******************************************************************************** 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/10/10.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10343 1.0000 500 10345 1.0000 500 10360 1.0000 500 10767 1.0000 500 11632 1.0000 500 11698 1.0000 500 12089 1.0000 500 1967 1.0000 500 2078 1.0000 500 20940 1.0000 500 233 1.0000 500 260844 1.0000 500 261499 1.0000 500 262307 1.0000 500 263924 1.0000 500 264181 1.0000 500 264421 1.0000 500 26759 1.0000 500 268324 1.0000 500 269147 1.0000 500 269696 1.0000 500 269699 1.0000 500 270370 1.0000 500 30851 1.0000 500 34030 1.0000 500 34125 1.0000 500 37338 1.0000 500 38724 1.0000 500 412 1.0000 500 4277 1.0000 500 4700 1.0000 500 4819 1.0000 500 4820 1.0000 500 6176 1.0000 500 6528 1.0000 500 6529 1.0000 500 7647 1.0000 500 7883 1.0000 500 8064 1.0000 500 8073 1.0000 500 bd838 1.0000 500 bd897 1.0000 52 ******************************************************************************** ******************************************************************************** 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/10/10.seqs.fa -oc motifs/10 -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= 20552 N= 42 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.270 C 0.230 G 0.227 T 0.273 Background letter frequencies (from dataset with add-one prior applied): A 0.270 C 0.230 G 0.227 T 0.273 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 29 llr = 333 E-value = 1.9e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1:1312::111:2::2::2:2 pos.-specific C 12:11:1:1:1::1:3::33: probability G :84174:38328149218147 matrix T 81452386:562761382431 bits 2.1 1.9 1.7 * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * * * * * ** * (16.6 bits) 0.9 ** *** * * ** * 0.6 *** * **** **** ** * 0.4 *** * ********* ** ** 0.2 *************** ***** 0.0 --------------------- Multilevel TGTTGGTTGTTGTTGTTGTGG consensus GA T G G T G C CCA sequence A AT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 30851 364 1.81e-09 GGTTGTGGCC TGTTCGTTGTTGTTGTTGTTG CATCTTCTCA 11632 148 2.54e-09 ATGGCCGCCG TGTTGTTTGGTGTTGCTTTGG TGGAAAAGTA 4700 356 7.75e-09 GTTCGTCTGG TGTTGATGGTTGATGGTGTCG CCGACCGACG 12089 249 1.84e-08 GTCGTCGTCG TCGTCGTTGTTGTTGTTGTTG TTATTGTTGT 37338 189 2.79e-08 GAGATGCCGT TGGTGTTGGTGGGTGGTGTGG CACGGATGGC 4819 19 3.19e-08 AGGTTGGTAG TGGAGGTGGTGGTTGATGGGG CGACATTGAT 10345 247 1.13e-07 GAAGCGATTC TGTATGTTGTTGTGTCTGCTG ATGGTTGTAT 10343 62 1.13e-07 GAAGCGATTC TGTATGTTGTTGTGTCTGCTG ATGGTTGTAT 269147 343 1.80e-07 TTGCGTGGTA TGTTGATTGGAGATGATGACG CCAATGCATG 8064 253 2.26e-07 GAGAGTTGTG AGTTGGTGGGTGTGGATTTGG CATGGATAGG 264421 49 2.83e-07 AGTTTATGGC CGAGGGCTGTTGTGGCTGCGG TGATAAGATG 261499 332 9.89e-07 AGGTCGTCAG TGGGGGTGGGGGTGGTGGCGT