******************************************************************************** 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/58/58.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 2027 1.0000 500 2058 1.0000 500 260392 1.0000 500 263864 1.0000 500 263917 1.0000 500 2958 1.0000 500 bd1037 1.0000 500 bd1150 1.0000 500 bd1160 1.0000 500 bd1161 1.0000 500 bd1192 1.0000 500 bd1216 1.0000 500 bd1304 1.0000 500 bd1306 1.0000 500 bd1342 1.0000 500 bd1350 1.0000 500 bd1387 1.0000 500 bd1403 1.0000 500 bd1449 1.0000 500 bd1527 1.0000 500 bd1542 1.0000 500 bd1658 1.0000 500 bd1755 1.0000 500 bd1765 1.0000 500 bd1766 1.0000 500 bd1778 1.0000 500 bd1820 1.0000 500 bd1837 1.0000 500 bd1863 1.0000 500 bd1983 1.0000 500 bd211 1.0000 500 bd218 1.0000 500 bd298 1.0000 500 bd439 1.0000 500 bd634 1.0000 500 bd672 1.0000 500 bd718 1.0000 500 bd783 1.0000 500 bd841 1.0000 500 bd950 1.0000 500 ThpsCp006 1.0000 500 ThpsCt017 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/58/58.seqs.fa -oc motifs/58 -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= 42 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= 21000 N= 42 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.298 C 0.212 G 0.206 T 0.285 Background letter frequencies (from dataset with add-one prior applied): A 0.298 C 0.212 G 0.206 T 0.285 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 13 llr = 203 E-value = 3.7e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::9:35352142:2:18:2 pos.-specific C :1:11::1::5::1148::11 probability G a649:7447238259428::7 matrix T :36::33::2:242:::2291 bits 2.3 * 2.1 * 1.8 * * * 1.6 * * * * Relative 1.4 * ** * * * Entropy 1.1 * **** * * * **** (22.6 bits) 0.9 ****** * * * ***** 0.7 ****** ** ** ******* 0.5 ************* ******* 0.2 ********************* 0.0 --------------------- Multilevel GGTGAGGAGACGAGGCCGATG consensus TG TAGAGG TA G sequence T TA GT A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 263917 7 1.23e-11 ACCAAT GGTGAGAAGGCGTGGGCGATG AGTCCATCCA 263864 137 1.23e-11 ATTCACCAAT GGTGAGAAGGCGTGGGCGATG AGTCCATCCA bd1161 439 3.10e-11 GATGCTGGAG GGGGAGGAGAGGAAGCCGATG CTATTCGTGC bd298 10 2.22e-09 GGACGGGTC GGTGATGGAGCGGAGGCGATG GGTGAGTTGA 2027 92 1.65e-08 AATGAATGTT GGTGAGAAATATGGGCCGATG AAGGTGAAGA bd1192 223 3.72e-08 CAAGACATCT GCGGAGTGGACTTTGACGATG CCAACTTGGC bd1160 299 7.18e-08 TAACTACTCT GGTGCGTAGAAGTCGCCGTTG TAGTGGCGTC bd218 13 9.09e-08 GGGAGTTGTG GGTGATTGGAGGAACGCGATA ATCGGGACGT bd1863 55 1.76e-07 TTACCAGGCA GGTGATGGGTGGGGGGGTATC ATCTCCGTTC bd1449 466 1.76e-07 TCATTACGAT GTGCATGCGACGATGACGATG