******************************************************************************** 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/219/219.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 15336 1.0000 500 15992 1.0000 500 1680 1.0000 500 17292 1.0000 500 20232 1.0000 500 20583 1.0000 500 20742 1.0000 500 21368 1.0000 500 21374 1.0000 500 21524 1.0000 500 21805 1.0000 500 21973 1.0000 500 22498 1.0000 500 22593 1.0000 500 22659 1.0000 500 23079 1.0000 500 23337 1.0000 500 24545 1.0000 500 24750 1.0000 500 25222 1.0000 500 25767 1.0000 500 25905 1.0000 500 261270 1.0000 500 261852 1.0000 500 264305 1.0000 500 264306 1.0000 500 268543 1.0000 500 270148 1.0000 500 29144 1.0000 500 32325 1.0000 500 32736 1.0000 500 34533 1.0000 500 34661 1.0000 500 34729 1.0000 500 35087 1.0000 500 36322 1.0000 500 36334 1.0000 500 36979 1.0000 500 39286 1.0000 500 40089 1.0000 500 41038 1.0000 500 41419 1.0000 500 9040 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/219/219.seqs.fa -oc motifs/219 -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 0.257 C 0.238 G 0.236 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.238 G 0.236 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 41 llr = 383 E-value = 2.8e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :6124::811183111 pos.-specific C 8:98:9a266624264 probability G :1::2:::::1::11: matrix T 13::31::321:3524 bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 ** ** * Entropy 1.0 * ** *** * (13.5 bits) 0.8 * ** *** * 0.6 **** ***** * * 0.4 ************* ** 0.2 **************** 0.0 ---------------- Multilevel CACCACCACCCACTCC consensus T T CTT CT T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 34729 356 2.64e-08 GTCGGCAATT CACCACCACCCAAACT CGTCCATCCG 22498 171 1.66e-07 TCCTCTCCTA CACCTCCATCGACTCC CTTGTAGTCA 32736 398 2.36e-07 CACCGTGCCT CACCGCCATTCATTCC ACTCATTCCA 34533 282 4.42e-07 CCCAACTTCT CTCCACCCCCCACTCA TTTCTTTTTC 264305 346 4.42e-07 TGAACCTCAG CACCACCATCTAATCT GTTTTCGTCG 20232 282 4.42e-07 CCCAACTTCT CTCCACCCCCCACTCA TTTCTTTTTC 22593 470 5.14e-07 ATTCGTTCTG CACAACCACCAATTCT GCCTCTCTCC 21524 439 7.99e-07 TCTGAACACC TACCACCACACAATCC ACCTTTCGGA 40089 451 1.84e-06 TCTGTTGAAC CTCATCCACCCATTTT CTCTTCCCAC 39286 424 2.10e-06 CGCGACGCGC CACAGCCACCGAATCT GCCTCGGTGG 32325 179 2.38e-06 GCTGGTATTG TACCACCAACCCCTCT TCGATGTGAA 41419 259 2.70e-06 CTCCTGCCAC TGCCACCACTCATTCC ATCCGCAGCG 25222 436 3.06e-06 TCCCACGTGT TACCTCCACTCATTTC TCGCTCTCTC 35087 431 4.38e-06 TCTTCTCTCT CTCCTCCACTCACCGT TGCGACCACA 268543 462 4.38e-06 CGCAGACCTC CTCCTCCCCTCAAACC ATACCCACTT 20583 335 4.38e-06 TGAAACCGTC CAACACCACCCATAAC AACTGAGACG 24750 465 5.53e-06 CACACCATCA CACCAACACCCCATCT AAGCCGACAC 21805 458 6.94e-06 CTCGGTCCTC CTCCTCCAACGACGCC TCAAAAGAGA 29144 450 7.74e-06 TTGATTCCAA CTCCACCCTCCCTGCT TAAGCTCATA 20742 448 7.74e-06 CGGTCGCAGC CACAGCCACACATTGC CCGTCCACCT 22659 453 1.77e-05 CAGCCACACA CGCAGCCACTCAAGCC CTCTCCCTCC 270148 432 1.95e-05 