GCAGGTCGTG 4277 369 1.32e-06 TCGTCTGTAT TGTAGATTATTTGTGTTGAGG TTCGGAGTTC 6528 17 1.46e-06 TGTGATGGAT TGGTGTTGAGATTGGTTGCTG CAATTATAAA 262307 284 3.02e-06 CGGCTGTCGC TGTCGGCTGTCGTCGCTGATG CACCTGATGC 1967 73 4.28e-06 CAAGTTGTAG TTGATATTGTAGTTGTTGCCA ACAATGACGG 4820 142 4.66e-06 TATCGTGAGA CCATGGTTGATGATGTTGATG CAAATGGAGG 263924 102 5.50e-06 ATGTTGTGAA TCTGTTTGGGTGTGGCTTTGA TGATTGATTG 8073 36 6.48e-06 GATGTTGTGC TGTCGACGAGTGAGGATGTCG CTGCTGGGAG 11698 128 7.62e-06 GCTTCGCTGC CGGTGATTGGATTTGCAGCCG TCTTATCGGT 268324 200 8.25e-06 TCTTCGCTCA TGGTGTTTGTTTGGGCGTGTG GTGCGGGGTG bd838 260 8.92e-06 ATATTGGTTG AGAGGTCGGTTGTCGCTGTCG AACTTGCTTT 6529 46 9.65e-06 CTGAAAGACT TGTTGCTTCGGTTTGGTGACG ACACGTCGAC 2078 419 1.31e-05 CAACTTCCTC TCGTCGTCGATGTGGTTGACA CGCATAAGTC 412 382 1.41e-05 AAGCATACAA TGTAAATTGATGTTGGTTTGT GGGTGAAGTT 34030 19 1.52e-05 CGTATTCTAA TGGTATTTGGGTGGGAGGCGG CACCGGCTTT 38724 13 2.34e-05 ATCGTCAGAG GGGAGGATCTTGTTGTTGTGA CTTTTTTCAG 270370 122 2.51e-05 AGGGCTCAAA TTGATGTGGATGTTTGTGTCA TTGGCTGTGT 10360 292 4.56e-05 CTCCTACCCT TCACGTTTGTCGATGTGGCCA CAAATATTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 30851 1.8e-09 363_[+1]_116 11632 2.5e-09 147_[+1]_332 4700 7.7e-09 355_[+1]_124 12089 1.8e-08 248_[+1]_231 37338 2.8e-08 188_[+1]_291 4819 3.2e-08 18_[+1]_461 10345 1.1e-07 246_[+1]_233 10343 1.1e-07 61_[+1]_418 269147 1.8e-07 342_[+1]_137 8064 2.3e-07 252_[+1]_227 264421 2.8e-07 48_[+1]_431 261499 9.9e-07 331_[+1]_148 4277 1.3e-06 368_[+1]_111 6528 1.5e-06 16_[+1]_463 262307 3e-06 283_[+1]_196 1967 4.3e-06 72_[+1]_407 4820 4.7e-06 141_[+1]_338 263924 5.5e-06 101_[+1]_378 8073 6.5e-06 35_[+1]_444 11698 7.6e-06 127_[+1]_352 268324 8.2e-06 199_[+1]_280 bd838 8.9e-06 259_[+1]_220 6529 9.7e-06 45_[+1]_434 2078 1.3e-05 418_[+1]_61 412 1.4e-05 381_[+1]_98 34030 1.5e-05 18_[+1]_461 38724 2.3e-05 12_[+1]_467 270370 2.5e-05 121_[+1]_358 10360 4.6e-05 291_[+1]_188 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=29 30851 ( 364) TGTTCGTTGTTGTTGTTGTTG 1 11632 ( 148) TGTTGTTTGGTGTTGCTTTGG 1 4700 ( 356) TGTTGATGGTTGATGGTGTCG 1 12089 ( 249) TCGTCGTTGTTGTTGTTGTTG 1 37338 ( 189) TGGTGTTGGTGGGTGGTGTGG 1 4819 ( 19) TGGAGGTGGTGGTTGATGGGG 1 10345 ( 247) TGTATGTTGTTGTGTCTGCTG 1 10343 ( 62) TGTATGTTGTTGTGTCTGCTG 1 269147 ( 343) TGTTGATTGGAGATGATGACG 1 8064 ( 253) AGTTGGTGGGTGTGGATTTGG 1 264421 ( 49) CGAGGGCTGTTGTGGCTGCGG 1 261499 ( 332) TGGGGGTGGGGGTGGTGGCGT 1 4277 ( 369) TGTAGATTATTTGTGTTGAGG 1 6528 ( 17) TGGTGTTGAGATTGGTTGCTG 1 262307 ( 284) TGTCGGCTGTCGTCGCTGATG 1 1967 ( 73) TTGATATTGTAGTTGTTGCCA 1 4820 ( 142) CCATGGTTGATGATGTTGATG 1 263924 ( 102) TCTGTTTGGGTGTGGCTTTGA 1 8073 ( 36) TGTCGACGAGTGAGGATGTCG 1 11698 ( 128) CGGTGATTGGATTTGCAGCCG 1 268324 ( 200) TGGTGTTTGTTTGGGCGTGTG 1 bd838 ( 260) AGAGGTCGGTTGTCGCTGTCG 1 6529 ( 