******************************************************************************** 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/212/212.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10519 1.0000 500 11133 1.0000 500 11479 1.0000 500 11945 1.0000 500 11947 1.0000 500 17002 1.0000 500 21239 1.0000 500 22473 1.0000 500 23528 1.0000 500 23557 1.0000 500 23618 1.0000 500 2447 1.0000 500 2467 1.0000 500 25276 1.0000 500 25338 1.0000 500 25837 1.0000 500 26136 1.0000 500 261381 1.0000 500 26146 1.0000 500 261827 1.0000 500 262721 1.0000 500 263742 1.0000 500 264451 1.0000 500 268761 1.0000 500 28984 1.0000 500 29053 1.0000 500 29237 1.0000 500 2985 1.0000 500 32805 1.0000 500 33219 1.0000 500 33780 1.0000 500 3564 1.0000 500 39847 1.0000 500 40586 1.0000 500 5622 1.0000 500 6093 1.0000 500 8369 1.0000 500 8675 1.0000 500 9029 1.0000 500 9184 1.0000 500 9186 1.0000 500 9527 1.0000 500 997 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/212/212.seqs.fa -oc motifs/212 -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= 43 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= 21500 N= 43 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.231 G 0.247 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.231 G 0.247 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 43 llr = 418 E-value = 2.5e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 135135126221513626215 pos.-specific C 64347268:448:87272492 probability G :1:3:11::3::11::1:1:: matrix T 3222:22:3:3:3::2:23:3 bits 2.1 1.9 1.7 1.5 * Relative 1.3 * * * * Entropy 1.1 * * * ** * (14.0 bits) 0.8 * ** * ** * 0.6 * * ** **** * * 0.4 * * * ************ ** 0.2 ********************* 0.0 --------------------- Multilevel CCACCACCACCCACCACACCA consensus TACGA T TGT T A ATT T sequence T AA C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 263742 44 6.86e-08 CTCTCATCCT CCACCACCACCCTCCTCGCCA GCTACGATCA 11945 280 1.47e-07 GACGCAACCA AAAACACCTCCCACCACTCCC CTCAACTGCC 9029 146 1.96e-07 ATATGAAGAA CCCGCACCAATAACCAAACCT AGGGGATGAC 268761 214 2.26e-07 AGAAGGGTCA CAACCTCCTGTCGCCACTCCT ACGTCGCCTG 264451 451 2.60e-07 TAGATACTAC CCACCGCCTCTCACCATACCA TCCGCCGTGC 997 475 3.42e-07 TCATTCCATT CCATCCTCAATCTCAACATCA AAACC 11479 446 3.42e-07 ACTCGAGTCT TCTCCACCAGCCAACACATCC AACCCTTGAA 5622 315 4.46e-07 ATCAATCCCA CCCAAACCACTCTCATCATCT CATTTTCGTT 3564 446 6.59e-07 TCTCTCTTCT CCTTATCCACTCACACCACCA AAGCAAGCTT 33219 454 7.48e-07 