******************************************************************************** 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/395/395.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1057 1.0000 500 11135 1.0000 500 11617 1.0000 500 11906 1.0000 500 11981 1.0000 500 12859 1.0000 500 17036 1.0000 500 20935 1.0000 500 21089 1.0000 500 21535 1.0000 500 22450 1.0000 500 23316 1.0000 500 2455 1.0000 500 25457 1.0000 500 25619 1.0000 500 25762 1.0000 500 262501 1.0000 500 263051 1.0000 500 264621 1.0000 500 264809 1.0000 500 36337 1.0000 500 41306 1.0000 500 4573 1.0000 500 4660 1.0000 500 4938 1.0000 500 5871 1.0000 500 6378 1.0000 500 6581 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/395/395.seqs.fa -oc motifs/395 -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= 28 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= 14000 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.228 G 0.237 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.228 G 0.237 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 23 llr = 217 E-value = 1.5e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :39:176:94:7 pos.-specific C 47129:3a:38: probability G :::::21::::3 matrix T 5::7:2::122: bits 2.1 1.9 * 1.7 * 1.5 * * ** * Relative 1.3 * * ** * Entropy 1.1 ** * ** ** (13.6 bits) 0.9 ***** ** ** 0.6 ********* ** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TCATCAACAACA consensus CA C C C G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 4938 467 1.17e-07 AAAAGAAACA TCATCAACAACA TCATCGTCAT 264809 23 2.20e-07 AGATACCAGT TCATCAACACCA GCAGTAGCAT 262501 16 6.70e-07 CTCTCTGTAC CAATCAACAACA AAAGGCAGTC 21089 470 9.92e-07 AAACAACAGA TCATCAACAACG CCACAAAGCA 11906 410 9.92e-07 AACTGGCCTC TCACCAACAACA GCCCCTGCCA 6581 170 3.82e-06 GACGCATCCA CAATCAACACCG AAGACCCTAC 264621 401 5.09e-06 CGCCGATGCA TCCTCAACAACA ACACCGCAAG 11135 471 5.78e-06 ACACATCAGA TCATCACCAATA CTCAATACAG 4573 195 9.79e-06 ACCGCCGACC TAATCGACATCA GTATTTGCAG 23316 323 9.79e-06 AGTCCTTCTT CAATCTCCAACA AATCATGTTT 22450 177 1.45e-05 ACCATCAGTG ACATCAACATCA TTGTCGACGT 263051 49 2.84e-05 TTCATCTTCT TCATCGGCATCA TGCCGATGAG 17036 103 2.84e-05 ACGTCACAAC CCCCCACCACCA TCCCACCCAG 12859 87 2.84e-05 CGCGTATTAG TAATCTCCACCG TCAAGGCAGA 21535 476 4.27e-05 TAAAGCAATA CAACAAACAACA AGAGATGAAG 41306 420 4.92e-05 TCACTATATT CCACCAACATTG CGCACGCCGA 25457 170 4.92e-05 GTTGGATCAG CCATATCCACCA ACGTAAAGGT 11981 435 4.92e-05 CCAGTTGCCA TAATCACCTTCA ATGCCGACTA 5871 55 5.65e-05 GCTAACGTAT CAATCACTAACA ACCGTATGCT 11617 191 6.55e-05 TTATAACTCG TCATGAACACTA ACAAACTTTT 6378 482 7.00e-05 GGGGCACGAA CCAGCGACACCG TATCACA 1057 392 9.08e-05 TCTAATAAAA CCATCGACTATA TATTCTACTT 25619 105 9.68e-05 ACTATCGTCG TCACCTGCACCG ATTACACTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4938 1.2e-07 466_[+1]_22 264809 2.2e-07 22_[+1]_466 262501 6.7e-07 15_[+1]_473 21089 9.9e-07 469_[+1]_19 11906 9.9e-07 409_[+1]_79 6581 3.8e-06 169_[+1]_319 264621 5.1e-06 400_[+1]_88 11135 5.8e-06 470_[+1]_18 4573 9.8e-06 194_[+1]_294 23316 9.8e-06 322_[+1]_166 22450 1.5e-05 176_[+1]_312 263051 2.8e-05 48_[+1]_440 17036 2.8e-05 102_[+1]_386 12859 2.8e-05 86_[+1]_402 21535 4.3e-05 475_[+1]_13 41306 4.9e-05 419_[+1]_69 25457 4.9e-05 169_[+1]_319 11981 4.9e-05 434_[+1]_54 5871 5.7e-05 54_[+1]_434 11617 6.5e-05 190_[+1]_298 6378 7e-05 481_[+1]_7 1057 9.1e-05 391_[+1]_97 25619 9.7e-05 104_[+1]_384 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=23 4938 ( 467) TCATCAACAACA 1 264809 ( 23) TCATCAACACCA 1 262501 ( 16) CAATCAACAACA 1 21089 ( 470) TCATCAACAACG 1 11906 ( 410) TCACCAACAACA 1 6581 ( 170) CAATCAACACCG 1 264621 ( 401) TCCTCAACAACA 1 11135 ( 471) TCATCACCAATA 1 4573 ( 195) TAATCGACATCA 1 23316 ( 323) CAATCTCCAACA 1 22450 ( 177) ACATCAACATCA 1 263051 ( 49) TCATCGGCATCA 1 17036 ( 103) CCCCCACCACCA 1 12859 ( 87) TAATCTCCACCG 1 21535 ( 476) CAACAAACAACA 1 41306 ( 420) CCACCAACATTG 1 25457 ( 170) CCATATCCACCA 1 11981 ( 435) TAATCACCTTCA 1 5871 ( 55) CAATCACTAACA 1 11617 ( 191) TCATGAACACTA 1 6378 ( 482) CCAGCGACACCG 1 1057 ( 392) CCATCGACTATA 1 25619 ( 105) TCACCTGCACCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13692 bayes= 10.2805 E= 1.5e-003 -258 93 -1117 93 41 152 -1117 -1117 181 -139 -1117 -1117 -1117 -7 -244 143 -158 193 -244 -1117 132 -1117 -45 -66 122 42 -144 -1117 -1117 207 -1117 -265 181 -1117 -1117 -166 74 61 -1117 -34 -1117 186 -1117 -66 150 -1117 14 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 23 E= 1.5e-003 0.043478 0.434783 0.000000 0.521739 0.347826 0.652174 0.000000 0.000000 0.913043 0.086957 0.000000 0.000000 0.000000 0.217391 0.043478 0.739130 0.086957 0.869565 0.043478 0.000000 0.652174 0.000000 0.173913 0.173913 0.608696 0.304348 0.086957 0.000000 0.000000 0.956522 0.000000 0.043478 0.913043 0.000000 0.000000 0.086957 0.434783 0.347826 0.000000 0.217391 0.000000 0.826087 0.000000 0.173913 0.739130 0.000000 0.260870 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC][CA]A[TC]CA[AC]CA[ACT]C[AG] -------------------------------------------------------------------------------- Time 7.26 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 23 llr = 237 E-value = 1.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :2::2::43:23:3:: pos.