******************************************************************************** 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/459/459.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 14719 1.0000 500 1720 1.0000 500 20974 1.0000 500 21333 1.0000 500 21438 1.0000 500 21449 1.0000 500 22002 1.0000 500 22215 1.0000 500 22708 1.0000 500 22855 1.0000 500 23314 1.0000 500 23419 1.0000 500 23521 1.0000 500 23700 1.0000 500 23701 1.0000 500 23735 1.0000 500 23794 1.0000 500 23881 1.0000 500 23888 1.0000 500 23933 1.0000 500 23947 1.0000 500 23949 1.0000 500 24108 1.0000 500 24144 1.0000 500 24415 1.0000 500 24559 1.0000 500 24571 1.0000 500 24748 1.0000 500 25439 1.0000 500 25594 1.0000 500 262153 1.0000 500 262247 1.0000 500 262646 1.0000 500 263096 1.0000 500 268220 1.0000 500 268234 1.0000 500 268366 1.0000 500 268966 1.0000 500 269264 1.0000 500 269446 1.0000 500 2928 1.0000 500 3110 1.0000 500 32693 1.0000 500 34418 1.0000 500 36889 1.0000 500 4193 1.0000 500 6273 1.0000 500 6424 1.0000 500 6750 1.0000 500 7333 1.0000 500 7815 1.0000 500 8028 1.0000 500 9406 1.0000 500 9860 1.0000 500 bd1748 1.0000 500 bd1871 1.0000 500 bd1880 1.0000 500 bd1882 1.0000 500 bd1883 1.0000 500 bd388 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/459/459.seqs.fa -oc motifs/459 -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= 60 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= 30000 N= 60 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.237 G 0.232 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.237 G 0.232 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 60 llr = 467 E-value = 1.5e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 56:76:83:451 pos.-specific C 41912a1:a548 probability G :11:2115:22: matrix T 13:21::2:::1 bits 2.1 * 1.9 * * 1.7 * * * 1.5 * * * Relative 1.3 * * * Entropy 1.1 * ** * (11.2 bits) 0.8 * ** * * 0.6 ** ** ** * 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel AACAACAGCCAC consensus CT T A AC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 32693 424 2.20e-07 GGGTACACCT CACAACAGCCCC GCCCCCGCCC 8028 295 1.14e-06 TAGTGACTCG ATCAACAGCCCC TTCCTTGGCC 25594 401 1.14e-06 CGCCCATCCG AACAACAACAAC AGCAGCAGCA 21438 433 1.51e-06 CAACCAAACC AACAACAACACC AAGCCAGCCC 22708 483 1.96e-06 TAGGAGCTAC AACAACAGCAGC AACAAC 269264 453 2.44e-06 GCATTAAATA CACTACAGCCAC TCTCAAACAA 21333 129 3.22e-06 GAGAGTGTTG AACAGCAGCAAC GAGGGCAACG 24108 426 3.81e-06 TCATGGATTG AACCACAGCCAC TGAGCTCTTT 268234 307 4.51e-06 GTCCAAGGCG AGCAACAGCCCC GTTTGGTTTT 23521 451 4.51e-06 GTGAAAGCTA CACAGCAGCACC CTTCTCTCCC 20974 382 6.25e-06 AGAGCCGGAG AACAACAACGCC CAAAAGATGC 22002 353 8.33e-06 TCGAGAGTAA CGCAACAGCAAC TGAAGACAAC 23888 281 1.00e-05 ATACAACACA ACCAACAGCCCC AACTCCTCTC 21449 23 1.19e-05 GCCATCTCTC CACAGCAACACC CTTTCATCCG 9860 457 1.34e-05 ACTATCAATA CTCAACATCAAC CATCGAAGCT bd1882 394 1.50e-05 TTCTCACGGA AACATCAGCCAC AAAATGACCC 268220 26 1.72e-05 CACCTTAAAG AACAACAACGGC GTGTAGTGGC 7333 338 2.54e-05 CCAAAGAGTG AGCACCAGCCCC ACTCTCGGTC 262247 450 2.54e-05 CACCTCACCC AACAACCTCCCC TCTTGTGCAC 24415 373 2.54e-05 TCTCGTGATT