CAGACGAAGA bd439 400 2.02e-07 GCAGAGGTGG GTGGAGGAAACAATGCCGATT TGGAGTTGAT bd672 178 3.87e-07 TAGCTTCATT GTTGAGAGGAGGAGGCGTTCG GTTGAGTTTG bd1216 357 6.59e-07 ATACACACAC GTGGAGTAATAGTGGACAATA AATGACAAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263917 1.2e-11 6_[+1]_473 263864 1.2e-11 136_[+1]_343 bd1161 3.1e-11 438_[+1]_41 bd298 2.2e-09 9_[+1]_470 2027 1.7e-08 91_[+1]_388 bd1192 3.7e-08 222_[+1]_257 bd1160 7.2e-08 298_[+1]_181 bd218 9.1e-08 12_[+1]_467 bd1863 1.8e-07 54_[+1]_425 bd1449 1.8e-07 465_[+1]_14 bd439 2e-07 399_[+1]_80 bd672 3.9e-07 177_[+1]_302 bd1216 6.6e-07 356_[+1]_123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=13 263917 ( 7) GGTGAGAAGGCGTGGGCGATG 1 263864 ( 137) GGTGAGAAGGCGTGGGCGATG 1 bd1161 ( 439) GGGGAGGAGAGGAAGCCGATG 1 bd298 ( 10) GGTGATGGAGCGGAGGCGATG 1 2027 ( 92) GGTGAGAAATATGGGCCGATG 1 bd1192 ( 223) GCGGAGTGGACTTTGACGATG 1 bd1160 ( 299) GGTGCGTAGAAGTCGCCGTTG 1 bd218 ( 13) GGTGATTGGAGGAACGCGATA 1 bd1863 ( 55) GGTGATGGGTGGGGGGGTATC 1 bd1449 ( 466) GTGCATGCGACGATGACGATG 1 bd439 ( 400) GTGGAGGAAACAATGCCGATT 1 bd672 ( 178) GTTGAGAGGAGGAGGCGTTCG 1 bd1216 ( 357) GTGGAGTAATAGTGGACAATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20160 bayes= 12.2285 E= 3.7e-008 -1035 -1035 228 -1035 -1035 -146 158 11 -1035 -1035 90 111 -1035 -146 216 -1035 163 -146 -1035 -1035 -1035 -1035 175 11 5 -1035 90 11 85 -146 90 -1035 5 -1035 175 -1035 85 -1035 16 -30 -37 112 58 -1035 -195 -1035 190 -89 37 -1035 16 43 -37 -146 116 -30 -1035 -146 216 -1035 -37 86 90 -1035 -1035 200 -42 -1035 -195 -1035 190 -89 151 -1035 -1035 -89 -1035 -146 -1035 170 -95 -146 175 -188 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 3.7e-008 0.000000 0.000000 1.000000 0.000000 0.000000 0.076923 0.615385 0.307692 0.000000 0.000000 0.384615 0.615385 0.000000 0.076923 0.923077 0.000000 0.923077 0.076923 0.000000 0.000000 0.000000 0.000000 0.692308 0.307692 0.307692 0.000000 0.384615 0.307692 0.538462 0.076923 0.384615 0.000000 0.307692 0.000000 0.692308 0.000000 0.538462 0.000000 0.230769 0.230769 0.230769 0.461538 0.307692 0.000000 0.076923 0.000000 0.769231 0.153846 0.384615 0.000000 0.230769 0.384615 0.230769 0.076923 0.461538 0.230769 0.000000 0.076923 0.923077 0.000000 0.230769 0.384615 0.384615 0.000000 0.000000 0.846154 0.153846 0.000000 0.076923 0.000000 0.769231 0.153846 0.846154 0.000000 0.000000 0.153846 0.000000 0.076923 0.000000 0.923077 0.153846 0.076923 0.692308 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[GT][TG]GA[GT][GAT][AG][GA][AGT][CGA]G[ATG][GAT]G[CGA]CGATG -------------------------------------------------------------------------------- Time 13.