AGCTGCAGTC ACCGCACCACACACCTCTACT AACACAATAC 40586 383 1.08e-06 CAAAAAGATC CAACACTCAGCCTCCCCCCCT CACAGAACCG 21239 259 1.22e-06 AAAAGCAACA CACGAACAACTCACCAGAACA AAGAGAGCGC 9184 85 1.38e-06 CGCCAAAACG TTCGCAACAACCACAACAACA AACACCGCAA 33780 447 1.55e-06 TCACAATCAA CTCTCCCCTGCCACCAATTCC ACTCCATTTA 39847 454 2.19e-06 AAGAACTCTC CCCCCGCCACACTCTACACAA CGGCCGGTTT 2985 472 2.19e-06 CGTTGCATAG CCACCGCTACACACCACAGCA GCAGCGAC 261827 325 2.19e-06 ACAGCTTCGC CATTCACAACCCAACAAACCA ACAGAAGAAA 29053 139 2.75e-06 ACATTTGTTG TCAGCAGCAGCAACAACAACA AGTCCACACT 2467 478 3.42e-06 GGTGCACCGT TCACAACAACACTCCTCACAA CT 9527 462 3.81e-06 CGCCTTCAAA TAACCACCTGCAACCAAACAT AGCCACAAAC 26146 466 7.11e-06 GGCTCTTCCG AACGAGCCTCCCTCCTCCTCA CAAAATAAAC 25338 220 8.68e-06 TCACATGCCC CTCACTCCAATAGCCACACCT CCCTCCACTC 29237 435 9.57e-06 AAACAAACCT CATCCTCCTGCCGCCTCTGCA ACTGCTGCAC 25837 337 1.16e-05 GGTGGCGGAC AAACCGCAAACCTCCCCCCCT TGATAAAATA 23528 470 1.16e-05 CCTGCAACAC CACGCAGCAACAACAAATCCA CGGAGAAGAC 17002 424 1.40e-05 CTCATGTTTT TCCAACTCTGACACCAAATCC TACTCCTCCC 8675 451 2.02e-05 TAGATTCAGT CTAGCAGCTGCCTCCGCTCCC AGTTCTCATA 22473 266 2.42e-05 CCCCCTCTGC CGACCGACACACACCAGTTCT TGTTCTGCGA 26136 400 2.88e-05 CGTGCTCATT TCTGAACCAAACACCAATTAT GATTGTGTTG 10519 190 2.88e-05 TTGGAGGAGC AAAACATCAGCGTCACCACCA GACTGCTGCA 262721 335 3.71e-05 ATGGTAGTCA TTACCAACTATCACCCGAGCA GGATCTTATC 25276 131 3.71e-05 TTTCCATTAC TACGCTACGCTCTCAACAACA CAATAAAACC 261381 239 4.38e-05 CGACTGCTTC CCCTCACCGCCGTCCCCAGCC TTATGGCCGC 11947 468 4.38e-05 AAAACGATTG CCAAACTAACTCGGCACATCA ACAAGAAACA 23557 450 4.75e-05 CGGAATCCTT CGCCCTTCAGTCAGCCCCTCA AGATTCAACA 9186 195 6.03e-05 GAATTGATGA TATCAATCTGACTAAACATCT CATGTTTCTG 28984 49 7.05e-05 GTCAGATCAA CTATACTCTGTCGCAAATCCC GAATCATTCT 8369 480 8.22e-05 CCCCTCTCTG CCGTCAGCTCACACCAACACC 32805 215 9.54e-05 GGTCGAGGGG TCAGCAACAGCCGGACCCACA GAGTATGGAC 6093 417 1.11e-04 CATGGTTCAA TAATGCCCACTCTCTTCACCT CTGCTTACTT 23618 21 2.36e-04 CATCCTTCAT CTTCACCATAACTCCAACCAA CGAGAGTCGA 2447 400 3.66e-04 CATAATAAAT AGATAATATGTCAAAACATCT CCCCCTTTTA 11133 260 3.66e-04 GACACAAAGC CTCGCTTCATCCACCTGATAC AAGTATCTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263742 6.9e-08 43_[+1]_436 11945 1.5e-07 279_[+1]_200 9029 2e-07 145_[+1]_334 268761 2.3e-07 213_[+1]_266 264451 2.6e-07 450_[+1]_29 997 3.4e-07 474_[+1]_5 11479 3.4e-07 445_[+1]_34 5622 4.5e-07 314_[+1]_165 3564 6.6e-07 445_[+1]_34 33219 7.5e-07 453_[+1]_26 40586 1.1e-06 382_[+1]_97 