TACACCAGCCCC ACTCACTCCA 23881 424 2.54e-05 CGGCAAACGC CTCAGCAGCCGC AACAGAGGCA 24559 99 2.86e-05 GAAGGACAGA CACAAGAGCCCC CATTTTTACT 23700 168 2.86e-05 TGCGGCCCCC CAGAACAGCCCC AGATTTCATT 2928 311 3.24e-05 AGAATTCATT TTCAACAACCAC AGGTGGAGGT 23419 101 3.67e-05 GGGAAACGCC AGCCACAGCCAC AGAACAGACA 36889 157 4.11e-05 TTGCCAAAGG CACAACCTCAAC GGCACAGCAA 23933 4 4.11e-05 GCA ATCAGCAGCGCC TCGAGTATTG 23701 445 4.11e-05 TGGGGGGCCG CACAACGACCAC ACCGGCAAGA 4193 396 5.72e-05 ATAATATCTT CTCAACAACGGC GAGAAACGCC 24748 447 5.72e-05 CCTTGCTTTG CACAACAACCGT TGTTAAACTG 23314 485 7.04e-05 CGGACAACAA CACAACAACGCA AACC 9406 126 9.69e-05 GCTCGAAGAC TACTCCAGCCCC CCAAAAGACG bd1748 351 1.07e-04 AGTCATCAAC CAAAACAGCCCC CCTCAAGGCA 6750 406 1.07e-04 TCGTCTGATC AACCACAGCACT GACTGCCATA bd388 275 1.17e-04 GATATGCTAG ATCTACAGCAAA TACTACCTAC 262646 205 1.30e-04 TTGCGTTAAG AACTACCTCAAC GGTGGAGCTG 6273 483 1.55e-04 ATCATTAAAC AACAAGAACAGC TACACA bd1871 480 1.86e-04 CCTTGCTTTG CACAACAACGGT TATTGAACT 23794 377 1.86e-04 GACCCCAACG CTCAACGGCGAC GGACGCGCGA 34418 38 2.02e-04 GTTTCATACA CTCCACAGCACA CATTGGACAA 22215 323 2.02e-04 GTTGATTCCT CTCAGCCTCCAC TCGATGGCTC bd1880 457 2.21e-04 AGTGAACCAA ACCCCCAGCCCC CCAAACCGTA 24144 254 2.21e-04 AGAGTTGGCT AAGAACATCGAC GTCTTGTGTT 1720 443 2.21e-04 ACATCATACC TACACCCGCAAC TTCAACCTTC 7815 328 2.63e-04 CCAACGGGCA AACTCCAACAAA GGCTCCAACA 23949 373 2.63e-04 TTAACATCGC AACACCGTCAAC CACTTCATCG 3110 415 2.85e-04 ATGTTGAAGT ACCAACCTCAAC TTCGCTTGCT bd1883 307 3.09e-04 GAAATGGCCG AACTGCATCCAT CGCACAAAAT 23947 116 3.09e-04 CATGAATTCT CTCACCATCAAA AATCGTAATG 23735 363 3.34e-04 TTGCAATACC AGCAGGAGCCAC GGTGGAAATT 25439 403 3.62e-04 GCTTTCATTT GACTGCAGCCCC TCCGATGGTT 263096 66 4.54e-04 TCATTGTCGT AACTCCATCAAT TTCATCATGC 22855 191 6.07e-04 ACAACTTGGA AACAACAACGGG TTACTCAAGA 262153 90 6.50e-04 ATTTCATTGA CGCTGCAACCAA GTGCTACCTG 6424 33 6.96e-04 TCGCTCACTC TTCCACCACCAC TAATTCTAAC 268366 411 7.45e-04 CAGGTACATC TTGTACAGCCCC TCCCCCCCTA 269446 379 9.07e-04 CGGGTGGTGT ACCTCCAACCAA ATCATCCCAG 24571 481 9.07e-04 CGTCGTTTCA CTCTTCATCAGC TCATAAAT 268966 237 9.66e-04 TCATCTTCAT CTCAACAACATA TTCACAGTAT 14719 488 1.03e-03 ATGCAGCAAA CACCTCAGCCGT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32693 2.2e-07 423_[+1]_65 8028 1.1e-06 294_[+1]_194 25594 1.1e-06 400_[+1]_88 21438 1.5e-06 432_[+1]_56 22708 2e-06 482_[+1]_6 269264 2.4e-06 452_[+1]_36 21333 3.2e-06 128_[+1]_360 24108 3.8e-06 425_[+1]_63 268234 4.5e-06 306_[+1]_182 23521 4.5e-06 450_[+1]_38 20974 6.3e-06 381_[+1]_107 22002 8.3e-06 352_[+1]_136 23888 1e-05 280_[+1]_208 21449 1.2e-05 22_[+1]_466 9860 1.3e-05 456_[+1]_32 bd1882 1.5e-05 393_[+1]_95 268220 1.7e-05 25_[+1]_463 7333 2.5e-05 337_[+1]_151 262247 2.5e-05 449_[+1]_39 24415 2.5e-05 372_[+1]_116 23881 2.5e-05 423_[+1]_65 24559 2.9e-05 98_[+1]_390 23700 2.9e-05 167_[+1]_321 2928 3.2e-05 310_[+1]_178 23419 3.7e-05 100_[+1]_388 36889 4.1e-05 156_[+1]_332 23933 4.1e-05 3_[+1]_485 23701 4.1e-05 444_[+1]_44 4193 5.7e-05 395_[+1]_93 24748 5.7e-05 446_[+1]_42 23314 7e-05 484_[+1]_4 9406 9.7e-05 125_[+1]_363 bd1748 0.00011 350_[+1]_138 6750 0.00011 405_[+1]_83 bd388 