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 30 llr = 303 E-value = 1.4e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 9:8525244:83:85: pos.-specific C 1a:342731a:3a:28 probability G ::2::121::12:1:: matrix T ::1242:25:12::42 bits 2.3 * 2.1 * * * 1.8 * * * 1.6 * * * * Relative 1.4 * * * * Entropy 1.1 ** * ** * (14.6 bits) 0.9 *** * * ** * 0.7 *** * ** ** * 0.5 ***** * *** **** 0.2 ***** ***** **** 0.0 ---------------- Multilevel ACAACACATCAACAAC consensus CTC CA C T sequence AT T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- bd672 474 3.29e-08 ATCCCATCTC ACAACACATCATCATC ACACAACAAC bd211 363 1.33e-07 ATCGCTTGAC ACATCACCACAACAAC GTCGTCGTCG bd1192 472 1.33e-07 ACATGATGTT ACATCACCACAACAAC TACGACGCAG bd783 413 7.39e-07 CGTCACGCTC ACACTTCAACATCATC CCGGCAGTTC bd718 485 9.85e-07 CCTCGCCTAA CCACCACAACACCACC 2058 343 9.85e-07 TTCAGAATCG ACAATCCACCATCAAC TGACAACAAC ThpsCt017 361 1.93e-06 AATTCCATTA ACACCTGTTCAACAAC CGGATTCAAT bd1387 236 1.93e-06 AATTCCATTA ACACCTGTTCAACAAC CGGATTCAAT bd1837 290 2.47e-06 GTGACGTGTG ACACCACTCCACCGAC ATAATCGTTA bd1778 482 3.12e-06 TAACACACCT ACTCCACAACACCACC GCC bd1983 470 3.92e-06 TCTACCTCAA ACACACACACACCAAC TATCTCATCC bd950 367 6.02e-06 AAACTCGTAC ACATTGCCTCAACGAC GTACCCTCTT bd1755 287 6.66e-06 ATTGGACGCT ACAACACTTCTGCACC CACCAATTTC bd1820 421 8.13e-06 AGCACTAAAA ACGAAACGTCAGCACC CTTTTCCCGC bd1216 485 1.08e-05 TCCTTCGGCA ACAACAATACACCAAT bd841 202 1.18e-05 GAGAAGTTGA ACATCGCCTCTACATC TTGTGTACAG bd1161 191 1.18e-05 TCTCTTCCTT CCAAACCATCGACAAC AACTTTGGCA bd1449 112 1.54e-05 GAGCCATCAT ACAATCCATCATCTTC CAATCACTAC bd1342 127 1.54e-05 GCTAGTAAAA ACATTAGGCCACCAAC TAATAAAAGC 263917 201 1.54e-05 CCTATTACCA ACAATTAATCGGCATC ATGAGATGGA 263864 331 1.54e-05 CCTATTACCA ACAATTAATCGGCATC ATGAGATGGA bd1658 122 1.82e-05 ATGACGACCG ACGATCGCTCACCGTC CATGATACAA 260392 453 1.82e-05 TTTCATTCAT ACACATCATCATCACT GACACCTCCA bd218 309 2.32e-05 CGTCAACTCC AAGACACAACAACATC CAACCATGAA bd298 418 2.51e-05 CATCCCCACC ACTCTCGCACAGCATC CTCTGCTGCC 2958 404 3.16e-05 CATTTGCAAA ACAACAACAGAGCATC TCATCCCTGC bd1863 443 3.93e-05 GTTCTTTGAC ACGCTACCCCGCCAAT ACTGCTCTCT bd1765 235 3.93e-05 ACAATCGAGG ACAAAGCTTCAACGAT GAATATCACC bd439 166 5.89e-05 GCTGCTGCCA CCGAAGCGACATCATC TCGTCCACGC bd1160 398 8.03e-05 CTCTCTCTCT CCAATACAACCACAAT TCAGGAGGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd672 3.3e-08 473_[+2]_11 bd211 1.3e-07 362_[+2]_122 bd1192 1.3e-07 471_[+2]_13 bd783 7.4e-07 412_[+2]_72 bd718 9.8e-07 484_[+2] 2058 9.8e-07 