21239 1.2e-06 258_[+1]_221 9184 1.4e-06 84_[+1]_395 33780 1.6e-06 446_[+1]_33 39847 2.2e-06 453_[+1]_26 2985 2.2e-06 471_[+1]_8 261827 2.2e-06 324_[+1]_155 29053 2.7e-06 138_[+1]_341 2467 3.4e-06 477_[+1]_2 9527 3.8e-06 461_[+1]_18 26146 7.1e-06 465_[+1]_14 25338 8.7e-06 219_[+1]_260 29237 9.6e-06 434_[+1]_45 25837 1.2e-05 336_[+1]_143 23528 1.2e-05 469_[+1]_10 17002 1.4e-05 423_[+1]_56 8675 2e-05 450_[+1]_29 22473 2.4e-05 265_[+1]_214 26136 2.9e-05 399_[+1]_80 10519 2.9e-05 189_[+1]_290 262721 3.7e-05 334_[+1]_145 25276 3.7e-05 130_[+1]_349 261381 4.4e-05 238_[+1]_241 11947 4.4e-05 467_[+1]_12 23557 4.7e-05 449_[+1]_30 9186 6e-05 194_[+1]_285 28984 7.1e-05 48_[+1]_431 8369 8.2e-05 479_[+1] 32805 9.5e-05 214_[+1]_265 6093 0.00011 416_[+1]_63 23618 0.00024 20_[+1]_459 2447 0.00037 399_[+1]_80 11133 0.00037 259_[+1]_220 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=43 263742 ( 44) CCACCACCACCCTCCTCGCCA 1 11945 ( 280) AAAACACCTCCCACCACTCCC 1 9029 ( 146) CCCGCACCAATAACCAAACCT 1 268761 ( 214) CAACCTCCTGTCGCCACTCCT 1 264451 ( 451) CCACCGCCTCTCACCATACCA 1 997 ( 475) CCATCCTCAATCTCAACATCA 1 11479 ( 446) TCTCCACCAGCCAACACATCC 1 5622 ( 315) CCCAAACCACTCTCATCATCT 1 3564 ( 446) CCTTATCCACTCACACCACCA 1 33219 ( 454) ACCGCACCACACACCTCTACT 1 40586 ( 383) CAACACTCAGCCTCCCCCCCT 1 21239 ( 259) CACGAACAACTCACCAGAACA 1 9184 ( 85) TTCGCAACAACCACAACAACA 1 33780 ( 447) CTCTCCCCTGCCACCAATTCC 1 39847 ( 454) CCCCCGCCACACTCTACACAA 1 2985 ( 472) CCACCGCTACACACCACAGCA 1 261827 ( 325) CATTCACAACCCAACAAACCA 1 29053 ( 139) TCAGCAGCAGCAACAACAACA 1 2467 ( 478) TCACAACAACACTCCTCACAA 1 9527 ( 462) TAACCACCTGCAACCAAACAT 1 26146 ( 466) AACGAGCCTCCCTCCTCCTCA 1 25338 ( 220) CTCACTCCAATAGCCACACCT 1 29237 ( 435) CATCCTCCTGCCGCCTCTGCA 1 25837 ( 337) AAACCGCAAACCTCCCCCCCT 1 23528 ( 470) CACGCAGCAACAACAAATCCA 1 17002 ( 424) TCCAACTCTGACACCAAATCC 1 8675 ( 451) CTAGCAGCTGCCTCCGCTCCC 1 22473 ( 266) CGACCGACACACACCAGTTCT 1 26136 ( 400) TCTGAACCAAACACCAATTAT 1 10519 ( 190) AAAACATCAGCGTCACCACCA 1 262721 ( 335) TTACCAACTATCACCCGAGCA 1 25276 ( 131) TACGCTACGCTCTCAACAACA 1 261381 ( 239) CCCTCACCGCCGTCCCCAGCC 1 11947 ( 468) CCAAACTAACTCGGCACATCA 1 23557 ( 450) CGCCCTTCAGTCAGCCCCTCA 1 9186 ( 195) TATCAATCTGACTAAACATCT 1 28984 ( 49) CTATACTCTGTCGCAAATCCC 1 8369 ( 480) CCGTCAGCTCACACCAACACC 1 32805 ( 215) TCAGCAACAGCCGGACCCACA 1 6093 ( 417) TAATGCCCACTCTCTTCACCT 1 23618 ( 21) CTTCACCATAACTCCAACCAA 1 2447 ( 400) AGATAATATGTCAAAACATCT 