-specific C :3:1:113::7::2:: probability G 7:28:382161:9::7 matrix T 368:871:63:7:693 bits 2.1 1.9 1.7 1.5 * Relative 1.3 ** * Entropy 1.1 * *** * * * (14.9 bits) 0.9 * *** * **** ** 0.6 ******* **** ** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GTTGTTGATGCTGTTG consensus TC AG CATAA A T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11906 15 3.35e-10 GTGGGTAGAG GTTGTTGATGCTGTTG TTCATCTTGT 25762 200 1.53e-08 GGATCCTAAT GCTGTTGCTGCTGATG CTTTCAATGT 264621 21 5.45e-08 ATGTTGTGAT GTTGTTGCTGCTGCTT TGGGGTGGTC 4573 258 2.46e-07 CATTGAAGAA GTTGTTGCTGAAGTTT GTCTTTACTA 36337 128 9.80e-07 AGGCTTGTTT GTTGTTGGAGGAGTTG GGTGATCCGA 22450 23 1.10e-06 TTTACCAAAT GTTGTGTATGATGTTG AACTGTAGAT 21535 95 1.37e-06 AATCTACTCC GTTGTTGAATATGATT CAAAGGGCAG 263051 177 1.70e-06 GGGTGTGATG GTTGACGAAGCTGATG GGTGGTGGTG 25457 259 4.66e-06 AGGCGGGCAT GTTGTGGATTCTGTCT ACTTAGTCCT 12859 206 6.14e-06 TGTTGTTTGG GCGGATGCATCTGCTG CTGCCTGGAC 5871 311 6.73e-06 TGGGAGCATG GTGGTGGATTGAGTTG GAGCTTGGTT 41306 71 7.35e-06 GTTGGTCCAC TCGGTGGATGATGATG GGATGAGTGA 20935 230 9.54e-06 ATCGACTTGT GTTGTTCATTCTATTG GGGTTCTCTC 262501 418 1.13e-05 TGAACCATGC TCTGTTGCATCAGTTC CTTTCGTCAT 1057 106 1.33e-05 AGTGTTTCTT GTTCTGGGGTCAGTTG GGTCGGGCCA 11981 473 1.98e-05 GAATCCGTGG GCTGATCCATCAGTTT ATATCAATTT 11617 92 2.31e-05 TCATTGGTTG GAGGTTGAGGCTGTGG CGTCATGGAA 6581 142 2.68e-05 TTCCAACGAC TATGACGATGATGATG ACGACGCATC 25619 231 3.83e-05 CCTGGAAATC TTTCTTGGTGCTTCTG AAAAGGTTAA 2455 97 3.83e-05 AGGCGAGAGA GATGAGTGAGCAGATG GAGTCGATAA 6378 92 4.39e-05 GTTTCCCCTG TTTATTGCTCCTGCTG ACCTCTACCT 4660 297 4.70e-05 TTTCGTAATT TCTCTTGGTGCTGTAT TTCCGACTTC 17036 297 5.03e-05 TGGCGAGGAG TATGTTTCCGCAGTTT CCGGAGGGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11906 3.4e-10 14_[+2]_470 25762 1.5e-08 199_[+2]_285 264621 5.5e-08 20_[+2]_464 4573 2.5e-07 257_[+2]_227 36337 9.8e-07 127_[+2]_357 22450 1.1e-06 22_[+2]_462 21535 1.4e-06 94_[+2]_390 263051 1.7e-06 176_[+2]_308 25457 4.7e-06 258_[+2]_226 12859 6.1e-06 205_[+2]_279 5871 6.7e-06 310_[+2]_174 41306 7.4e-06 70_[+2]_414 20935 9.5e-06 229_[+2]_255 262501 1.1e-05 417_[+2]_67 1057 1.3e-05 105_[+2]_379 11981 2e-05 472_[+2]_12 11617 2.3e-05 91_[+2]_393 6581 2.7e-05 141_[+2]_343 25619 3.8e-05 230_[+2]_254 2455 3.8e-05 96_[+2]_388 6378 4.4e-05 91_[+2]_393 4660 4.7e-05 296_[+2]_188 17036 5e-05 296_[+2]_188 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=23 11906 ( 15) GTTGTTGATGCTGTTG 1 25762 ( 200) GCTGTTGCTGCTGATG 1 264621 ( 21) GTTGTTGCTGCTGCTT 1 4573 ( 258) GTTGTTGCTGAAGTTT 1 36337 ( 128) GTTGTTGGAGGAGTTG 1 22450 ( 23) GTTGTGTATGATGTTG 1 21535 ( 95) GTTGTTGAATATGATT 1 263051 ( 177) GTTGACGAAGCTGATG 1 25457 ( 259) GTTGTGGATTCTGTCT 1 12859 ( 206) GCGGATGCATCTGCTG 1 5871 ( 311) GTGGTGGATTGAGTTG 1 41306 ( 71) TCGGTGGATGATGATG 1 20935 ( 230) GTTGTTCATTCTATTG 1 262501 ( 418) TCTGTTGCATCAGTTC 1 1057 ( 106) GTTCTGGGGTCAGTTG 1 11981 ( 473) GCTGATCCATCAGTTT 1 11617 ( 92) GAGGTTGAGGCTGTGG 1 6581 ( 142) TATGACGATGATGATG 1 25619 ( 231) TTTCTTGGTGCTTCTG 1 2455 ( 97) GATGAGTGAGCAGATG 1 6378 ( 92) TTTATTGCTCCTGCTG 1 4660 ( 297) TCTCTTGGTGCTGTAT 1 17036 ( 297) TATGTTTCCGCAGTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13580 bayes= 9.60633 E= 1.8e-003 -1117 -1117 155 15 -59 20 -1117 104 -1117 -1117 -45 159 -258 -80 180 -1117 -26 -1117 -1117 151 -1117 -139 14 125 -1117 -139 172 -107 74 61 -12 -1117 22 -239 -144 104 -1117 -239 136 34 -26 161 -144 -1117 41 -1117 -1117 125 -258 -1117 195 -265 0 -39 -1117 104 -258 -239 -244 166 -1117 -239 146 15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 23 E= 1.8e-003 0.000000 0.000000 0.695652 0.304348 0.173913 0.260870 0.000000 0.565217 0.000000 0.000000 0.173913 0.826087 0.043478 0.130435 0.826087 0.000000 0.217391 0.000000 0.000000 0.782609 0.000000 0.086957 0.260870 0.652174 0.000000 0.086957 0.782609 0.130435 0.434783 0.347826 0.217391 0.000000 0.304348 0.043478 0.086957 0.565217 0.000000 0.043478 0.608696 0.347826 0.217391 0.695652 0.086957 0.000000 0.347826 0.000000 0.000000 0.652174 0.043478 0.000000 0.913043 0.043478 0.260870 0.173913 0.000000 0.565217 0.043478 0.043478 0.043478 0.869565 0.000000 0.043478 0.652174 0.304348 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][TC]TG[TA][TG]G[ACG][TA][GT][CA][TA]G[TA]T[GT] -------------------------------------------------------------------------------- Time 14.23 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 28 llr = 250 E-value = 4.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 12:15::::31::3: pos.-specific C :1:1:2111::313: probability G 6139183:47:38:5 matrix T 367:4:695:94144 bits 2.1 1.9 1.7 1.5 * Relative 1.3 * * * Entropy 1.1 ** * * ** * (12.9 bits) 0.9 ** *** ** * 0.6 * ********* * * 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel GTTGAGTTTGTTGTG consensus TAG TCG GA G CT sequence C A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 4660 110 4.80e-07 GAGCCATCTG ATTGAGTTTGTTGCG AAGCAGGAAC 2455 77 9.01e-07 TGCCGTTGGC GTTGAGTTTGAGGCG AGAGAGATGA 25762 34 1.43e-06 AAAACAAAGG TATGTGTTGGTTGCG GGCATCATTA 4573 88 2.16e-06 GTGCTGAATC GTTGTCGTTGTCGTT TGATTGGTGC 6581 277 4.59e-06 TGATTTGCAG TTTGTGTTTGATGTT TGTGAGAAGA 22450 271 5.19e-06 TAGTGAGCTA GATGTGTTGGTGCTT CGAGGTCTGT 11906 86 5.19e-06 GCTGTGCACA GTGGAGGTGATCGTT TCACTGCTAG 25457 231 5.84e-06 CAGTTGTGGC GTGGGGGTGGTGGTT CGGAGGCGGG 17036 37 5.84e-06 TGCCGAAGAC GATGACTTTGTCGAT CCTCCCCAAC 5871 215 6.54e-06 GGTGTATCTA GTTGTGGTTGTGTAG TACGTTCTTG 263051 98 7.33e-06 GAGTCGAGAG GTGATGTTTGTTGCG ACGGCGAAGT 25619 169 9.16e-06 AAGTGCTTGC TTTGGCTTTGTTGCG AACCGCGATC 264809 208 1.14e-05 AATCTATTCA TTGGAGTTGGTGCTT TCTTCGTGTT 6378 231 1.26e-05 ATTATCATTG TATGAGTTTGTTCCT TCTCTTCTGC 21089 272 1.26e-05 TCAAAATCGT GGTGTCGTTGTCGTG TCAGTGCATC 12859 364 1.26e-05 TCGGTAACGC ATTGTGTTGGTGCAG CACATCGGAG 11617 134 