46) TGTTGCTTCGGTTTGGTGACG 1 2078 ( 419) TCGTCGTCGATGTGGTTGACA 1 412 ( 382) TGTAAATTGATGTTGGTTTGT 1 34030 ( 19) TGGTATTTGGGTGGGAGGCGG 1 38724 ( 13) GGGAGGATCTTGTTGTTGTGA 1 270370 ( 122) TTGATGTGGATGTTTGTGTCA 1 10360 ( 292) TCACGTTTGTCGATGTGGCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19712 bayes= 10.0482 E= 1.9e-012 -197 -115 -272 154 -1150 -41 174 -198 -97 -1150 87 72 3 -115 -72 82 -197 -115 153 -66 -16 -273 98 2 -297 -73 -1150 160 -1150 -273 60 118 -139 -173 187 -1150 -97 -1150 60 92 -97 -173 -40 118 -1150 -1150 180 -40 -65 -1150 -72 134 -1150 -173 74 101 -1150 -1150 198 -140 -65 43 -40 34 -297 -1150 -72 160 -1150 -1150 187 -66 -39 43 -172 60 -1150 59 74 2 -39 -1150 167 -198 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 29 E= 1.9e-012 0.068966 0.103448 0.034483 0.793103 0.000000 0.172414 0.758621 0.068966 0.137931 0.000000 0.413793 0.448276 0.275862 0.103448 0.137931 0.482759 0.068966 0.103448 0.655172 0.172414 0.241379 0.034483 0.448276 0.275862 0.034483 0.137931 0.000000 0.827586 0.000000 0.034483 0.344828 0.620690 0.103448 0.068966 0.827586 0.000000 0.137931 0.000000 0.344828 0.517241 0.137931 0.068966 0.172414 0.620690 0.000000 0.000000 0.793103 0.206897 0.172414 0.000000 0.137931 0.689655 0.000000 0.068966 0.379310 0.551724 0.000000 0.000000 0.896552 0.103448 0.172414 0.310345 0.172414 0.344828 0.034483 0.000000 0.137931 0.827586 0.000000 0.000000 0.827586 0.172414 0.206897 0.310345 0.068966 0.413793 0.000000 0.344828 0.379310 0.275862 0.206897 0.000000 0.724138 0.068966 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TG[TG][TA]G[GTA]T[TG]G[TG]T[GT]T[TG]G[TC]TG[TCA][GCT][GA] -------------------------------------------------------------------------------- Time 13.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 32 llr = 351 E-value = 3.5e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3:576346452319316574 pos.-specific C 81853266433349:38:433 probability G 2:1::::::3:13::2:41:3 matrix T :61:121::124::132:::: bits 2.1 1.9 1.7 1.5 ** Relative 1.3 * * ** Entropy 1.1 * * ** ** (15.8 bits) 0.9 * ** ** ** ** * 0.6 ***** *** ** **** 0.4 ********* * *** ***** 0.2 *********** *** ***** 0.0 --------------------- Multilevel CTCCAACCAAATCCACCAAAA consensus A ACCAACCCCA A GCCC sequence T GT G T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 11632 454 1.59e-09 CACAGACCTT CTCCAACCAACAACAACACAA CATCCATCTA 233 68 3.45e-09 AGCATGTGCC CTCCAACCACCACCACCGAAC AGGCAAAGGA 4277 475 8.63e-09 ATCACAAGTC CTCCACCAAAATCCAACACAG CCATC 6529 464 2.77e-08 AGCAACCAAT CTCAACACCAATCCATCACAG ATATCTTTCT 10345 458 4.62e-08 TCACATAATG CACCAAACCAATACAGCAAAC ACAACATAGA 10343 273 4.62e-08 TCACATAATG CACCAAACCAATACAGCAAAC ACAACATAGA 264421 304 9.99e-08 GAGGCACTGC CTCCAAACACAAACAACGACA GCACCAAGTC 269147 141 