107 ( 263) CAACACTCAAATGTAACTCTT 1 1326 ( 422) CACCACTCACAGGAAGCTCTC 1 12097 ( 362) CACCGCCAGCACCCAGCACCC 1 3461 ( 89) CTACTCAAAAACCAACAAACC 1 3588 ( 434) CATCAAACTCACCAACGCAAC 1 bd1221 ( 478) CAACAAACAACAAAGCGTCTC 1 9943 ( 352) CATCGAACAACACCAATACAC 1 18796 ( 455) CAACAAAAATTACAGAGACAC 1 bd1069 ( 408) CCACGTAGACAACAACTATAC 1 24247 ( 73) CACCTCCACCACCTACTCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 9.72188 E= 4.8e-017 -1123 207 -260 -1123 171 -146 -1123 -166 120 54 -1123 -166 -1123 207 -1123 -266 148 -1123 -60 -108 20 154 -1123 -266 139 -46 -1123 -66 20 145 -160 -1123 164 -245 -102 -266 71 124 -1123 -266 156 -46 -1123 -166 56 54 -260 -8 -102 179 -160 -1123 148 -87 -1123 -66 164 -87 -160 -1123 56 100 -60 -1123 -161 145 -60 -108 85 35 -160 -66 -61 124 -1123 15 20 54 -1123 51 -1123 145 -102 -8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 4.8e-017 0.000000 0.958333 0.041667 0.000000 0.833333 0.083333 0.000000 0.083333 0.583333 0.333333 0.000000 0.083333 0.000000 0.958333 0.000000 0.041667 0.708333 0.000000 0.166667 0.125000 0.291667 0.666667 0.000000 0.041667 0.666667 0.166667 0.000000 0.166667 0.291667 0.625000 0.083333 0.000000 0.791667 0.041667 0.125000 0.041667 0.416667 0.541667 0.000000 0.041667 0.750000 0.166667 0.000000 0.083333 0.375000 0.333333 0.041667 0.250000 0.125000 0.791667 0.083333 0.000000 0.708333 0.125000 0.000000 0.166667 0.791667 0.125000 0.083333 0.000000 0.375000 0.458333 0.166667 0.000000 0.083333 0.625000 0.166667 0.125000 0.458333 0.291667 0.083333 0.166667 0.166667 0.541667 0.000000 0.291667 0.291667 0.333333 0.000000 0.375000 0.000000 0.625000 0.125000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[AC]CA[CA]A[CA]A[CA]A[ACT]CAA[CA]C[AC][CT][TCA][CT] -------------------------------------------------------------------------------- Time 7.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 21 llr = 263 E-value = 1.8e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 11:33:3:1:1121:3:1:1: pos.-specific C :::::1:2::1::1::::::: probability G 6:9:34427a:2618:44a21 matrix T 391734362:87162765:78 bits 2.1 1.9 1.7 * * 1.5 ** * * Relative 1.3 ** * * Entropy 1.1 ** * *** * (18.1 bits) 0.9 *** ** *** * * 0.6 **** ****** *** *** 0.4 **** **************** 0.2 ********************* 0.0 --------------------- Multilevel GTGTAGGTGGTTGTGTTTGTT consensus T AGTA GA AGG sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 1109 45 3.23e-10 TGTGTGATTA GTGTTGGTGGTTGTTTTTGTT TTGATGTCCC 1889 358 2.52e-08 GTGCTTGCTG GTGTGGGGGGTTTGGTTTGTT TGGTGATAAG 1888 188 5.87e-08 GCGAGCATGA TTTTATTTTGTTGTGTTGGTT