1 11133 ( 260) CTCGCTTCATCCACCTGATAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20640 bayes= 8.90388 E= 2.5e-017 -89 133 -1207 8 34 85 -182 -50 85 59 -340 -70 -89 68 18 -33 23 154 -340 -1207 99 -32 -82 -70 -115 127 -141 -18 -66 181 -1207 -350 123 -1207 -241 40 -30 85 50 -350 -15 85 -1207 40 -115 185 -241 -1207 99 -1207 -82 40 -147 185 -182 -1207 11 154 -1207 -250 123 -32 -340 -50 -15 149 -141 -350 117 -51 -340 -18 -66 93 -141 20 -89 189 -1207 -1207 92 -15 -1207 20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 43 E= 2.5e-017 0.139535 0.581395 0.000000 0.279070 0.325581 0.418605 0.069767 0.186047 0.465116 0.348837 0.023256 0.162791 0.139535 0.372093 0.279070 0.209302 0.302326 0.674419 0.023256 0.000000 0.511628 0.186047 0.139535 0.162791 0.116279 0.558140 0.093023 0.232558 0.162791 0.813953 0.000000 0.023256 0.604651 0.000000 0.046512 0.348837 0.209302 0.418605 0.348837 0.023256 0.232558 0.418605 0.000000 0.348837 0.116279 0.837209 0.046512 0.000000 0.511628 0.000000 0.139535 0.348837 0.093023 0.837209 0.069767 0.000000 0.279070 0.674419 0.000000 0.046512 0.604651 0.186047 0.023256 0.186047 0.232558 0.651163 0.093023 0.023256 0.581395 0.162791 0.023256 0.232558 0.162791 0.441860 0.093023 0.302326 0.139535 0.860465 0.000000 0.000000 0.488372 0.209302 0.000000 0.302326 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CA][AC][CGT][CA]A[CT]C[AT][CGA][CTA]C[AT]C[CA]A[CA][AT][CT]C[ATC] -------------------------------------------------------------------------------- Time 15.02 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 23 llr = 255 E-value = 1.9e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 6253:272:4:57::6 pos.-specific C :23:::::2:121::2 probability G :634a8:8739328a2 matrix T 4::3::3:23:::2:: bits 2.1 * * 1.9 * * 1.7 * * * 1.5 * * * Relative 1.3 ** * ** Entropy 1.1 * **** * ** (16.0 bits) 0.8 * **** * *** 0.6 ** ***** * **** 0.4 ********* ****** 0.2 **************** 0.0 ---------------- Multilevel AGAGGGAGGAGAAGGA consensus TCCA T T GG C sequence GT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 21239 76 1.58e-09 TGACGAAGTG AGAGGGAGGGGAAGGA CGCAAGCTAC 9029 244 5.95e-09 ACAGTGCACA AGCAGGAGGAGAAGGA GAAATCCGAG 25837 6 7.53e-08 TATAG TGCTGGAGGTGGAGGA GTGGAGGATT 11479 248 7.53e-08 CAAAAATTCA TGAGGGAGTAGAAGGA TACCCCCCCC 8675 173 1.56e-07 TTGCTCCTGT TGAAGGAGCTGAAGGA CGACATGCTT 262721 138 3.78e-07 TGCGTCAGCG ACGAGGAGGAGAAGGC CATCACAGTA 26146 