1.26e-05 AGGCGAGGAA GTTGTGGTGAAGGCG ACAGCACAAA 11981 182 2.76e-05 CTTGGTGATA GTTGAGTTCAATGTG AATGATGGTG 1057 144 3.95e-05 GTATCGGGCT GAGAAGTTTGTTGAT GTGGGGACGT 4938 335 6.52e-05 CACTGGCTGT GTTCAGCTTGTCGAT ATCCGACACA 41306 1 7.64e-05 . AAGGAGTCGGTTGTG AGATGATAAC 21535 414 8.91e-05 TTGAAGCGAA GCTGTGTCTATCGTG AAACTTTATG 264621 38 1.11e-04 CTGCTGCTTT GGGGTGGTCATGGTG AGCGTGTGGT 23316 65 1.38e-04 ACAACACTCG TCTGTCGTGATTGCT ACCGGCTCAA 36337 257 1.48e-04 TGAATTACCG ATTGATTTGATCGCT TCTCACACTT 20935 322 2.50e-04 GAAGAGCCTG GTTGAGCTGGTTTAA TAGCAATCAT 262501 310 4.00e-04 GCACTACCTT GGGGGCTTGGTTGAC CGAGCTACAT 11135 390 5.51e-04 CTATCGTAGG TTTCAGTTTCTGTTG TGATGTCACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4660 4.8e-07 109_[+3]_376 2455 9e-07 76_[+3]_409 25762 1.4e-06 33_[+3]_452 4573 2.2e-06 87_[+3]_398 6581 4.6e-06 276_[+3]_209 22450 5.2e-06 270_[+3]_215 11906 5.2e-06 85_[+3]_400 25457 5.8e-06 230_[+3]_255 17036 5.8e-06 36_[+3]_449 5871 6.5e-06 214_[+3]_271 263051 7.3e-06 97_[+3]_388 25619 9.2e-06 168_[+3]_317 264809 1.1e-05 207_[+3]_278 6378 1.3e-05 230_[+3]_255 21089 1.3e-05 271_[+3]_214 12859 1.3e-05 363_[+3]_122 11617 1.3e-05 133_[+3]_352 11981 2.8e-05 181_[+3]_304 1057 4e-05 143_[+3]_342 4938 6.5e-05 334_[+3]_151 41306 7.6e-05 [+3]_485 21535 8.9e-05 413_[+3]_72 264621 0.00011 37_[+3]_448 23316 0.00014 64_[+3]_421 36337 0.00015 256_[+3]_229 20935 0.00025 321_[+3]_164 262501 0.0004 309_[+3]_176 11135 0.00055 389_[+3]_96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=28 4660 ( 110) ATTGAGTTTGTTGCG 1 2455 ( 77) GTTGAGTTTGAGGCG 1 25762 ( 34) TATGTGTTGGTTGCG 1 4573 ( 88) GTTGTCGTTGTCGTT 1 6581 ( 277) TTTGTGTTTGATGTT 1 22450 ( 271) GATGTGTTGGTGCTT 1 11906 ( 86) GTGGAGGTGATCGTT 1 25457 ( 231) GTGGGGGTGGTGGTT 1 17036 ( 37) GATGACTTTGTCGAT 1 5871 ( 215) GTTGTGGTTGTGTAG 1 263051 ( 98) GTGATGTTTGTTGCG 1 25619 ( 169) TTTGGCTTTGTTGCG 1 264809 ( 208) TTGGAGTTGGTGCTT 1 6378 ( 231) TATGAGTTTGTTCCT 1 21089 ( 272) GGTGTCGTTGTCGTG 1 12859 ( 364) ATTGTGTTGGTGCAG 1 11617 ( 134) GTTGTGGTGAAGGCG 1 11981 ( 182) GTTGAGTTCAATGTG 1 1057 ( 144) GAGAAGTTTGTTGAT 1 4938 ( 335) GTTCAGCTTGTCGAT 1 41306 ( 1) AAGGAGTCGGTTGTG 1 21535 ( 414) GCTGTGTCTATCGTG 1 264621 ( 38) GGGGTGGTCATGGTG 1 23316 ( 65) TCTGTCGTGATTGCT 1 36337 ( 257) ATTGATTTGATCGCT 1 20935 ( 322) GTTGAGCTGGTTTAA 1 262501 ( 310) GGGGGCTTGGTTGAC 1 11135 ( 390) TTTCAGTTTCTGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 13608 bayes= 8.92184 E= 4.8e-001 -87 -1145 136 -13 -28 -167 -114 115 -1145 -1145 27 138 -187 -167 186 -1145 83 -1145 -114 64 -1145 -9 166 -294 -1145 -167 27 123 -1145 -167 -1145 176 -1145 -167 86 87 -6 -267 159 -1145 -87 -1145 -1145 164 -1145 13 44 64 -1145 -67 166 -136 -6 50 -1145 64 -287 -267 108 64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 