0.00012 274_[+1]_214 262646 0.00013 204_[+1]_284 6273 0.00016 482_[+1]_6 bd1871 0.00019 479_[+1]_9 23794 0.00019 376_[+1]_112 34418 0.0002 37_[+1]_451 22215 0.0002 322_[+1]_166 bd1880 0.00022 456_[+1]_32 24144 0.00022 253_[+1]_235 1720 0.00022 442_[+1]_46 7815 0.00026 327_[+1]_161 23949 0.00026 372_[+1]_116 3110 0.00028 414_[+1]_74 bd1883 0.00031 306_[+1]_182 23947 0.00031 115_[+1]_373 23735 0.00033 362_[+1]_126 25439 0.00036 402_[+1]_86 263096 0.00045 65_[+1]_423 22855 0.00061 190_[+1]_298 262153 0.00065 89_[+1]_399 6424 0.0007 32_[+1]_456 268366 0.00074 410_[+1]_78 269446 0.00091 378_[+1]_110 24571 0.00091 480_[+1]_8 268966 0.00097 236_[+1]_252 14719 0.001 487_[+1]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=60 32693 ( 424) CACAACAGCCCC 1 8028 ( 295) ATCAACAGCCCC 1 25594 ( 401) AACAACAACAAC 1 21438 ( 433) AACAACAACACC 1 22708 ( 483) AACAACAGCAGC 1 269264 ( 453) CACTACAGCCAC 1 21333 ( 129) AACAGCAGCAAC 1 24108 ( 426) AACCACAGCCAC 1 268234 ( 307) AGCAACAGCCCC 1 23521 ( 451) CACAGCAGCACC 1 20974 ( 382) AACAACAACGCC 1 22002 ( 353) CGCAACAGCAAC 1 23888 ( 281) ACCAACAGCCCC 1 21449 ( 23) CACAGCAACACC 1 9860 ( 457) CTCAACATCAAC 1 bd1882 ( 394) AACATCAGCCAC 1 268220 ( 26) AACAACAACGGC 1 7333 ( 338) AGCACCAGCCCC 1 262247 ( 450) AACAACCTCCCC 1 24415 ( 373) TACACCAGCCCC 1 23881 ( 424) CTCAGCAGCCGC 1 24559 ( 99) CACAAGAGCCCC 1 23700 ( 168) CAGAACAGCCCC 1 2928 ( 311) TTCAACAACCAC 1 23419 ( 101) AGCCACAGCCAC 1 36889 ( 157) CACAACCTCAAC 1 23933 ( 4) ATCAGCAGCGCC 1 23701 ( 445) CACAACGACCAC 1 4193 ( 396) CTCAACAACGGC 1 24748 ( 447) CACAACAACCGT 1 23314 ( 485) CACAACAACGCA 1 9406 ( 126) TACTCCAGCCCC 1 bd1748 ( 351) CAAAACAGCCCC 1 6750 ( 406) AACCACAGCACT 1 bd388 ( 275) ATCTACAGCAAA 1 262646 ( 205) AACTACCTCAAC 1 6273 ( 483) AACAAGAACAGC 1 bd1871 ( 480) CACAACAACGGT 1 23794 ( 377) CTCAACGGCGAC 1 34418 ( 38) CTCCACAGCACA 1 22215 ( 323) CTCAGCCTCCAC 1 bd1880 ( 457) ACCCCCAGCCCC 1 24144 ( 254) AAGAACATCGAC 1 1720 ( 443) TACACCCGCAAC 1 7815 ( 328) AACTCCAACAAA 1 23949 ( 373) AACACCGTCAAC 1 3110 ( 415) ACCAACCTCAAC 1 bd1883 ( 307) AACTGCATCCAT 1 23947 ( 116) CTCACCATCAAA 1 23735 ( 363) AGCAGGAGCCAC 1 25439 ( 403) GACTGCAGCCCC 1 263096 ( 66) AACTCCATCAAT 1 22855 ( 191) AACAACAACGGG 1 262153 ( 90) CGCTGCAACCAA 1 6424 ( 33) TTCCACCACCAC 1 268366 ( 411) TTGTACAGCCCC 1 269446 ( 379) ACCTCCAACCAA 1 24571 ( 481) CTCTTCATCAGC 1 268966 ( 237) CTCAACAACATA 1 14719 ( 488) CACCTCAGCCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 29340 bayes= 8.93074 E= 1.5e-010 86 75 -380 -141 114 -183 -121 -9 -399 198 -221 -1255 136 -102 -1255 -41 122 -51 -48 -241 -1255 200 -221 -1255 165 -102 -221 -1255 18 -1255 111 -41 -1255 208 -1255 -1255 47 103 -63 -1255 76 63 -48 -399 -99 166 -380 -141 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 60 E= 1.5e-010 0.483333 0.400000 0.016667 0.100000 0.583333 0.066667 0.100000 0.250000 0.016667 0.933333 0.050000 0.000000 0.683333 0.116667 0.000000 0.200000 0.616667 0.166667 0.166667 0.050000 0.000000 0.950000 0.050000 0.000000 0.833333 0.116667 0.050000 0.000000 0.300000 0.000000 0.500000 0.200000 0.000000 1.000000 0.000000 0.000000 0.366667 0.483333 0.150000 0.000000 0.450000 0.366667 0.166667 0.016667 0.133333 0.750000 0.016667 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC][AT]C[AT]ACA[GAT]C[CA][AC]C -------------------------------------------------------------------------------- Time 24.31 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 19 llr = 224 E-value = 5.6e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 23:::::12::3 pos.