283 6.44e-07 GCTGCACGGC AGAAGGAAGGGAAGGC GGTTCAGTCT 263742 480 1.06e-06 CTGTCTTCGG AGGAGGAGGAGGGGGG GCGCC 2447 118 1.69e-06 CCCATGGCGA AGAGGAAAGGGGAGGA ACGAGCAACG 11133 336 2.56e-06 ACGAAAGTTC TGGTGGAGTTGAAGGG TGCACGTCTG 5622 29 3.11e-06 TGACGATGAC TGATGAAGGAGGATGA AATTGGACAT 2467 299 3.11e-06 ACACACGACC ACCTGGTGGGGAGGGA TCGGTGTGTG 32805 128 4.13e-06 CTGGAAGACG TGGGGGTAGTGCAGGA GATGCAGCGA 39847 160 4.52e-06 AAGATAGTTC AAAGGGTGGCGGAGGA GGGTTTGTCA 26136 443 4.52e-06 GTATCAGTGT TGAGGGAGGACACGGA TGTCATTTGT 28984 410 8.84e-06 CCTTTGATTG AAAAGGAGTGGAGGGC AGTGTATGTT 29053 98 1.37e-05 TGCAGTAGAA TGATGGATGTGCAGGG CGTAGTAGGT 3564 173 1.79e-05 AATTTGCAAC AACGGGTGCAGGGGGC AGCTAGGAAT 33780 207 1.79e-05 GTTGTGGTTT ACGTGGTGTGGCAGGC AGGGCAGGCA 22473 163 1.79e-05 GTGGACGGCC ACGAGGAGGTCCGGGA AGTCCGGAGC 997 80 2.15e-05 AGCTGATGTC TGCGGATGCAGGATGA GTGTGCATGA 33219 96 3.19e-05 TTTGATGACG AACTGGAGCTGACTGA AGGAAGCTGC 23528 70 3.19e-05 CCATTTGCAG ACAGGAAAGAGGATGG CGAGAACAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21239 1.6e-09 75_[+2]_409 9029 5.9e-09 243_[+2]_241 25837 7.5e-08 5_[+2]_479 11479 7.5e-08 247_[+2]_237 8675 1.6e-07 172_[+2]_312 262721 3.8e-07 137_[+2]_347 26146 6.4e-07 282_[+2]_202 263742 1.1e-06 479_[+2]_5 2447 1.7e-06 117_[+2]_367 11133 2.6e-06 335_[+2]_149 5622 3.1e-06 28_[+2]_456 2467 3.1e-06 298_[+2]_186 32805 4.1e-06 127_[+2]_357 39847 4.5e-06 159_[+2]_325 26136 4.5e-06 442_[+2]_42 28984 8.8e-06 409_[+2]_75 29053 1.4e-05 97_[+2]_387 3564 1.8e-05 172_[+2]_312 33780 1.8e-05 206_[+2]_278 22473 1.8e-05 162_[+2]_322 997 2.2e-05 79_[+2]_405 33219 3.2e-05 95_[+2]_389 23528 3.2e-05 69_[+2]_415 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=23 21239 ( 76) AGAGGGAGGGGAAGGA 1 9029 ( 244) AGCAGGAGGAGAAGGA 1 25837 ( 6) TGCTGGAGGTGGAGGA 1 11479 ( 248) TGAGGGAGTAGAAGGA 1 8675 ( 173) TGAAGGAGCTGAAGGA 1 262721 ( 138) ACGAGGAGGAGAAGGC 1 26146 ( 283) AGAAGGAAGGGAAGGC 1 263742 ( 480) AGGAGGAGGAGGGGGG 1 2447 ( 118) AGAGGAAAGGGGAGGA 1 11133 ( 336) TGGTGGAGTTGAAGGG 1 5622 ( 29) TGATGAAGGAGGATGA 1 2467 ( 299) ACCTGGTGGGGAGGGA 1 32805 ( 128) TGGGGGTAGTGCAGGA 1 39847 ( 160) AAAGGGTGGCGGAGGA 1 26136 ( 443) TGAGGGAGGACACGGA 1 28984 ( 410) AAAAGGAGTGGAGGGC 1 29053 ( 98) TGATGGATGTGCAGGG 1 3564 ( 173) AACGGGTGCAGGGGGC 1 33780 ( 207) ACGTGGTGTGGCAGGC 1 22473 ( 163) ACGAGGAGGTCCGGGA 1 997 ( 80) TGCGGATGCAGGATGA 1 33219 ( 96) AACTGGAGCTGACTGA 1 23528 ( 70) ACAGGAAAGAGGATGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 