342_[+2]_142 ThpsCt017 1.9e-06 360_[+2]_124 bd1387 1.9e-06 235_[+2]_249 bd1837 2.5e-06 289_[+2]_195 bd1778 3.1e-06 481_[+2]_3 bd1983 3.9e-06 469_[+2]_15 bd950 6e-06 366_[+2]_118 bd1755 6.7e-06 286_[+2]_198 bd1820 8.1e-06 420_[+2]_64 bd1216 1.1e-05 484_[+2] bd841 1.2e-05 201_[+2]_283 bd1161 1.2e-05 190_[+2]_294 bd1449 1.5e-05 111_[+2]_373 bd1342 1.5e-05 126_[+2]_358 263917 1.5e-05 200_[+2]_284 263864 1.5e-05 330_[+2]_154 bd1658 1.8e-05 121_[+2]_363 260392 1.8e-05 452_[+2]_32 bd218 2.3e-05 308_[+2]_176 bd298 2.5e-05 417_[+2]_67 2958 3.2e-05 403_[+2]_81 bd1863 3.9e-05 442_[+2]_42 bd1765 3.9e-05 234_[+2]_250 bd439 5.9e-05 165_[+2]_319 bd1160 8e-05 397_[+2]_87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=30 bd672 ( 474) ACAACACATCATCATC 1 bd211 ( 363) ACATCACCACAACAAC 1 bd1192 ( 472) ACATCACCACAACAAC 1 bd783 ( 413) ACACTTCAACATCATC 1 bd718 ( 485) CCACCACAACACCACC 1 2058 ( 343) ACAATCCACCATCAAC 1 ThpsCt017 ( 361) ACACCTGTTCAACAAC 1 bd1387 ( 236) ACACCTGTTCAACAAC 1 bd1837 ( 290) ACACCACTCCACCGAC 1 bd1778 ( 482) ACTCCACAACACCACC 1 bd1983 ( 470) ACACACACACACCAAC 1 bd950 ( 367) ACATTGCCTCAACGAC 1 bd1755 ( 287) ACAACACTTCTGCACC 1 bd1820 ( 421) ACGAAACGTCAGCACC 1 bd1216 ( 485) ACAACAATACACCAAT 1 bd841 ( 202) ACATCGCCTCTACATC 1 bd1161 ( 191) CCAAACCATCGACAAC 1 bd1449 ( 112) ACAATCCATCATCTTC 1 bd1342 ( 127) ACATTAGGCCACCAAC 1 263917 ( 201) ACAATTAATCGGCATC 1 263864 ( 331) ACAATTAATCGGCATC 1 bd1658 ( 122) ACGATCGCTCACCGTC 1 260392 ( 453) ACACATCATCATCACT 1 bd218 ( 309) AAGACACAACAACATC 1 bd298 ( 418) ACTCTCGCACAGCATC 1 2958 ( 404) ACAACAACAGAGCATC 1 bd1863 ( 443) ACGCTACCCCGCCAAT 1 bd1765 ( 235) ACAAAGCTTCAACGAT 1 bd439 ( 166) CCGAAGCGACATCATC 1 bd1160 ( 398) CCAATACAACCACAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 20370 bayes= 10.0802 E= 1.4e-008 154 -67 -1155 -1155 -316 219 -1155 -1155 136 -1155 -31 -209 75 65 -1155 -77 -57 103 -1155 37 65 -8 -63 -51 -84 165 -31 -1155 43 50 -104 -51 43 -67 -1155 71 -1155 219 -263 -1155 136 -266 -63 -209 16 33 -4 -51 -1155 224 -1155 -1155 148 -1155 -63 -309 65 -34 -1155 37 -1155 198 -1155 -77 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 30 E= 1.4e-008 0.866667 0.133333 0.000000 0.000000 0.033333 0.966667 0.000000 0.000000 0.766667 0.000000 0.166667 0.066667 0.500000 0.333333 0.000000 0.166667 0.200000 0.433333 0.000000 0.366667 0.466667 0.200000 0.133333 0.200000 0.166667 0.666667 0.166667 0.000000 0.400000 0.300000 0.100000 0.200000 0.400000 0.133333 0.000000 0.466667 0.000000 0.966667 0.033333 0.000000 0.766667 0.033333 0.133333 0.066667 0.333333 0.266667 0.200000 0.200000 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.133333 0.033333 0.466667 0.166667 0.000000 0.366667 0.000000 0.833333 0.000000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- ACA[AC][CTA][ACT]C[ACT][TA]CA[ACGT]CA[AT]C -------------------------------------------------------------------------------- Time 25.