2.94e-07 CCTCCGTAAT CTCAAACAAAACCTACCACAA ATAGATTGGC 269699 411 6.02e-07 CCAACCTCTC GTCCACACAATCGCATCGCAA TCGCATCAAC 269696 412 6.02e-07 CCAACCTCTC GTCCACACAATCGCATCGCAA TCGCATCAAC 30851 474 7.56e-07 ATTTGCAAAT CTCCATCACAATACACGACAA TTACTG 7647 93 1.05e-06 CCTCAATCCT CTCCCTCCAGTCACACCAGCC TTCTTTCTTC 26759 435 1.60e-06 AAGCAAACAG CCCAAACACCATCCACTGACC TCTTTCGTTG 20940 441 1.60e-06 AAGCAAACAG CCCAAACACCATCCACTGACC TCTTTCGTTG 262307 185 1.77e-06 TTTTTGTGAT CTCCTCACCGACACAACAACA CAAGGAAACA 1967 169 2.16e-06 TCGACAACTA CACAATTACCCCGCACCACAG TCAACAACTT 10767 65 2.62e-06 ACTAACCATA CACAAACCAGTTGCAAAACAC GAAGCAAGTT 6176 473 3.48e-06 CAGTTCTTTC CTCATATAAACCACATCAACA CCAAAAC 11698 224 4.58e-06 ATGTTTGCTT CTGAAAAAAGTCACAACAACA AGATCCTCCC 268324 10 5.00e-06 CGTCGACAT CTCCAACAATCCACATTGGAC CAGCCCACAT 2078 365 7.69e-06 TTTAACTAGC CTCACTCCCCTGCCTTCGAAA TGCAACGTCA 8064 467 9.83e-06 AGATCTTTTC CCGCCACCCACTCCATCAGCC TGATAGTGCT 38724 128 2.27e-05 ACGGCTGCAA ATCCAATCACCGGCAGCGAAG CCAGCCTTTC 261499 203 2.27e-05 TTGCTTCTTC CTCACTCACACGCAACTGAAA TTGGAACTTC 270370 8 2.44e-05 ACCTCCT GATACTCCAAATCCAACAGAG GCTTTCTTCA 10360 337 2.61e-05 AGGTCGAAAA GATACACCAGATCCACAACAA AACGATCCTG 4820 459 2.80e-05 TTCCCTGGTT CTCAGTTCAACACCTCCACAA CTTAATTCCG 6528 427 3.68e-05 GACGTGTCGT CACCAAACCGAAGCAACAAGT CTTTCAGATT 34030 402 3.68e-05 GCATCTCTCA GTCTCCACCGAGCCAGCGCAA ACGCTACACT 264181 313 3.68e-05 TGATACGAGT CACAACCACTAAGCTCCGACG CTCATCCTAA 12089 472 4.77e-05 GGTACCCCTC GCTACACAACTCACAGCACAG TTTAGTTA 34125 141 5.76e-05 CTTGATATGT CTCCAACAAGCTGAATTCAAG CTCTGCTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11632 1.6e-09 453_[+2]_26 233 3.5e-09 67_[+2]_412 4277 8.6e-09 474_[+2]_5 6529 2.8e-08 463_[+2]_16 10345 4.6e-08 457_[+2]_22 10343 4.6e-08 272_[+2]_207 264421 1e-07 303_[+2]_176 269147 2.9e-07 140_[+2]_339 269699 6e-07 410_[+2]_69 269696 6e-07 411_[+2]_68 30851 7.6e-07 473_[+2]_6 7647 1e-06 92_[+2]_387 26759 1.6e-06 434_[+2]_45 20940 1.6e-06 440_[+2]_39 262307 1.8e-06 184_[+2]_295 1967 2.2e-06 168_[+2]_311 10767 2.6e-06 64_[+2]_415 6176 3.5e-06 472_[+2]_7 11698 4.6e-06 223_[+2]_256 268324 5e-06 9_[+2]_470 2078 7.7e-06 364_[+2]_115 8064 9.8e-06 466_[+2]_13 38724 2.3e-05 127_[+2]_352 261499 2.3e-05 202_[+2]_277 270370 2.4e-05 7_[+2]_472 10360 2.6e-05 336_[+2]_143 4820 2.8e-05 458_[+2]_21 6528 3.7e-05 426_[+2]_53 34030 3.7e-05 401_[+2]_78 264181 3.7e-05 312_[+2]_167 12089 4.8e-05 471_[+2]_8 34125 5.8e-05 140_[+2]_339 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=32 11632 ( 454) CTCCAACCAACAACAACACAA 1 233 ( 68) CTCCAACCACCACCACCGAAC 1 4277 ( 475) CTCCACCAAAATCCAACACAG 1 6529 ( 464) CTCAACACCAATCCATCACAG 1 10345 ( 458) CACCAAACCAATACAGCAAAC 1 10343 ( 273) CACCAAACCAATACAGCAAAC 1 264421 ( 304) CTCCAAACACAAACAACGACA 1 269147 ( 