20855 bayes= 10.8879 E= 1.9e-005 124 -1117 -1117 57 -57 -9 130 -1117 89 17 8 -1117 24 -1117 67 21 -1117 -1117 202 -1117 -57 -1117 174 -1117 152 -1117 -1117 -2 -57 -1117 167 -260 -1117 -41 140 -60 60 -241 8 21 -1117 -141 189 -1117 89 -41 50 -1117 143 -141 -18 -1117 -1117 -1117 174 -60 -1117 -1117 202 -1117 124 -9 -50 -1117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 23 E= 1.9e-005 0.608696 0.000000 0.000000 0.391304 0.173913 0.217391 0.608696 0.000000 0.478261 0.260870 0.260870 0.000000 0.304348 0.000000 0.391304 0.304348 0.000000 0.000000 1.000000 0.000000 0.173913 0.000000 0.826087 0.000000 0.739130 0.000000 0.000000 0.260870 0.173913 0.000000 0.782609 0.043478 0.000000 0.173913 0.652174 0.173913 0.391304 0.043478 0.260870 0.304348 0.000000 0.086957 0.913043 0.000000 0.478261 0.173913 0.347826 0.000000 0.695652 0.086957 0.217391 0.000000 0.000000 0.000000 0.826087 0.173913 0.000000 0.000000 1.000000 0.000000 0.608696 0.217391 0.173913 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AT][GC][ACG][GAT]GG[AT]GG[ATG]G[AG][AG]GG[AC] -------------------------------------------------------------------------------- Time 29.39 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 15 llr = 189 E-value = 2.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 31:::23::1::141: pos.-specific C 1::1::311::311:1 probability G :9::a::7138:5:29 matrix T 6:a9:8429527357: bits 2.1 * 1.9 * * 1.7 ** * * 1.5 **** * Relative 1.3 ***** * * * Entropy 1.1 ***** ** ** * (18.2 bits) 0.8 ***** ** ** ** 0.6 ****** ***** *** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TGTTGTTGTTGTGTTG consensus A AAT GTCTAG sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 8369 287 7.65e-09 GCTGAGGAAC AGTTGTCGTTGTGTTG CGTTGTTTAC 10519 75 2.22e-08 TTGATGTTGT TGTTGTAGTAGTGTTG GTACTATTTG 8675 235 3.46e-08 CGAGAGTGGT TGTTGTCGTTGTCATG GTAGTGTAGT 11133 42 1.21e-07 AGTTTGGCCA TGTTGTTGTGGTTAGG TGGAGCACAA 264451 158 2.56e-07 CAGTGGTTGG TGTTGTTGGTGTTTTG ACAATGAGTG 6093 71 8.07e-07 CCATCCATAT TGTTGATGTGTCGATG ATGTCGGAGG 29053 74 8.70e-07 TAGTATCTAG CGTTGATTTGGTGTTG CAGTAGAATG 997 198 9.40e-07 AGTTGAACGG AATTGTAGTTGCGTTG ATAGAAGAAT 261827 383 1.10e-06 ATACAAACAC AGTTGTTCTTGCTTTG GAATTGGTTG 23528 298 1.10e-06 GATGAATTCT TGTTGAAGTGGTGAAG AAGTCTTGAA 2467 247 1.19e-06 TATTGTACGC CGTTGTAGTTTTGCTG TGATACGGCG 2985 179 1.78e-06 TGCTAAACGC TGTCGTCTTGGTTTTG TTTCATGTTC 17002 304 2.23e-06 TGGTGAGTAA