28 E= 4.8e-001 0.142857 0.000000 0.607143 0.250000 0.214286 0.071429 0.107143 0.607143 0.000000 0.000000 0.285714 0.714286 0.071429 0.071429 0.857143 0.000000 0.464286 0.000000 0.107143 0.428571 0.000000 0.214286 0.750000 0.035714 0.000000 0.071429 0.285714 0.642857 0.000000 0.071429 0.000000 0.928571 0.000000 0.071429 0.428571 0.500000 0.250000 0.035714 0.714286 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.250000 0.321429 0.428571 0.000000 0.142857 0.750000 0.107143 0.250000 0.321429 0.000000 0.428571 0.035714 0.035714 0.500000 0.428571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT][TA][TG]G[AT][GC][TG]T[TG][GA]T[TGC]G[TCA][GT] -------------------------------------------------------------------------------- Time 21.49 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1057 4.62e-04 105_[+2(1.33e-05)]_22_\ [+3(3.95e-05)]_233_[+1(9.08e-05)]_97 11135 1.98e-02 470_[+1(5.78e-06)]_18 11617 1.09e-04 94_[+3(5.84e-06)]_24_[+3(1.26e-05)]_\ 42_[+1(6.55e-05)]_298 11906 9.09e-11 14_[+2(3.35e-10)]_55_[+3(5.19e-06)]_\ 66_[+3(8.26e-05)]_228_[+1(9.92e-07)]_79 11981 2.86e-04 181_[+3(2.76e-05)]_238_\ [+1(4.92e-05)]_26_[+2(1.98e-05)]_12 12859 3.31e-05 86_[+1(2.84e-05)]_107_\ [+2(6.14e-06)]_142_[+3(1.26e-05)]_122 17036 1.05e-04 36_[+3(5.84e-06)]_51_[+1(2.84e-05)]_\ 182_[+2(5.03e-05)]_188 20935 1.68e-02 229_[+2(9.54e-06)]_255 21089 1.99e-04 271_[+3(1.26e-05)]_183_\ [+1(9.92e-07)]_19 21535 6.89e-05 94_[+2(1.37e-06)]_303_\ [+3(8.91e-05)]_47_[+1(4.27e-05)]_13 22450 1.81e-06 22_[+2(1.10e-06)]_138_\ [+1(1.45e-05)]_82_[+3(5.19e-06)]_215 23316 1.11e-02 322_[+1(9.79e-06)]_166 2455 3.11e-04 76_[+3(9.01e-07)]_5_[+2(3.83e-05)]_\ 388 25457 2.13e-05 169_[+1(4.92e-05)]_49_\ [+3(5.84e-06)]_13_[+2(4.66e-06)]_226 25619 3.45e-04 104_[+1(9.68e-05)]_52_\ [+3(9.16e-06)]_47_[+2(3.83e-05)]_254 25762 3.03e-07 33_[+3(1.43e-06)]_151_\ [+2(1.53e-08)]_285 262501 4.05e-05 15_[+1(6.70e-07)]_390_\ [+2(1.13e-05)]_67 263051 6.60e-06 48_[+1(2.84e-05)]_37_[+3(7.33e-06)]_\ 64_[+2(1.70e-06)]_308 264621 7.29e-07 [+2(4.70e-05)]_4_[+2(5.45e-08)]_364_\ [+1(5.09e-06)]_88 264809 6.15e-05 22_[+1(2.20e-07)]_173_\ [+3(1.14e-05)]_278 36337 9.06e-04 127_[+2(9.80e-07)]_357 41306 2.90e-04 [+3(7.64e-05)]_55_[+2(7.35e-06)]_\ 333_[+1(4.92e-05)]_69 4573 1.48e-07 87_[+3(2.16e-06)]_92_[+1(9.79e-06)]_\ 51_[+2(2.46e-07)]_227 4660 3.17e-04 109_[+3(4.80e-07)]_172_\ [+2(4.70e-05)]_188 4938 3.00e-05 334_[+3(6.52e-05)]_117_\ [+1(1.17e-07)]_22 5871 3.66e-05 54_[+1(5.65e-05)]_148_\ [+3(6.54e-06)]_81_[+2(6.73e-06)]_174 6378 3.89e-04 91_[+2(4.39e-05)]_123_\ [+3(1.26e-05)]_236_[+1(7.00e-05)]_7 6581 8.48e-06 141_[+2(2.68e-05)]_12_\ [+1(3.82e-06)]_95_[+3(4.59e-06)]_209 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************