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 22 llr = 272 E-value = 6.9e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:2::2:41114153:6:1:9 pos.-specific C 31::::::1::::21::1321 probability G 693382941582634a3558: matrix T ::57161265:4312:141:: bits 2.3 * 2.1 * 1.8 * 1.6 * * * * Relative 1.4 * * * * * Entropy 1.1 * * * * * ** (17.8 bits) 0.9 ** ** * * * ** 0.7 ** ** * ** * * * ** 0.5 ** ********** *** ** 0.2 ********************* 0.0 --------------------- Multilevel GGTTGTGATGGTGAGGAGGGA consensus C GG G G T ATGA GTC sequence T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd718 220 4.82e-10 CAAGGTGACG GGTTGTGTTGGAGAGGAGAGA GGATACACAG 263917 228 6.62e-09 TGAGATGGAT GGTTGAGATTGGTAGGATCGA CATTGATACA 263864 358 6.62e-09 TGAGATGGAT GGTTGAGATTGGTAGGATCGA CATTGATACA bd298 195 1.07e-07 GAAACGAAGT CGTCGTGTCGGTGGGGATGGA TCAGCTGTCG bd1527 443 2.10e-07 GTGTCCACGT GGTTGGTTTGGGGGGGGGCGC TCGCGTCGCG bd950 86 2.34e-07 TGATTCACGT GGATGGGAAGGAGAAGAGTGA TGCGACGTAT bd783 4 2.60e-07 GCA GGAGGTGATGGGTTGGATTGA TTGGTTGTGG bd672 71 5.84e-07 ATGTACCGAC GGGTGAGGTTGGGCCGTCCGA GTACGGTGTG bd439 422 5.84e-07 ATGCCGATTT GGAGTTGATTGTTGAGACGGA GGATGTGGAA bd1542 265 7.78e-07 CATAGGGTTA GGGTATGATTGAAAAGGGGGA ACTAAAGTAA bd1192 320 7.78e-07 ATTTCGCCCC CGTGGTGGATAAGATGGTGGA TGAGATCGTG 2027 57 8.55e-07 GTATCAGCAA AGGGGTGGTGGTGCTGAGCCC TTCCAATGAA bd1160 329 9.38e-07 GTAGTGGCGT CGTTGTGATGGTGTTGACACA TGAAATGCTC bd218 432 1.23e-06 CTTCGCCAAC GGCTTGGTGGGAGGAGAGGGA CCCGAGCCCA bd1216 63 1.47e-06 ACGACGACGA CGTTGTTGTGGTGATGTGTCA AGCGATGGTG bd1161 79 1.75e-06 GAAGAGAAAC ACTGGGGATTGTAAGGATGGA GGGGGATTGC bd634 28 2.25e-06 AGTGGCTTTA GGTTGTGGCAGAGAAGTGGCC CTACCGTTGT bd1983 267 2.66e-06 TGAATCCGAT CAGGGGGGGTGAGATGGTGGA GACATTTAAC bd1778 107 3.66e-06 AGACTAGCGA GGGTGTTGTATTTGGGAGCGA ATACTTCTCT bd841 71 3.96e-06 ATTGATGCAT CGGTTAGATGATTGAGGTGGA CTTTGTGGTG bd1658 194 6.69e-06 TCTCGGACGG AGATCTGTCTGTTCGGATGGA TCGTGGATAT bd1837 240 7.72e-06 TCTGCCTCTT GCTTGTGGGTAAGCCGGGAGA GTGACATACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd718 4.8e-10 219_[+3]_260 263917 6.6e-09 227_[+3]_252 263864 6.6e-09 357_[+3]_122 bd298 1.1e-07 194_[+3]_285 bd1527 2.1e-07 442_[+3]_37 bd950 2.3e-07 85_[+3]_394 bd783 2.6e-07 3_[+3]_476 