AGTTGTTGTTGTATTC ACTTGTAGAA 263742 367 2.39e-06 TTCGTATCTT TGTTGTCGCAGTGAGG TTCGTTGCCA 9527 347 4.90e-06 AAGTGGCATC TGTTGTATTTTCCAGG CAAAAACATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8369 7.6e-09 286_[+3]_198 10519 2.2e-08 74_[+3]_410 8675 3.5e-08 234_[+3]_250 11133 1.2e-07 41_[+3]_443 264451 2.6e-07 157_[+3]_327 6093 8.1e-07 70_[+3]_414 29053 8.7e-07 73_[+3]_411 997 9.4e-07 197_[+3]_287 261827 1.1e-06 382_[+3]_102 23528 1.1e-06 297_[+3]_187 2467 1.2e-06 246_[+3]_238 2985 1.8e-06 178_[+3]_306 17002 2.2e-06 303_[+3]_181 263742 2.4e-06 366_[+3]_118 9527 4.9e-06 346_[+3]_138 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=15 8369 ( 287) AGTTGTCGTTGTGTTG 1 10519 ( 75) TGTTGTAGTAGTGTTG 1 8675 ( 235) TGTTGTCGTTGTCATG 1 11133 ( 42) TGTTGTTGTGGTTAGG 1 264451 ( 158) TGTTGTTGGTGTTTTG 1 6093 ( 71) TGTTGATGTGTCGATG 1 29053 ( 74) CGTTGATTTGGTGTTG 1 997 ( 198) AATTGTAGTTGCGTTG 1 261827 ( 383) AGTTGTTCTTGCTTTG 1 23528 ( 298) TGTTGAAGTGGTGAAG 1 2467 ( 247) CGTTGTAGTTTTGCTG 1 2985 ( 179) TGTCGTCTTGGTTTTG 1 17002 ( 304) AGTTGTTGTTGTATTC 1 263742 ( 367) TGTTGTCGCAGTGAGG 1 9527 ( 347) TGTTGTATTTTCCAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 20855 bayes= 11.1148 E= 2.7e-002 5 -80 -1055 118 -195 -1055 192 -1055 -1055 -1055 -1055 192 -1055 -179 -1055 182 -1055 -1055 202 -1055 -37 -1055 -1055 160 37 20 -1055 60 -1055 -179 157 -40 -1055 -179 -188 172 -95 -1055 43 101 -1055 -1055 170 -40 -1055 20 -1055 147 -195 -80 111 2 63 -179 -1055 101 -195 -1055 -30 147 -1055 -179 192 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 15 E= 2.7e-002 0.266667 0.133333 0.000000 0.600000 0.066667 0.000000 0.933333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.066667 0.000000 0.933333 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.333333 0.266667 0.000000 0.400000 0.000000 0.066667 0.733333 0.200000 0.000000 0.066667 0.066667 0.866667 0.133333 0.000000 0.333333 0.533333 0.000000 0.000000 0.800000 0.200000 0.000000 0.266667 0.000000 0.733333 0.066667 0.133333 0.533333 0.266667 0.400000 0.066667 0.000000 0.533333 0.066667 0.000000 0.200000 0.733333 0.000000 0.066667 0.933333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA]GTTG[TA][TAC][GT]T[TG][GT][TC][GT][TA][TG]G -------------------------------------------------------------------------------- Time 44.30 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10519 1.87e-05 74_[+3(2.22e-08)]_99_[+1(2.88e-05)]_\ 290 