141) CTCAAACAAAACCTACCACAA 1 269699 ( 411) GTCCACACAATCGCATCGCAA 1 269696 ( 412) GTCCACACAATCGCATCGCAA 1 30851 ( 474) CTCCATCACAATACACGACAA 1 7647 ( 93) CTCCCTCCAGTCACACCAGCC 1 26759 ( 435) CCCAAACACCATCCACTGACC 1 20940 ( 441) CCCAAACACCATCCACTGACC 1 262307 ( 185) CTCCTCACCGACACAACAACA 1 1967 ( 169) CACAATTACCCCGCACCACAG 1 10767 ( 65) CACAAACCAGTTGCAAAACAC 1 6176 ( 473) CTCATATAAACCACATCAACA 1 11698 ( 224) CTGAAAAAAGTCACAACAACA 1 268324 ( 10) CTCCAACAATCCACATTGGAC 1 2078 ( 365) CTCACTCCCCTGCCTTCGAAA 1 8064 ( 467) CCGCCACCCACTCCATCAGCC 1 38724 ( 128) ATCCAATCACCGGCAGCGAAG 1 261499 ( 203) CTCACTCACACGCAACTGAAA 1 270370 ( 8) GATACTCCAAATCCAACAGAG 1 10360 ( 337) GATACACCAGATCCACAACAA 1 4820 ( 459) CTCAGTTCAACACCTCCACAA 1 6528 ( 427) CACCAAACCGAAGCAACAAGT 1 34030 ( 402) GTCTCCACCGAGCCAGCGCAA 1 264181 ( 313) CACAACCACTAAGCTCCGACG 1 12089 ( 472) GCTACACAACTCACAGCACAG 1 34125 ( 141) CTCCAACAAGCTGAATTCAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19712 bayes= 9.26444 E= 3.5e-011 -311 177 -28 -1164 -11 -88 -1164 119 -1164 188 -186 -154 79 112 -1164 -312 128 12 -286 -213 106 -7 -1164 -32 21 129 -1164 -113 59 137 -1164 -1164 106 93 -1164 -1164 69 12 14 -213 79 44 -1164 -32 -53 44 -86 46 35 82 14 -1164 -211 198 -1164 -312 174 -1164 -1164 -154 -11 58 -54 -13 -211 171 -286 -80 113 -287 72 -1164 79 82 -86 -1164 135 29 -286 -1164 69 29 14 -312 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 32 E= 3.5e-011 0.031250 0.781250 0.187500 0.000000 0.250000 0.125000 0.000000 0.625000 0.000000 0.843750 0.062500 0.093750 0.468750 0.500000 0.000000 0.031250 0.656250 0.250000 0.031250 0.062500 0.562500 0.218750 0.000000 0.218750 0.312500 0.562500 0.000000 0.125000 0.406250 0.593750 0.000000 0.000000 0.562500 0.437500 0.000000 0.000000 0.437500 0.250000 0.250000 0.062500 0.468750 0.312500 0.000000 0.218750 0.187500 0.312500 0.125000 0.375000 0.343750 0.406250 0.250000 0.000000 0.062500 0.906250 0.000000 0.031250 0.906250 0.000000 0.000000 0.093750 0.250000 0.343750 0.156250 0.250000 0.062500 0.750000 0.031250 0.156250 0.593750 0.031250 0.375000 0.000000 0.468750 0.406250 0.125000 0.000000 0.687500 0.281250 0.031250 0.000000 0.437500 0.281250 0.250000 0.031250 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TA]C[CA][AC][ACT][CA][CA][AC][ACG][ACT][TC][CAG]CA[CAT]C[AG][AC][AC][ACG] -------------------------------------------------------------------------------- Time 27.22 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 158 E-value = 1.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3:2::2:::::::113214:: pos.