bd672 5.8e-07 70_[+3]_409 bd439 5.8e-07 421_[+3]_58 bd1542 7.8e-07 264_[+3]_215 bd1192 7.8e-07 319_[+3]_160 2027 8.5e-07 56_[+3]_423 bd1160 9.4e-07 328_[+3]_151 bd218 1.2e-06 431_[+3]_48 bd1216 1.5e-06 62_[+3]_417 bd1161 1.7e-06 78_[+3]_401 bd634 2.3e-06 27_[+3]_452 bd1983 2.7e-06 266_[+3]_213 bd1778 3.7e-06 106_[+3]_373 bd841 4e-06 70_[+3]_409 bd1658 6.7e-06 193_[+3]_286 bd1837 7.7e-06 239_[+3]_240 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=22 bd718 ( 220) GGTTGTGTTGGAGAGGAGAGA 1 263917 ( 228) GGTTGAGATTGGTAGGATCGA 1 263864 ( 358) GGTTGAGATTGGTAGGATCGA 1 bd298 ( 195) CGTCGTGTCGGTGGGGATGGA 1 bd1527 ( 443) GGTTGGTTTGGGGGGGGGCGC 1 bd950 ( 86) GGATGGGAAGGAGAAGAGTGA 1 bd783 ( 4) GGAGGTGATGGGTTGGATTGA 1 bd672 ( 71) GGGTGAGGTTGGGCCGTCCGA 1 bd439 ( 422) GGAGTTGATTGTTGAGACGGA 1 bd1542 ( 265) GGGTATGATTGAAAAGGGGGA 1 bd1192 ( 320) CGTGGTGGATAAGATGGTGGA 1 2027 ( 57) AGGGGTGGTGGTGCTGAGCCC 1 bd1160 ( 329) CGTTGTGATGGTGTTGACACA 1 bd218 ( 432) GGCTTGGTGGGAGGAGAGGGA 1 bd1216 ( 63) CGTTGTTGTGGTGATGTGTCA 1 bd1161 ( 79) ACTGGGGATTGTAAGGATGGA 1 bd634 ( 28) GGTTGTGGCAGAGAAGTGGCC 1 bd1983 ( 267) CAGGGGGGGTGAGATGGTGGA 1 bd1778 ( 107) GGGTGTTGTATTTGGGAGCGA 1 bd841 ( 71) CGGTTAGATGATTGAGGTGGA 1 bd1658 ( 194) AGATCTGTCTGTTCGGATGGA 1 bd1837 ( 240) GCTTGTGGGTAAGCCGGGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20160 bayes= 10.1936 E= 6.9e-007 -113 37 152 -1110 -271 -122 207 -1110 -71 -222 40 81 -1110 -222 40 126 -271 -222 191 -106 -71 -1110 14 105 -1110 -1110 207 -106 46 -1110 82 -32 -171 -63 -60 116 -171 -1110 114 68 -113 -1110 199 -264 29 -1110 14 52 -171 -1110 152 16 61 -22 40 -164 -13 -122 99 -32 -1110 -1110 228 -1110 99 -1110 40 -106 -1110 -63 114 52 -113 37 114 -106 -1110 -22 199 -1110 154 -63 -1110 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 22 E= 6.9e-007 0.136364 0.272727 0.590909 0.000000 0.045455 0.090909 0.863636 0.000000 0.181818 0.045455 0.272727 0.500000 0.000000 0.045455 0.272727 0.681818 0.045455 0.045455 0.772727 0.136364 0.181818 0.000000 0.227273 0.590909 0.000000 0.000000 0.863636 0.136364 0.409091 0.000000 0.363636 0.227273 0.090909 0.136364 0.136364 0.636364 0.090909 0.000000 0.454545 0.454545 0.136364 0.000000 0.818182 0.045455 0.363636 0.000000 0.227273 0.409091 0.090909 0.000000 0.590909 0.318182 0.454545 0.181818 0.272727 0.090909 0.272727 0.090909 0.409091 0.227273 0.000000 0.000000 1.000000 0.000000 0.590909 0.000000 0.272727 0.136364 0.000000 0.136364 0.454545 0.409091 0.136364 0.272727 0.454545 0.136364 0.000000 0.181818 0.818182 0.000000 0.863636 0.136364 