CACTGAGTAA 263700 58 9.27e-08 TTGTACCTGG TTGAAGTTGGCTGTTTGTGTT GTTGCACAAG 9511 184 1.04e-07 TGTTGAATGA TTGATGATGGTTGTGTGGCTT AAGTGAGGCA 3741 237 1.77e-07 AACTGCTACG GTGGGCATGGTTGAGTTTGTT GGTGTATCGA 23228 332 1.77e-07 GTCATGTTGC GTGTGGTGTGTTGCGTGTGGT GGTGCCGGTG 37450 107 2.93e-07 TTTGGAGCTC ATGTTGACGGTGGTGTTGGTG TGTTGAGAGG 3588 206 2.93e-07 AAAGTACATA ATGTGTTTGGTTGTTTGAGAT CGTCTGTCGA 1326 44 3.23e-07 CAATGCGTTC GTGTGTGTTGTGTTGATGGAT CTTCGAAGAG 8546 412 3.56e-07 TTGCGAGGCA GTGACGACGGCTGTGATGGTT TTGGATGAAA 40107 352 7.46e-07 GTCTGTGTCT GTGTTTGTCGTTGTGAGAGTG CAGTGTCGTG bd1069 62 1.36e-06 CTGTGATAAT GTGTTCATGGTGTCGATGGAT CGGTTGTGCT 33008 39 1.36e-06 CGTCGCCATT GTGTATGCAGATATGTGTGGT TTGGAACTTC 270372 40 1.36e-06 CGTCGCCATT GTGTATGCAGATATGTGTGGT TTGGAACTTC 261637 69 1.88e-06 AGAGTGGACG GTGTGTGGGGCTGGCTTAGTT TGTAGCAGGA 22579 229 1.88e-06 TCTCCTATAC GATTTTGTGGTAGCGTTTGTT TGTTGGACAG 41778 46 2.03e-06 TAGGGTACGT TTGTGTTGGATGATGATGGTT GAACAAGTTT 12097 118 3.72e-06 GAGGGCGAGC TTGAACATTGTGAAGAGTGTT TGGGTGTTTG 269148 45 9.01e-06 TGGAGATCGA TTGAAGTTGGTTAGTTGTGGC AATGATGGCG bd1221 406 1.09e-05 ATCAATAATG AAGAAGATGGTAGTGATGGTA CGAAGAAGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1109 3.2e-10 44_[+2]_435 1889 2.5e-08 357_[+2]_122 1888 5.9e-08 187_[+2]_292 263700 9.3e-08 57_[+2]_422 9511 1e-07 183_[+2]_296 3741 1.8e-07 236_[+2]_243 23228 1.8e-07 331_[+2]_148 37450 2.9e-07 106_[+2]_373 3588 2.9e-07 205_[+2]_274 1326 3.2e-07 43_[+2]_436 8546 3.6e-07 411_[+2]_68 40107 7.5e-07 351_[+2]_128 bd1069 1.4e-06 61_[+2]_418 33008 1.4e-06 38_[+2]_441 270372 1.4e-06 39_[+2]_440 261637 1.9e-06 68_[+2]_411 22579 1.9e-06 228_[+2]_251 41778 2e-06 45_[+2]_434 12097 3.7e-06 117_[+2]_362 269148 9e-06 44_[+2]_435 bd1221 1.1e-05 405_[+2]_74 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=21 1109 ( 45) GTGTTGGTGGTTGTTTTTGTT 1 1889 ( 358) GTGTGGGGGGTTTGGTTTGTT 1 1888 ( 188) TTTTATTTTGTTGTGTTGGTT 1 263700 ( 58) TTGAAGTTGGCTGTTTGTGTT 1 9511 ( 184) TTGATGATGGTTGTGTGGCTT 1 3741 ( 237) GTGGGCATGGTTGAGTTTGTT 1 23228 ( 332) GTGTGGTGTGTTGCGTGTGGT 1 37450 ( 107) ATGTTGACGGTGGTGTTGGTG 1 3588 ( 206) ATGTGTTTGGTTGTTTGAGAT 1 1326 ( 44) GTGTGTGTTGTGTTGATGGAT 1 8546 ( 412) GTGACGACGGCTGTGATGGTT 1 40107 ( 352) GTGTTTGTCGTTGTGAGAGTG 1 bd1069 ( 62) GTGTTCATGGTGTCGATGGAT 1 33008 ( 39) GTGTATGCAGATATGTGTGGT 1 270372 ( 40) GTGTATGCAGATATGTGTGGT 1 261637 ( 69) GTGTGTGGGGCTGGCTTAGTT 1 22579 ( 229) GATTTTGTGGTAGCGTTTGTT 1 41778 ( 46) TTGTGTTGGATGATGATGGTT 1 12097 ( 118) TTGAACATTGTGAAGAGTGTT 1 269148 ( 45) TTGAAGTTGGTTAGTTGTGGC 1 bd1221 ( 406) AAGAAGATGGTAGTGATGGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 9.77197 E= 1.8e-008 -83 -1104 117 12 -142 -1104 -1104 178 -1104 -1104 184 -147 17 -1104 -241 134 39 -226 40 12 -1104 -68 76 70 39 -1104 59 12 -1104 -26 -41 123 -142 -226 140 -47 -241 -1104 191 -1104 -142 -68 -1104 153 -142 -1104 -9 134 -10 -1104 129 -88 -142 -68 -82 123 -1104 -226 159 -47 39 -1104 -1104 134 -1104 -1104 76 112 -83 -1104 59 85 -1104 -226 191 -1104 -83 -1104 -41 134 -241 -226 -141 162 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 21 E= 1.8e-008 0.142857 0.000000 0.571429 0.285714 0.095238 0.000000 0.000000 0.904762 0.000000 0.000000 0.904762 0.095238 0.285714 0.000000 0.047619 0.666667 0.333333 0.047619 0.333333 0.285714 0.000000 0.142857 0.428571 0.428571 0.333333 0.000000 0.380952 0.285714 0.000000 0.190476 0.190476 0.619048 0.095238 0.047619 0.666667 0.190476 0.047619 0.000000 0.952381 0.000000 0.095238 0.142857 0.000000 0.761905 0.095238 0.000000 0.238095 0.666667 0.238095 0.000000 0.619048 0.142857 0.095238 0.142857 0.142857 0.619048 0.000000 0.047619 0.761905 0.190476 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.428571 0.571429 0.142857 0.000000 0.380952 0.476190 0.000000 0.047619 0.952381 0.000000 0.142857 0.000000 0.190476 0.666667 0.047619 0.047619 0.095238 0.809524 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]TG[TA][AGT][GT][GAT]TGGT[TG][GA]TG[TA][TG][TG]GTT -------------------------------------------------------------------------------- Time 14.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 16 llr = 217 E-value = 9.7e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 313:1812:3:3:4:13:336 pos.-specific C 89:892686773a28333751 probability G :1:2::3:1:1::1:3231:1 matrix T ::8::1::3125:32435:21 bits 2.1 * 1.9 * 1.7 * * 1.5 * ** * * * Relative 1.3 ** ** * * * Entropy 1.1 ****** * * * * (19.6 bits) 0.9 ******** ** * * * 0.6 *********** * * ** 0.4 ************* * **** 0.2 *************** **** 0.0 --------------------- Multilevel CCTCCACCCCCTCACTTTCCA consensus A A G TA A T CACAA sequence C GCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9511 394 3.02e-09 GGAAGTACGC CCTGCCCCCCCCCACGTTCCA CGTGTCATAA 23228 463 8.74e-09 CACGCACCCA CCTCCACCCTCCCTCCACCCA CTTTCTTCCT 269148 462 1.12e-08 TCAACGCCCG CCTCCACCCAGCCACTTTACA AAGTCCTTCT 28425 464 2.28e-08 TTTCACTCTG CCTCCACCCCTTCTCTACACC GGTCCACTTC 1889 37 3.99e-08 AACACCGCCT CCTCCAGCTCCTCCTTCTCCG CGAGCCCGTT 40107 471 6.08e-08 GGAGCCGACG CCTCCACCTCCACGCCGTCAC TTTTGCTAC 24247 434 1.62e-07 TCAACTTCCA CGTGCACACCCACTCTCTCCA CCATCAACAC 18796 81 1.78e-07 TAGACAGCAG