11133 2.18e-06 41_[+3(1.21e-07)]_278_\ [+2(2.56e-06)]_149 11479 7.95e-07 247_[+2(7.53e-08)]_182_\ [+1(3.42e-07)]_34 11945 2.77e-03 279_[+1(1.47e-07)]_200 11947 1.34e-01 467_[+1(4.38e-05)]_12 17002 4.78e-04 303_[+3(2.23e-06)]_104_\ [+1(1.40e-05)]_56 21239 5.34e-08 75_[+2(1.58e-09)]_167_\ [+1(1.22e-06)]_221 22473 1.38e-03 162_[+2(1.79e-05)]_87_\ [+1(2.42e-05)]_214 23528 7.30e-06 69_[+2(3.19e-05)]_212_\ [+3(1.10e-06)]_156_[+1(1.16e-05)]_10 23557 7.31e-02 449_[+1(4.75e-05)]_30 23618 1.93e-01 500 2447 5.95e-03 117_[+2(1.69e-06)]_367 2467 3.25e-07 246_[+3(1.19e-06)]_36_\ [+2(3.11e-06)]_163_[+1(3.42e-06)]_2 25276 1.25e-01 130_[+1(3.71e-05)]_349 25338 5.31e-02 219_[+1(8.68e-06)]_42_\ [+1(5.58e-05)]_197 25837 2.67e-05 5_[+2(7.53e-08)]_315_[+1(1.16e-05)]_\ 143 26136 1.00e-03 399_[+1(2.88e-05)]_22_\ [+2(4.52e-06)]_42 261381 9.09e-02 238_[+1(4.38e-05)]_241 26146 7.17e-05 282_[+2(6.44e-07)]_167_\ [+1(7.11e-06)]_14 261827 5.73e-05 324_[+1(2.19e-06)]_37_\ [+3(1.10e-06)]_102 262721 2.01e-04 137_[+2(3.78e-07)]_181_\ [+1(3.71e-05)]_145 263742 6.49e-09 22_[+1(2.88e-05)]_[+1(6.86e-08)]_63_\ [+2(2.15e-05)]_44_[+2(6.41e-06)]_163_[+3(2.39e-06)]_97_[+2(1.06e-06)]_5 264451 2.79e-06 157_[+3(2.56e-07)]_277_\ [+1(2.60e-07)]_29 268761 1.43e-03 213_[+1(2.26e-07)]_266 28984 4.36e-03 48_[+1(7.05e-05)]_340_\ [+2(8.84e-06)]_75 29053 7.69e-07 73_[+3(8.70e-07)]_8_[+2(1.37e-05)]_\ 25_[+1(2.75e-06)]_341 29237 1.60e-02 434_[+1(9.57e-06)]_45 2985 5.20e-05 178_[+3(1.78e-06)]_277_\ [+1(2.19e-06)]_8 32805 2.95e-03 127_[+2(4.13e-06)]_71_\ [+1(9.54e-05)]_237_[+2(9.59e-05)]_12 33219 1.38e-04 95_[+2(3.19e-05)]_342_\ [+1(7.48e-07)]_26 33780 1.85e-04 106_[+1(6.03e-05)]_79_\ [+2(1.79e-05)]_224_[+1(1.55e-06)]_33 3564 4.52e-05 172_[+2(1.79e-05)]_229_\ [+1(2.46e-06)]_7_[+1(6.59e-07)]_34 39847 1.12e-04 35_[+2(2.42e-05)]_108_\ [+2(4.52e-06)]_278_[+1(2.19e-06)]_26 40586 8.44e-03 382_[+1(1.08e-06)]_97 5622 3.29e-05 28_[+2(3.11e-06)]_270_\ [+1(4.46e-07)]_165 6093 4.00e-04 70_[+3(8.07e-07)]_414 8369 6.50e-06 286_[+3(7.65e-09)]_177_\ [+1(8.22e-05)] 8675 4.18e-09 172_[+2(1.56e-07)]_46_\ [+3(3.46e-08)]_200_[+1(2.02e-05)]_29 9029 6.63e-08 145_[+1(1.96e-07)]_77_\ [+2(5.95e-09)]_241 9184 1.13e-02 84_[+1(1.38e-06)]_395 9186 8.77e-02 194_[+1(6.03e-05)]_285 9527 9.21e-05 346_[+3(4.90e-06)]_99_\ [+1(3.81e-06)]_18 997 1.88e-07 79_[+2(2.15e-05)]_102_\ [+3(9.40e-07)]_261_[+1(3.42e-07)]_5 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************