-specific C :a::a:8113::a:214:::9 probability G ::12:::::266:::61:4:1 matrix T 7:78:8299444:97:291a: bits 2.1 * * * 1.9 * * * * 1.7 * * * ** 1.5 * * ** * ** Relative 1.3 * * *** ** * ** Entropy 1.1 * ****** **** * ** (25.4 bits) 0.9 ** ****** **** * ** 0.6 ********* ****** **** 0.4 **************** **** 0.2 ********************* 0.0 --------------------- Multilevel TCTTCTCTTTGGCTTGCTATC consensus A AG AT CTT CAA G sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10345 402 5.99e-11 TGAAGGGGTA TCTTCTCTTGGTCTTGATGTC GCTCGTCACG 10343 217 5.99e-11 TGAAGGGGTA TCTTCTCTTGGTCTTGATGTC GCTCGTCACG 26759 400 5.08e-10 ACCTCATATT TCTTCTCTTTTGCTCATTATC CAACAAGCAA 20940 406 5.08e-10 ACCTCATATT TCTTCTCTTTTGCTCATTATC CAACAAGCAA 269699 318 9.57e-09 TCGGCCAACG TCAGCATTTCGTCTTGCTATC CTCTTGCTTT 269696 319 9.57e-09 TCGGCCAACG TCAGCATTTCGTCTTGCTATC CTCTTGCTTT 270370 270 1.95e-08 ACGTCTACAG ACGTCTCTTTTGCTTGCTTTG CTTTGTATCC 8064 4 3.21e-08 CCA ACTTCTCCTTGGCAAACTGTC CAAGGGCCTC 34125 452 6.40e-08 AGAGTTCATC ACTTCTCTCCTGCTTCGAGTC GCCTTCTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10345 6e-11 401_[+3]_78 10343 6e-11 216_[+3]_263 26759 5.1e-10 399_[+3]_80 20940 5.1e-10 405_[+3]_74 269699 9.6e-09 317_[+3]_162 269696 9.6e-09 318_[+3]_161 270370 2e-08 269_[+3]_210 8064 3.2e-08 3_[+3]_476 34125 6.4e-08 451_[+3]_28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 10345 ( 402) TCTTCTCTTGGTCTTGATGTC 1 10343 ( 217) TCTTCTCTTGGTCTTGATGTC 1 26759 ( 400) TCTTCTCTTTTGCTCATTATC 1 20940 ( 406) TCTTCTCTTTTGCTCATTATC 1 269699 ( 318) TCAGCATTTCGTCTTGCTATC 1 269696 ( 319) TCAGCATTTCGTCTTGCTATC 1 270370 ( 270) ACGTCTCTTTTGCTTGCTTTG 1 8064 ( 4) ACTTCTCCTTGGCAAACTGTC 1 34125 ( 452) ACTTCTCTCCTGCTTCGAGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19712 bayes= 11.2306 E= 1.3e-002 30 -982 -982 129 -982 212 -982 -982 -28 -982 -103 129 -982 -982 -3 151 -982 212 -982 -982 -28 -982 -982 151 -982 176 -982 -30 -982 -105 -982 170 -982 -105 -982 170 -982 54 -3 70 -982 -982 129 70 -982 -982 129 70 -982 212 -982 -982 -128 -982 -982 170 -128 -5 -982 129 30 -105 129 -982 -28 95 -103 -30 -128 -982 -982 170 72 -982 97 -129 -982 -982 -982 187 -982 195 -103 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 1.3e-002 0.333333 0.000000 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.222222 0.000000 0.111111 0.666667 0.000000 0.000000 0.222222 0.777778 0.000000 1.000000 0.000000 0.000000 0.222222 0.000000 0.000000 0.777778 0.000000 0.777778 0.000000 0.222222 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.000000 0.333333 0.222222 0.444444 0.000000 0.000000 0.555556 0.444444 0.000000 0.000000 0.555556 0.444444 0.000000 1.