GGAAGTCGTA CTCCTCCACCACCCGT TGAGCAACTT 25905 338 2.36e-05 TCACTTCCCG CAACACCCTCCATTTA TGAGAGCGTG 41038 460 2.85e-05 TGACGAACCA CTCCTTCCCTCCCTCC TCTTTTGGTT 36322 77 2.85e-05 AAAACAAAGA CTCCTTCACCAATTAC ACCGCCGACG 15992 406 3.72e-05 CCGTATCTCT CGCGACCATCCATCCT GTCCACACGC 9040 272 4.43e-05 CAGCCTTTTT CACCCCCATCAAATAT CTGTACCCCC 17292 466 4.43e-05 CCACCATTTG CAAATCCACTCACATC ACATCTCCTT 261270 85 4.83e-05 ACATCATCAG CAACACCATCTACCAC ACACACCGCA 21973 11 4.83e-05 TCCTCGATAG CACCTCCATTTCCCTC TTCTTGGCAG 15336 191 4.83e-05 GCTCAACCTT TGCCACCAACCACTGA ATGAATAGAG 23079 141 6.21e-05 CCGAAACGAA CATCACCACCGCTACC ATCATCGTTC 36979 459 6.74e-05 ATTTGCAAAT CACCTTCACAAACCTC ATATCAACGC 34661 478 1.08e-04 TCCGTGATTC AACAACCACACAAACT CAAGACA 23337 72 1.08e-04 AGTGATGCCC CACCTGCCACCATTGT TGCTACTGCT 25767 337 1.16e-04 GGTCTGCCGC TGCCGCCCTCCCCTTT GCCAGCCTCA 21374 455 1.16e-04 AACATCACCT GAACACCAACCAATCA GTGGTTCAAA 264306 343 1.55e-04 CCCTACAAGA CGCCGCCGTTCACGCT ACCGTTCAAC 1680 37 1.78e-04 CTTTCATGTT CACCGTCAAAGAAGCC AGGCCGATTT 36334 353 2.50e-04 ATCTCACTAT CTCCTCCCCATCACTT CCCTCATAGC 21368 313 2.84e-04 CCGAATCTCA CACAGCCATCACTGAA TTAATTTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34729 2.6e-08 355_[+1]_129 22498 1.7e-07 170_[+1]_314 32736 2.4e-07 397_[+1]_87 34533 4.4e-07 281_[+1]_203 264305 4.4e-07 345_[+1]_139 20232 4.4e-07 281_[+1]_203 22593 5.1e-07 469_[+1]_15 21524 8e-07 438_[+1]_46 40089 1.8e-06 450_[+1]_34 39286 2.1e-06 423_[+1]_61 32325 2.4e-06 178_[+1]_306 41419 2.7e-06 258_[+1]_226 25222 3.1e-06 435_[+1]_49 35087 4.4e-06 430_[+1]_54 268543 4.4e-06 461_[+1]_23 20583 4.4e-06 334_[+1]_150 24750 5.5e-06 464_[+1]_20 21805 6.9e-06 457_[+1]_27 29144 7.7e-06 449_[+1]_35 20742 7.7e-06 447_[+1]_37 22659 1.8e-05 452_[+1]_32 270148 2e-05 431_[+1]_53 25905 2.4e-05 337_[+1]_147 41038 2.8e-05 459_[+1]_25 36322 2.8e-05 76_[+1]_408 15992 3.7e-05 405_[+1]_79 9040 4.4e-05 271_[+1]_213 17292 4.4e-05 465_[+1]_19 261270 4.8e-05 84_[+1]_400 21973 4.8e-05 10_[+1]_474 15336 4.8e-05 190_[+1]_294 23079 6.2e-05 140_[+1]_344 36979 6.7e-05 458_[+1]_26 34661 0.00011 477_[+1]_7 23337 0.00011 71_[+1]_413 25767 0.00012 336_[+1]_148 21374 0.00012 454_[+1]_30 264306 0.00016 342_[+1]_142 1680 0.00018 36_[+1]_448 36334 0.00025 352_[+1]_132 21368 0.00028 312_[+1]_172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=41 34729 ( 356) CACCACCACCCAAACT 1 22498 ( 171) CACCTCCATCGACTCC 1 32736 ( 398) CACCGCCATTCATTCC 1 34533 ( 282) CTCCACCCCCCACTCA 1 264305 ( 346) CACCACCATCTAATCT 1 20232 ( 282) CTCCACCCCCCACTCA 1 22593 ( 470) CACAACCACCAATTCT 1 21524 ( 439) TACCACCACACAATCC 1 40089 ( 451) CTCATCCACCCATTTT 1 39286 ( 424) CACAGCCACCGAATCT 1 32325 ( 179) TACCACCAACCCCTCT 1 41419 ( 259) TGCCACCACTCATTCC 1 25222 ( 436) TACCTCCACTCATTTC 1 35087 ( 431) CTCCTCCACTCACCGT 1 268543 ( 462) CTCCTCCCCTCAAACC 1 20583 ( 335) CAACACCACCCATAAC 1 24750 ( 465) CACCAACACCCCATCT 1 21805 ( 458) CTCCTCCAACGACGCC 1 29144 ( 450) CTCCACCCTCCCTGCT 