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC]G[TG][TG]G[TG]G[AGT]T[GT]G[TAG][GT][AG][GAT]G[AG][GT][GC]GA -------------------------------------------------------------------------------- Time 37.99 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2027 6.46e-07 56_[+3(8.55e-07)]_14_[+1(1.65e-08)]_\ 388 2058 6.31e-03 342_[+2(9.85e-07)]_142 260392 1.95e-02 452_[+2(1.82e-05)]_32 263864 9.80e-14 136_[+1(1.23e-11)]_173_\ [+2(1.54e-05)]_11_[+3(6.62e-09)]_122 263917 9.80e-14 6_[+1(1.23e-11)]_173_[+2(1.54e-05)]_\ 11_[+3(6.62e-09)]_252 2958 1.38e-01 403_[+2(3.16e-05)]_81 bd1037 1.00e+00 500 bd1150 4.57e-01 500 bd1160 1.47e-07 298_[+1(7.18e-08)]_9_[+3(9.38e-07)]_\ 48_[+2(8.03e-05)]_87 bd1161 3.49e-11 78_[+3(1.75e-06)]_91_[+2(1.18e-05)]_\ 232_[+1(3.10e-11)]_41 bd1192 1.87e-10 11_[+2(5.17e-05)]_123_\ [+2(7.56e-05)]_56_[+1(3.72e-08)]_10_[+3(4.61e-05)]_45_[+3(7.78e-07)]_131_\ [+2(1.33e-07)]_13 bd1216 2.71e-07 62_[+3(1.47e-06)]_172_\ [+3(2.34e-05)]_80_[+1(6.59e-07)]_107_[+2(1.08e-05)] bd1304 5.82e-01 500 bd1306 5.54e-01 500 bd1342 1.24e-01 126_[+2(1.54e-05)]_358 bd1350 9.97e-01 500 bd1387 2.52e-02 235_[+2(1.93e-06)]_249 bd1403 9.28e-01 500 bd1449 2.15e-05 111_[+2(1.54e-05)]_338_\ [+1(1.76e-07)]_14 bd1527 8.22e-04 442_[+3(2.10e-07)]_37 bd1542 8.66e-04 189_[+3(5.97e-05)]_54_\ [+3(7.78e-07)]_215 bd1658 7.41e-04 121_[+2(1.82e-05)]_56_\ [+3(6.69e-06)]_286 bd1755 4.85e-02 286_[+2(6.66e-06)]_198 bd1765 1.39e-01 234_[+2(3.93e-05)]_250 bd1766 7.67e-01 500 bd1778 1.05e-04 106_[+3(3.66e-06)]_354_\ [+2(3.12e-06)]_3 bd1820 3.48e-02 420_[+2(8.13e-06)]_64 bd1837 3.81e-04 239_[+3(7.72e-06)]_29_\ [+2(2.47e-06)]_195 bd1863 1.28e-05 54_[+1(1.76e-07)]_367_\ [+2(3.93e-05)]_42 bd1983 4.42e-05 266_[+3(2.66e-06)]_182_\ [+2(3.92e-06)]_15 bd211 1.05e-03 362_[+2(1.33e-07)]_24_\ [+2(2.72e-05)]_33_[+2(6.68e-05)]_33 bd218 7.64e-08 12_[+1(9.09e-08)]_275_\ [+2(2.32e-05)]_107_[+3(1.23e-06)]_48 bd298 2.81e-10 9_[+1(2.22e-09)]_85_[+3(1.02e-05)]_\ 58_[+3(1.07e-07)]_202_[+2(2.51e-05)]_67 bd439 1.86e-07 165_[+2(5.89e-05)]_218_\ [+1(2.02e-07)]_1_[+3(5.84e-07)]_58 bd634 3.19e-03 27_[+3(2.25e-06)]_452 bd672 3.46e-10 70_[+3(5.84e-07)]_49_[+3(5.12e-05)]_\ 16_[+1(3.87e-07)]_275_[+2(3.29e-08)]_11 bd718 7.17e-09 219_[+3(4.82e-10)]_244_\ [+2(9.85e-07)] bd783 5.16e-06 3_[+3(2.60e-07)]_388_[+2(7.39e-07)]_\ 22_[+2(9.57e-05)]_34 bd841 7.38e-04 70_[+3(3.96e-06)]_110_\ [+2(1.18e-05)]_283 bd950 3.38e-06 85_[+3(2.34e-07)]_260_\ [+2(6.02e-06)]_118 ThpsCp006 1.00e+00 500 ThpsCt017 2.49e-02 360_[+2(1.93e-06)]_124 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************