-specific C 1:::9:1::2:: probability G 77a9119127:7 matrix T :::119:871a: bits 2.1 * 1.9 ** * * 1.7 ** ** * 1.5 ***** * Relative 1.3 ****** ** Entropy 1.1 ******** *** (17.0 bits) 0.8 ******** *** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GGGGCTGTTGTG consensus AA C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 6273 211 4.23e-08 TAAAATAGTG GGGGCTGTTGTG GAACCTAGGC 2928 377 4.23e-08 GTTGTACCTG GGGGCTGTTGTG AGTACGCCCC 23521 406 1.76e-07 AAGAATAGGT GGGGCTGTGGTG AATACAACCC 23701 425 2.19e-07 AATGAAATCT GGGGCTGTTCTG GGGGGCCGCA 8028 278 3.10e-07 TCTTCAATCG GGGGCTGTAGTG ACTCGATCAA 23314 402 3.10e-07 CATTTGTCCT GGGGCTGTAGTG GCGCCCCCGG 23419 350 1.14e-06 CATTTCTACC AGGGCTGTTCTG CCGACGACAT 3110 339 1.58e-06 TTGGAGAGTC GAGGCTGATGTG CCATCATTTT 22002 311 1.58e-06 CCCGACCAAG GGGGCTGATGTA AAATCATCTC 34418 323 2.83e-06 CTTGTTTGGT GGGGCGGTTGTA TTTGAGAGAC bd388 174 3.29e-06 GCTCCTTCAA GAGGGTGTTGTG CCTCAAGGCA 24144 348 3.29e-06 ACGCTAGCTG AGGGCTGTGCTG GCTGTCTCTT 269264 209 3.67e-06 GATGGTCGCA GAGTCTGTTGTG AAGAAGTATG 23933 297 3.67e-06 GTTCACGATA CGGGCTGTAGTG AGTCGGGCAA 23888 37 4.12e-06 GGTTATCATC AGGGCTGTTTTG TCTGGTATTG 24571 232 4.53e-06 AATATCAAAT GAGGCTGGGGTG ATATTTTCTA 14719 289 5.22e-06 GTGGGTTGGC AGGGCTGGTGTA ACTGCAGAAA 6424 254 7.95e-06 TTGTTCGGTA GAGGTTGTTGTA GACATCATCA 25594 340 8.90e-06 TAGGGGCTTA GGGGCTCTTCTA CGACACTCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6273 4.2e-08 210_[+2]_278 2928 4.2e-08 376_[+2]_112 23521 1.8e-07 405_[+2]_83 23701 2.2e-07 424_[+2]_64 8028 3.1e-07 277_[+2]_211 23314 3.1e-07 401_[+2]_87 23419 1.1e-06 349_[+2]_139 3110 1.6e-06 338_[+2]_150 22002 1.6e-06 310_[+2]_178 34418 2.8e-06 322_[+2]_166 bd388 3.3e-06 173_[+2]_315 24144 3.3e-06 347_[+2]_141 269264 3.7e-06 208_[+2]_280 23933 3.7e-06 296_[+2]_192 23888 4.1e-06 36_[+2]_452 24571 4.5e-06 231_[+2]_257 14719 5.2e-06 288_[+2]_200 6424 7.9e-06 253_[+2]_235 25594 8.9e-06 339_[+2]_149 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=19 6273 ( 211) GGGGCTGTTGTG 1 2928 ( 377) GGGGCTGTTGTG 1 23521 ( 406) GGGGCTGTGGTG 1 23701 ( 425) GGGGCTGTTCTG 1 8028 ( 278) GGGGCTGTAGTG 1 23314 ( 402) GGGGCTGTAGTG 1 23419 ( 350) AGGGCTGTTCTG 1 3110 ( 339) GAGGCTGATGTG 1 22002 ( 311) GGGGCTGATGTA 1 34418 ( 323) GGGGCGGTTGTA 1 bd388 ( 174) GAGGGTGTTGTG 1 24144 ( 348) AGGGCTGTGCTG 1 269264 ( 209) GAGTCTGTTGTG 1 23933 ( 297) CGGGCTGTAGTG 1 23888 ( 37) AGGGCTGTTTTG 1 24571 ( 232) GAGGCTGGGGTG 1 14719 ( 289) AGGGCTGGTGTA 1 6424 ( 254) GAGGTTGTTGTA 1 25594 ( 340) GGGGCTCTTCTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 29340 bayes= 12.0329 E= 5.6e-009 -33 -217 167 -1089 -1 -1089 167 -1089 -1089 -1089 211 -1089 -1089 -1089 203 -233 -1089 192 -214 -233 -1089 -1089 -214 184 -1089 -217 203 -1089 -133 -1089 -114 157 -75 -1089 -55 137 -1089 -17 167 -233 -1089 -1089 -1089 191 -1 -1089 167 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 19 E= 5.6e-009 0.210526 0.052632 0.736842 0.000000 0.263158 0.000000 0.736842 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.947368 0.052632 0.000000 0.894737 0.052632 0.052632 0.000000 0.000000 0.052632 0.947368 0.000000 0.052632 0.947368 0.000000 0.105263 0.000000 0.105263 0.789474 0.157895 0.000000 0.157895 0.684211 0.000000 0.210526 0.736842 0.052632 0.000000 0.000000 0.000000 1.000000 0.263158 0.000000 0.736842 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA][GA]GGCTGTT[GC]T[GA] -------------------------------------------------------------------------------- Time 47.47 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 48 llr = 461 E-value = 1.5e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1211:11:111::2:1122:: pos.-specific C 1:3132322112::::31213 probability G 62261:5:161:a23735135 matrix T 254277286278:67142663 bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 * ** Entropy 1.1 * ** * (13.8 bits) 0.8 * * ** ** * 0.6 * ** * ****** ** 0.4 * ************* *** 0.2 ********************* 0.0 --------------------- Multilevel GTTGTTGTTGTTGTTGTGTTG consensus ACTCCCC AG CA GC sequence GG T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9860 195 2.67e-13 TGTTGTTGTT GTTGTTGTTGTTGTTGTGTTG TTCGGGACGA 14719 153 9.29e-09 CGTCGTCGTT GTTGTTGTTGTTGTTGTTGTC GGTCATGGTG 34418 165 3.11e-08 GGAGGTTAGT GCTGTTCTTGTTGTGGCGTGG TCTGACATTG 21438 226 8.11e-08 GATGTTGTTG GTTGTTGCTGTTGATAAGTTG CCTTCGTTTG 22215 444 9.45e-08 GTTTGGATAT GGTGTCGTTTTTGTTGTATGC CAATTCACCG 6424 431 1.48e-07 CTCGTGGCAA GTAGTTCCTGTTGAGGTGTGG TCGCAACGGT 22708 375 4.57e-07 AAGGGTCACA GAGGCTGTTGATGTTGTGCTT CCGTGAACAA 7815 462 5.23e-07 GTATGTCGTC GTGGCTATCGTCGTTGCGTTG CAGTTGGGAT bd1880 45 1.46e-06 AGCATGGTTG GGTATCGTTATTGTTGTAATG TGATATCTAA 23419 12 1.86e-06 GAGACGTCAT GGTGTATTAGTTGTTGCTTTG TATCAACTGA 25594 45 2.10e-06 CTTCTTTTGC TTTGTTTCCATTGTTGGGATG CATCGAGAGG 4193 330 2.65e-06 TGGCGGTGGT GGCATCCTTGATGTTGTGCTG AGATTTAGTA 24415 161 4.19e-06 AATAACACAT ATCGTTTCTTTTGAGGTGTTT GTGAATGACC 20974 262 5.23e-06 TTTTGCTGTG AGGGCTGCTGTTGTTTGGTTC CGAGAGCTCG 2928 14 5.83e-06 GCAATGTACG CATTTCGTCTTTGTTGCTTTG TTTTGTTTGA 269264 230 6.50e-06 GAAGAAGTAT GGTATTGTAAGTGATGCGTTG AGTGATGAGT 262247 348 7.23e-06 AACTCACCTC ATCGTTCTTCGTGTTGGTTTC TCTCTTCATG 23701 349 7.23e-06 CGAAATAAGC TGGGCCTTTGTTGTTGTAATT CACTAGACGA 3110 239 8.93e-06 TGAAGATATC GTCGTCGTAGATGATGTAATG TATTGCGACG 268966 7 8.93e-06 GCAGAT GATGTAGTTTGTGGTGGCTTG GATACGATTA 9406 52 1.10e-05 CGCCGAGGTG GTTGCTGTTCTCGTCGGGTGC ATTGAGTTCC bd1748 114 1.34e-05 AGTTGAGACG TGCTTCTCCTTTGTTGGGTTG GCACGACGGA 24144 284 1.34e-05 TTATCTCAAA GAGCTTGTTGTTGGTTGGTCG GCCGGGGGAG 6273 84 1.49e-05 GTGGAGCAAA GTGCTCTTGGTTGTTGCGAGT CGTGTTATCG 268366 192 1.49e-05 TAATGGCATA GTAGCAGTGTTTGTTGTGCTC ATTCGTACAG 23888 4 1.64e-05 TTT GTTTTTGTTCTCGAGGCTCTT TAGGTTATCA 32693 268 1.81e-05 GAATTGGTTT TGTGTTTCAGTTGGTGTTTGC CGGCGGTTAA 23700 142 1.99e-05 