CATCCACCCACTCACCTGATA AGGCTTTCCA 21939 443 2.54e-07 ATCTGCTTCA ACACAACCTCCTCTCTCCCAA TACATACTGA 1888 435 3.59e-07 GGAGCTTTCT CCTCCAGACAGCCACAATCAA TCTTATCACC 269759 353 3.90e-07 TTAATCGGCA CCACCACCGCTTCATGGTCTA GCAGAAGCAG 12070 407 6.84e-07 GTACGTGGTG ACTCCACAGCCACACGCTCTT AAGATTTGGA 261637 470 1.07e-06 ACAACCAGGG ACAGCAGCTCCTCCCTGGCCT CCATGCAATC 1326 133 1.33e-06 CTGCCGAAAA ACTCCCGCCACACACGTGGAA GAGCACGGAT 41778 449 1.64e-06 CTCGGTGTCG CCTCCCACTCCTCCTCTGCCG TCTACAGCAA 3741 351 2.01e-06 AGGGACCCCC CCACCTGCCCTTCTCAACAAA ATATTTAGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9511 3e-09 393_[+3]_86 23228 8.7e-09 462_[+3]_17 269148 1.1e-08 461_[+3]_18 28425 2.3e-08 463_[+3]_16 1889 4e-08 36_[+3]_443 40107 6.1e-08 470_[+3]_9 24247 1.6e-07 433_[+3]_46 18796 1.8e-07 80_[+3]_399 21939 2.5e-07 442_[+3]_37 1888 3.6e-07 434_[+3]_45 269759 3.9e-07 352_[+3]_127 12070 6.8e-07 406_[+3]_73 261637 1.1e-06 469_[+3]_10 1326 1.3e-06 132_[+3]_347 41778 1.6e-06 448_[+3]_31 3741 2e-06 350_[+3]_129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=16 9511 ( 394) CCTGCCCCCCCCCACGTTCCA 1 23228 ( 463) CCTCCACCCTCCCTCCACCCA 1 269148 ( 462) CCTCCACCCAGCCACTTTACA 1 28425 ( 464) CCTCCACCCCTTCTCTACACC 1 1889 ( 37) CCTCCAGCTCCTCCTTCTCCG 1 40107 ( 471) CCTCCACCTCCACGCCGTCAC 1 24247 ( 434) CGTGCACACCCACTCTCTCCA 1 18796 ( 81) CATCCACCCACTCACCTGATA 1 21939 ( 443) ACACAACCTCCTCTCTCCCAA 1 1888 ( 435) CCTCCAGACAGCCACAATCAA 1 269759 ( 353) CCACCACCGCTTCATGGTCTA 1 12070 ( 407) ACTCCACAGCCACACGCTCTT 1 261637 ( 470) ACAGCAGCTCCTCCCTGGCCT 1 1326 ( 133) ACTCCCGCCACACACGTGGAA 1 41778 ( 449) CCTCCCACTCCTCCTCTGCCG 1 3741 ( 351) CCACCTGCCCTTCTCAACAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 10.5971 E= 9.7e-006 -3 171 -1064 -1064 -202 193 -201 -1064 -3 -1064 -1064 151 -1064 183 -43 -1064 -202 203 -1064 -1064 156 -29 -1064 -207 -202 145 30 -1064 -44 183 -1064 -1064 -1064 130 -102 24 -3 159 -1064 -207 -1064 159 -102 -49 -3 13 -1064 92 -1064 213 -1064 -1064 78 -29 -201 24 -1064 183 -1064 -49 -102 13 -2 51 -3 13 -43 24 -1064 13 -2 92 -3 159 -201 -1064 30 113 -1064 -49 130 -87 -102 -108 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 9.7e-006 0.250000 0.750000 0.000000 0.000000 0.062500 0.875000 0.062500 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.812500 0.187500 0.000000 0.062500 0.937500 0.000000 0.000000 0.750000 0.187500 0.000000 0.062500 0.062500 0.625000 0.312500 0.000000 0.187500 0.812500 0.000000 0.000000 0.000000 0.562500 0.125000 0.312500 0.250000 0.687500 0.000000 0.062500 0.000000 0.687500 0.125000 0.187500 0.250000 