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.888889 0.111111 0.222222 0.000000 0.666667 0.333333 0.111111 0.555556 0.000000 0.222222 0.444444 0.111111 0.222222 0.111111 0.000000 0.000000 0.888889 0.444444 0.000000 0.444444 0.111111 0.000000 0.000000 0.000000 1.000000 0.000000 0.888889 0.111111 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA]C[TA][TG]C[TA][CT]TT[TCG][GT][GT]CT[TC][GA][CAT]T[AG]TC -------------------------------------------------------------------------------- Time 40.38 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10343 2.61e-14 61_[+1(1.13e-07)]_134_\ [+3(5.99e-11)]_35_[+2(4.62e-08)]_139_[+3(4.59e-05)]_47 10345 2.61e-14 246_[+1(1.13e-07)]_134_\ [+3(5.99e-11)]_35_[+2(4.62e-08)]_22 10360 9.05e-04 291_[+1(4.56e-05)]_24_\ [+2(2.61e-05)]_14_[+3(9.30e-05)]_108 10767 1.02e-02 64_[+2(2.62e-06)]_415 11632 1.85e-10 147_[+1(2.54e-09)]_257_\ [+2(1.33e-07)]_7_[+2(1.59e-09)]_26 11698 4.41e-04 127_[+1(7.62e-06)]_75_\ [+2(4.58e-06)]_256 12089 8.90e-06 248_[+1(1.84e-08)]_6_[+1(7.62e-06)]_\ 175_[+2(4.77e-05)]_8 1967 5.47e-05 72_[+1(4.28e-06)]_75_[+2(2.16e-06)]_\ 311 2078 6.97e-04 364_[+2(7.69e-06)]_33_\ [+1(1.31e-05)]_61 20940 3.42e-08 405_[+3(5.08e-10)]_14_\ [+2(1.60e-06)]_39 233 9.93e-06 67_[+2(3.45e-09)]_412 260844 3.33e-01 500 261499 2.45e-04 202_[+2(2.27e-05)]_108_\ [+1(9.89e-07)]_148 262307 6.18e-06 15_[+3(6.47e-05)]_148_\ [+2(1.77e-06)]_78_[+1(3.02e-06)]_20_[+1(4.28e-05)]_155 263924 2.16e-02 101_[+1(5.50e-06)]_378 264181 1.03e-01 312_[+2(3.68e-05)]_167 264421 1.07e-06 48_[+1(2.83e-07)]_234_\ [+2(9.99e-08)]_51_[+2(6.92e-05)]_104 26759 3.42e-08 399_[+3(5.08e-10)]_14_\ [+2(1.60e-06)]_45 268324 2.89e-04 9_[+2(5.00e-06)]_169_[+1(8.25e-06)]_\ 84_[+2(6.92e-05)]_175 269147 1.36e-06 140_[+2(2.94e-07)]_75_\ [+2(1.82e-05)]_85_[+1(1.80e-07)]_69_[+1(3.30e-06)]_47 269696 2.08e-07 318_[+3(9.57e-09)]_72_\ [+2(6.02e-07)]_68 269699 1.99e-07 317_[+3(9.57e-09)]_72_\ [+2(6.02e-07)]_69 270370 3.00e-07 7_[+2(2.44e-05)]_93_[+1(2.51e-05)]_\ 127_[+3(1.95e-08)]_210 30851 8.02e-08 363_[+1(1.81e-09)]_89_\ [+2(7.56e-07)]_6 34030 5.66e-03 18_[+1(1.52e-05)]_362_\ [+2(3.68e-05)]_78 34125 9.44e-05 140_[+2(5.76e-05)]_290_\ [+3(6.40e-08)]_28 37338 2.12e-04 188_[+1(2.79e-08)]_36_\ [+1(5.18e-05)]_[+1(2.88e-05)]_213 38724 3.49e-03 12_[+1(2.34e-05)]_94_[+2(2.27e-05)]_\ 352 412 1.79e-02 381_[+1(1.41e-05)]_98 4277 1.88e-07 368_[+1(1.32e-06)]_61_\ [+2(2.61e-05)]_3_[+2(8.63e-09)]_5 4700 1.39e-05 36_[+3(5.55e-05)]_298_\ [+1(7.75e-09)]_124 4819 1.98e-04 18_[+1(3.19e-08)]_9_[+1(8.40e-05)]_\ 431 4820 1.28e-03 141_[+1(4.66e-06)]_296_\ [+2(2.80e-05)]_21 6176 3.32e-02 472_[+2(3.48e-06)]_7 6528 1.86e-04 16_[+1(1.46e-06)]_389_\ [+2(3.68e-05)]_53 6529 2.54e-06 45_[+1(9.65e-06)]_254_\ [+2(1.25e-05)]_122_[+2(2.77e-08)]_16 7647 1.88e-03 92_[+2(1.05e-06)]_358_\ [+2(5.76e-05)]_8 7883 7.57e-01 500 8064 2.79e-09 3_[+3(3.21e-08)]_228_[+1(2.26e-07)]_\ 193_[+2(9.83e-06)]_13 8073 1.60e-02 35_[+1(6.48e-06)]_126_\ [+1(5.18e-05)]_297 bd838 5.72e-02 110_[+1(9.43e-05)]_128_\ [+1(8.92e-06)]_220 bd897 5.41e-01 52 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************