TTGCTCTCTT GCCGGTGTGGTCGTTGTGCGG CCCCCCAGAA 24748 42 2.19e-05 CCACCTTGGC CTTGGTTTTGGCGTTGGATTC ATCGGCATTT 22002 149 2.19e-05 TGCAAAGTTT GACTTTGTTAGTGGTGCCCTC TGTTTTACAT bd388 384 2.41e-05 TCACGAAAGA GACTTTGCTGTTGATGATTCT TACAAATCAT 7333 181 2.65e-05 AAATCACACA GATGTGTTTTTTGTTATCTTT TAACATACAC 23933 103 3.18e-05 TTCGTCTACC TTTCGTCTCATTGTTGTGTTT TAAAGTCCCA 8028 2 3.49e-05 G GGCTTCATTTTTGGGGGCTTG CCCGGTCCCT 6750 236 3.49e-05 CGAGCAAACA TTCTCTCTTTCTGAGGGGCTG CGACTGTGAT 1720 462 3.82e-05 AACTTCAACC TTCTCTCTCGTTGATACGATT GGTGAACGAC bd1882 253 4.17e-05 GTTCCCGCCA TTTGTTGTTATTGGGACAGGG GCTTCGGTTT 23794 410 4.17e-05 CGCGCACAGA GAGGCTCTTGCTGTTTCACGC ACAAGACAGG 23881 239 4.56e-05 CTTCAGCTCT CTCGTCCTGGTCGTTGAATGC ACATCATAAA 25439 377 4.97e-05 CAGCCCTCCT CATTTTGTCATTGTTAGCTTT CATTTGACTG 22855 22 6.43e-05 GAAGGAACGA GTGATTGTGGGCGATCCGTTG TATGTTGTTA 36889 411 6.99e-05 CACACGACCA CTTGCTCTTGCTGTGCTTTGC TCATTTCATT 262646 279 8.25e-05 TGCTCTGTGC ATAGTTATCGTTGGTGTATCG CACGACTGAT 262153 124 8.95e-05 TTGTCCGAGT GGATCTGCTGCTGAGGTGAGT TGCTGGTTGC 268220 240 1.14e-04 CGGCGTGAAG GTGTTGCTTGTTGTGAAGAGT TATTGAAGAA 24108 68 1.23e-04 GAAAGCGCTA GATACTTCTCCTGGGGGGTGG TTGGGTGTGG 23947 358 1.43e-04 ACGGATGAAA GACGTTGCTGTCTTGACGCTC AGTTCAGTAA 21333 378 1.43e-04 GATAAAATGA CTGATTCTTGTTGGGTGAGTG TTTGTAAAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9860 2.7e-13 194_[+3]_285 14719 9.3e-09 152_[+3]_327 34418 3.1e-08 164_[+3]_315 21438 8.1e-08 225_[+3]_254 22215 9.5e-08 443_[+3]_36 6424 1.5e-07 430_[+3]_49 22708 4.6e-07 374_[+3]_105 7815 5.2e-07 461_[+3]_18 bd1880 1.5e-06 44_[+3]_435 23419 1.9e-06 11_[+3]_468 25594 2.1e-06 44_[+3]_435 4193 2.7e-06 329_[+3]_150 24415 4.2e-06 160_[+3]_319 20974 5.2e-06 261_[+3]_218 2928 5.8e-06 13_[+3]_466 269264 6.5e-06 229_[+3]_250 262247 7.2e-06 347_[+3]_132 23701 7.2e-06 348_[+3]_131 3110 8.9e-06 238_[+3]_241 268966 8.9e-06 6_[+3]_473 9406 1.1e-05 51_[+3]_428 bd1748 1.3e-05 113_[+3]_366 24144 1.3e-05 283_[+3]_196 6273 1.5e-05 83_[+3]_396 268366 1.5e-05 191_[+3]_288 23888 1.6e-05 3_[+3]_476 32693 1.8e-05 267_[+3]_212 23700 2e-05 141_[+3]_338 24748 2.2e-05 41_[+3]_438 22002 2.2e-05 148_[+3]_331 bd388 2.4e-05 383_[+3]_96 7333 2.6e-05 180_[+3]_299 23933 3.2e-05 102_[+3]_377 8028 3.5e-05 1_[+3]_478 6750 3.5e-05 235_[+3]_244 1720 3.8e-05 461_[+3]_18 bd1882 4.2e-05 252_[+3]_227 23794 4.2e-05 409_[+3]_70 23881 4.6e-05 238_[+3]_241 25439 5e-05 376_[+3]_103 22855 6.4e-05 21_[+3]_458 36889 7e-05 410_[+3]_69 262646 8.2e-05 278_[+3]_201 262153 8.9e-05 123_[+3]_356 268220 0.00011 239_[+3]_240 24108 0.00012 67_[+3]_412 23947 0.00014 357_[+3]_122 21333 0.00014 377_[+3]_102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=48 9860 ( 195) GTTGTTGTTGTTGTTGTGTTG 1 14719 ( 153) GTTGTTGTTGTTGTTGTTGTC 1 34418 ( 165) GCTGTTCTTGTTGTGGCGTGG 1 21438 ( 226) GTTGTTGCTGTTGATAAGTTG 1 22215 ( 444) GGTGTCGTTTTTGTTGTATGC 1 6424 ( 431) GTAGTTCCTGTTGAGGTGTGG 1 22708 ( 375) GAGGCTGTTGATGTTGTGCTT 1 7815 ( 462) GTGGCTATCGTCGTTGCGTTG 1 bd1880 ( 45) GGTATCGTTATTGTTGTAATG 1 23419 ( 12) GGTGTATTAGTTGTTGCTTTG 1 25594 ( 45) TTTGTTTCCATTGTTGGGATG 1 4193 ( 330) GGCATCCTTGATGTTGTGCTG 