0.250000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.437500 0.187500 0.062500 0.312500 0.000000 0.812500 0.000000 0.187500 0.125000 0.250000 0.250000 0.375000 0.250000 0.250000 0.187500 0.312500 0.000000 0.250000 0.250000 0.500000 0.250000 0.687500 0.062500 0.000000 0.312500 0.500000 0.000000 0.187500 0.625000 0.125000 0.125000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CA]C[TA]CCA[CG]C[CT][CA]C[TAC]C[AT]C[TCG][TAC][TCG][CA][CA]A -------------------------------------------------------------------------------- Time 21.11 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1109 8.26e-06 44_[+2(3.23e-10)]_435 12070 1.38e-03 406_[+3(6.84e-07)]_73 12097 6.49e-06 117_[+2(3.72e-06)]_157_\ [+2(7.08e-05)]_45_[+1(1.15e-06)]_118 1326 1.67e-08 43_[+2(3.23e-07)]_68_[+3(1.33e-06)]_\ 17_[+3(8.84e-05)]_230_[+1(1.15e-06)]_58 18796 2.11e-05 80_[+3(1.78e-07)]_247_\ [+1(7.06e-05)]_85_[+1(6.86e-06)]_25 1888 4.57e-13 50_[+3(4.73e-05)]_116_\ [+2(5.87e-08)]_226_[+3(3.59e-07)]_6_[+1(3.04e-10)]_18 1889 8.39e-09 36_[+3(3.99e-08)]_300_\ [+2(2.52e-08)]_122 21939 9.93e-09 408_[+1(2.86e-09)]_13_\ [+3(2.54e-07)]_37 22579 1.80e-05 228_[+2(1.88e-06)]_228_\ [+1(6.22e-07)]_2 23228 5.74e-12 331_[+2(1.77e-07)]_88_\ [+1(6.10e-08)]_1_[+3(8.74e-09)]_17 24247 3.12e-05 72_[+1(1.35e-05)]_340_\ [+3(1.62e-07)]_46 25249 2.61e-05 290_[+1(6.82e-08)]_189 261637 1.09e-09 68_[+2(1.88e-06)]_329_\ [+1(1.28e-08)]_30_[+3(1.07e-06)]_10 263700 3.07e-07 57_[+2(9.27e-08)]_246_\ [+1(8.14e-07)]_155 269148 7.75e-10 44_[+2(9.01e-06)]_375_\ [+1(1.78e-07)]_[+3(1.12e-08)]_18 269759 1.78e-07 231_[+1(1.05e-07)]_100_\ [+3(3.90e-07)]_127 270372 2.20e-06 39_[+2(1.36e-06)]_365_\ [+1(3.55e-07)]_54 28425 1.63e-04 463_[+3(2.28e-08)]_16 33008 2.20e-06 38_[+2(1.36e-06)]_365_\ [+1(3.55e-07)]_55 3461 1.76e-03 88_[+1(1.26e-06)]_391 3588 2.20e-06 205_[+2(2.93e-07)]_207_\ [+1(1.75e-06)]_46 3691 2.27e-01 500 3741 2.27e-06 89_[+2(3.34e-05)]_126_\ [+2(1.77e-07)]_93_[+3(2.01e-06)]_129 37450 5.09e-07 106_[+2(2.93e-07)]_233_\ [+1(1.03e-05)]_73_[+1(3.55e-07)]_25 40107 1.93e-09 262_[+1(1.06e-06)]_68_\ [+2(7.46e-07)]_98_[+3(6.08e-08)]_9 41778 4.93e-10 4_[+2(2.44e-05)]_20_[+2(2.03e-06)]_\ 315_[+1(3.30e-09)]_46_[+3(1.64e-06)]_31 8546 6.42e-03 411_[+2(3.56e-07)]_68 9511 1.24e-11 19_[+2(3.18e-05)]_143_\ [+2(1.04e-07)]_36_[+1(9.04e-05)]_132_[+3(3.02e-09)]_11_[+1(6.81e-07)]_33_\ [+1(8.45e-06)] 9943 1.21e-02 351_[+1(3.30e-06)]_128 bd1069 1.18e-04 61_[+2(1.36e-06)]_325_\ [+1(1.03e-05)]_72 bd1221 2.69e-04 405_[+2(1.09e-05)]_51_\ [+1(2.06e-06)]_2 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************