1 24415 ( 161) ATCGTTTCTTTTGAGGTGTTT 1 20974 ( 262) AGGGCTGCTGTTGTTTGGTTC 1 2928 ( 14) CATTTCGTCTTTGTTGCTTTG 1 269264 ( 230) GGTATTGTAAGTGATGCGTTG 1 262247 ( 348) ATCGTTCTTCGTGTTGGTTTC 1 23701 ( 349) TGGGCCTTTGTTGTTGTAATT 1 3110 ( 239) GTCGTCGTAGATGATGTAATG 1 268966 ( 7) GATGTAGTTTGTGGTGGCTTG 1 9406 ( 52) GTTGCTGTTCTCGTCGGGTGC 1 bd1748 ( 114) TGCTTCTCCTTTGTTGGGTTG 1 24144 ( 284) GAGCTTGTTGTTGGTTGGTCG 1 6273 ( 84) GTGCTCTTGGTTGTTGCGAGT 1 268366 ( 192) GTAGCAGTGTTTGTTGTGCTC 1 23888 ( 4) GTTTTTGTTCTCGAGGCTCTT 1 32693 ( 268) TGTGTTTCAGTTGGTGTTTGC 1 23700 ( 142) GCCGGTGTGGTCGTTGTGCGG 1 24748 ( 42) CTTGGTTTTGGCGTTGGATTC 1 22002 ( 149) GACTTTGTTAGTGGTGCCCTC 1 bd388 ( 384) GACTTTGCTGTTGATGATTCT 1 7333 ( 181) GATGTGTTTTTTGTTATCTTT 1 23933 ( 103) TTTCGTCTCATTGTTGTGTTT 1 8028 ( 2) GGCTTCATTTTTGGGGGCTTG 1 6750 ( 236) TTCTCTCTTTCTGAGGGGCTG 1 1720 ( 462) TTCTCTCTCGTTGATACGATT 1 bd1882 ( 253) TTTGTTGTTATTGGGACAGGG 1 23794 ( 410) GAGGCTCTTGCTGTTTCACGC 1 23881 ( 239) CTCGTCCTGGTCGTTGAATGC 1 25439 ( 377) CATTTTGTCATTGTTAGCTTT 1 22855 ( 22) GTGATTGTGGGCGATCCGTTG 1 36889 ( 411) CTTGCTCTTGCTGTGCTTTGC 1 262646 ( 279) ATAGTTATCGTTGGTGTATCG 1 262153 ( 124) GGATCTGCTGCTGAGGTGAGT 1 268220 ( 240) GTGTTGCTTGTTGTGAAGAGT 1 24108 ( 68) GATACTTCTCCTGGGGGGTGG 1 23947 ( 358) GACGTTGCTGTCTTGACGCTC 1 21333 ( 378) CTGATTCTTGTTGGGTGAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 28800 bayes= 9.67451 E= 1.5e-008 -167 -92 143 -67 -21 -251 -2 91 -167 19 -16 72 -109 -192 133 -21 -1223 8 -189 137 -209 -19 -248 137 -209 8 105 -35 -1223 -5 -1223 154 -167 -51 -115 128 -86 -151 133 -50 -209 -119 -89 142 -1223 -51 -1223 165 -1223 -1223 208 -367 -21 -1223 -31 114 -1223 -351 22 142 -86 -251 165 -167 -167 19 22 50 -35 -119 117 -67 -67 -34 -189 114 -1223 -192 33 128 -1223 19 105 -9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 48 E= 1.5e-008 0.083333 0.125000 0.625000 0.166667 0.229167 0.041667 0.229167 0.500000 0.083333 0.270833 0.208333 0.437500 0.125000 0.062500 0.583333 0.229167 0.000000 0.250000 0.062500 0.687500 0.062500 0.208333 0.041667 0.687500 0.062500 0.250000 0.479167 0.208333 0.000000 0.229167 0.000000 0.770833 0.083333 0.166667 0.104167 0.645833 0.145833 0.083333 0.583333 0.187500 0.062500 0.104167 0.125000 0.708333 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.979167 0.020833 0.229167 0.000000 0.187500 0.583333 0.000000 0.020833 0.270833 0.708333 0.145833 0.041667 0.729167 0.083333 0.083333 0.270833 0.270833 0.375000 0.208333 0.104167 0.520833 0.166667 0.166667 0.187500 0.062500 0.583333 0.000000 0.062500 0.291667 0.645833 0.000000 0.270833 0.479167 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[TAG][TCG][GT][TC][TC][GCT][TC]TGTTG[TA][TG]G[TCG][GA]T[TG][GCT] -------------------------------------------------------------------------------- Time 70.63 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14719 9.22e-07 84_[+2(7.43e-05)]_56_[+3(9.29e-09)]_\ 115_[+2(5.22e-06)]_200 1720 5.01e-02 461_[+3(3.82e-05)]_18 20974 4.62e-05 261_[+3(5.23e-06)]_99_\ [+1(6.25e-06)]_107 21333 4.58e-03 128_[+1(3.22e-06)]_360 21438 2.58e-06 225_[+3(8.11e-08)]_9_[+3(5.91e-05)]_\ 120_[+1(7.91e-05)]_24_[+1(1.51e-06)]_56 21449 9.56e-02 22_[+1(1.19e-05)]_21_[+1(1.72e-05)]_\ 433 22002 5.49e-06 148_[+3(2.19e-05)]_141_\ [+2(1.58e-06)]_30_[+1(8.33e-06)]_136 22215 3.77e-04 417_[+3(4.97e-05)]_5_[+3(9.45e-08)]_\ 36 22708 4.75e-06 374_[+3(4.57e-07)]_87_\ [+1(1.96e-06)]_6 22855 1.36e-01 21_[+3(6.43e-05)]_458 23314 2.86e-04 401_[+2(3.10e-07)]_71_\ [+1(7.04e-05)]_4 23419 1.69e-06 11_[+3(1.86e-06)]_68_[+1(3.67e-05)]_\ 237_[+2(1.14e-06)]_139 23521 1.11e-05 92_[+2(8.90e-06)]_301_\ [+2(1.76e-07)]_33_[+1(4.51e-06)]_22_[+1(1.50e-05)]_4 23700 4.76e-03 141_[+3(1.99e-05)]_5_[+1(2.86e-05)]_\ 321 23701 1.44e-06 348_[+3(7.23e-06)]_55_\ [+2(2.19e-07)]_8_[+1(4.11e-05)]_44 23735 1.80e-01 500 23794 4.24e-02 409_[+3(4.17e-05)]_70 23881 1.24e-03 238_[+3(4.56e-05)]_164_\ [+1(2.54e-05)]_65 23888 1.17e-05 3_[+3(1.64e-05)]_12_[+2(4.12e-06)]_\ 232_[+1(1.00e-05)]_174_[+1(5.72e-05)]_22 23933 6.47e-05 3_[+1(4.11e-05)]_87_[+3(3.18e-05)]_\ 173_[+2(3.67e-06)]_192 23947 1.22e-01 500 23949 3.96e-01 500 24108 1.64e-03 425_[+1(3.81e-06)]_63 24144 1.16e-04 283_[+3(1.34e-05)]_43_\ [+2(3.29e-06)]_141 24415 6.44e-04 160_[+3(4.19e-06)]_191_\ [+1(2.54e-05)]_116 24559 9.96e-02 98_[+1(2.86e-05)]_390 24571 1.90e-02 231_[+2(4.53e-06)]_257 24748 1.12e-02 41_[+3(2.19e-05)]_384_\ [+1(5.72e-05)]_42 25439 5.90e-02 376_[+3(4.97e-05)]_103 25594 5.29e-07 7_[+3(1.99e-05)]_16_[+3(2.10e-06)]_\ 274_[+2(8.90e-06)]_49_[+1(1.14e-06)]_6_[+1(5.20e-05)]_57_[+1(9.69e-05)]_1 262153 1.01e-01 123_[+3(8.95e-05)]_356 262247 2.12e-03 347_[+3(7.23e-06)]_81_\ [+1(2.54e-05)]_39 262646 3.00e-02 278_[+3(8.25e-05)]_201 263096 4.30e-01 500 268220 7.13e-03 25_[+1(1.72e-05)]_365_\ [+1(7.04e-05)]_86 268234 1.97e-02 306_[+1(4.51e-06)]_182 268366 1.44e-03 191_[+3(1.49e-05)]_32_\ [+2(1.94e-05)]_244 268966 2.42e-02 6_[+3(8.93e-06)]_473 269264 1.31e-06 208_[+2(3.67e-06)]_9_[+3(6.50e-06)]_\ 202_[+1(2.44e-06)]_36 269446 7.68e-01 500 2928 2.17e-07 13_[+3(5.83e-06)]_276_\ [+1(3.24e-05)]_54_[+2(4.23e-08)]_96_[+1(8.80e-05)]_4 3110 5.30e-05 238_[+3(8.93e-06)]_79_\ [+2(1.58e-06)]_150 32693 6.06e-05 267_[+3(1.81e-05)]_135_\ [+1(2.20e-07)]_65 34418 4.32e-07 164_[+3(3.11e-08)]_137_\ [+2(2.83e-06)]_166 36889 2.08e-02 156_[+1(4.11e-05)]_242_\ [+3(6.99e-05)]_69 4193 3.82e-04 329_[+3(2.65e-06)]_45_\ [+1(5.72e-05)]_93 6273 2.01e-06 83_[+3(1.49e-05)]_106_\ [+2(4.23e-08)]_161_[+3(7.60e-05)]_96 6424 1.20e-05 253_[+2(7.95e-06)]_165_\ [+3(1.48e-07)]_49 6750 2.41e-02 235_[+3(3.49e-05)]_244 7333 6.93e-03 180_[+3(2.65e-05)]_136_\ [+1(2.54e-05)]_151 7815 4.26e-04 461_[+3(5.23e-07)]_18 8028 3.22e-07 1_[+3(3.49e-05)]_255_[+2(3.10e-07)]_\ 5_[+1(1.14e-06)]_62_[+1(3.22e-06)]_99_[+1(6.29e-05)]_9 9406 9.32e-03 51_[+3(1.10e-05)]_53_[+1(9.69e-05)]_\ 363 9860 1.52e-10 164_[+3(1.33e-08)]_9_[+3(2.67e-13)]_\ 241_[+1(1.34e-05)]_32 bd1748 4.47e-03 113_[+3(1.34e-05)]_366 bd1871 1.74e-01 500 bd1880 2.26e-03 44_[+3(1.46e-06)]_435 bd1882 1.53e-03 252_[+3(4.17e-05)]_120_\ [+1(1.50e-05)]_95 bd1883 2.73e-01 500 bd388 1.13e-04 173_[+2(3.29e-06)]_198_\ [+3(2.41e-05)]_96 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************