1 20742 ( 448) CACAGCCACACATTGC 1 22659 ( 453) CGCAGCCACTCAAGCC 1 270148 ( 432) CTCCTCCACCACCCGT 1 25905 ( 338) CAACACCCTCCATTTA 1 41038 ( 460) CTCCTTCCCTCCCTCC 1 36322 ( 77) CTCCTTCACCAATTAC 1 15992 ( 406) CGCGACCATCCATCCT 1 9040 ( 272) CACCCCCATCAAATAT 1 17292 ( 466) CAAATCCACTCACATC 1 261270 ( 85) CAACACCATCTACCAC 1 21973 ( 11) CACCTCCATTTCCCTC 1 15336 ( 191) TGCCACCAACCACTGA 1 23079 ( 141) CATCACCACCGCTACC 1 36979 ( 459) CACCTTCACAAACCTC 1 34661 ( 478) AACAACCACACAAACT 1 23337 ( 72) CACCTGCCACCATTGT 1 25767 ( 337) TGCCGCCCTCCCCTTT 1 21374 ( 455) GAACACCAACCAATCA 1 264306 ( 343) CGCCGCCGTTCACGCT 1 1680 ( 37) CACCGTCAAAGAAGCC 1 36334 ( 353) CTCCTCCCCATCACTT 1 21368 ( 313) CACAGCCATCACTGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 20855 bayes= 9.26681 E= 2.8e-016 -339 176 -327 -88 119 -1200 -69 -1 -107 184 -1200 -346 -40 171 -327 -1200 77 -328 -27 34 -339 184 -327 -146 -1200 207 -1200 -1200 156 -12 -327 -1200 -81 124 -1200 12 -81 136 -1200 -14 -81 141 -95 -146 156 4 -1200 -1200 19 62 -1200 34 -81 -48 -69 99 -107 124 -95 -46 -81 88 -1200 62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 41 E= 2.8e-016 0.024390 0.804878 0.024390 0.146341 0.585366 0.000000 0.146341 0.268293 0.121951 0.853659 0.000000 0.024390 0.195122 0.780488 0.024390 0.000000 0.439024 0.024390 0.195122 0.341463 0.024390 0.853659 0.024390 0.097561 0.000000 1.000000 0.000000 0.000000 0.756098 0.219512 0.024390 0.000000 0.146341 0.560976 0.000000 0.292683 0.146341 0.609756 0.000000 0.243902 0.146341 0.634146 0.121951 0.097561 0.756098 0.243902 0.000000 0.000000 0.292683 0.365854 0.000000 0.341463 0.146341 0.170732 0.146341 0.536585 0.121951 0.560976 0.121951 0.195122 0.146341 0.439024 0.000000 0.414634 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AT]CC[AT]CC[AC][CT][CT]C[AC][CTA]TC[CT] -------------------------------------------------------------------------------- Time 16.33 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 24 llr = 294 E-value = 5.5e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 51233:4377257::526332 pos.-specific C ::1:3::::1:::1143:31: probability G 3577:9563274299144548 matrix T 24::311:::1:1:::2::3: bits 2.1 1.9 1.7 * * 1.5 * ** * Relative 1.3 * ** * Entropy 1.0 * * * ** * * (17.6 bits) 0.8 ** * ** ***** * * 0.6 *** * ********* * * 0.4 **** *********** ** * 0.2 **************** ** * 0.0 --------------------- Multilevel AGGGAGGGAAGAAGGAGAGGG consensus GTAAC AAGGAG CCGCA sequence T T A AT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 22498 327 2.82e-08 GAGGACTGGC AGAGAGTGAAGAAGGAAAGTG GAAATGTTTG 29144 77 3.71e-08 CGCGAGCGGA GGGACGGGAAGGAGGGGAGCG TTGTAGAGTT 22593 28 6.26e-08 CTACTTCAGG AGGAAGAAGAGGAGGAAGAGG AAGAAGACTT 34533 364 9.10e-08 GCCCGTCTTC GTCGTGGGAAGAAGGCCACTG ATCTTGTCGT 20232 364 9.10e-08 GCCCGTCTTC GTCGTGGGAAGAAGGCCACTG ATCTTGTCGT 25767 36 2.05e-07 TTTGCATCTC AAGACGAAAAGGAGGCGAATG TTCTGCACAG 261852 379 2.84e-07 TTTTGGCACG AGGAAGAGAGAGAGGCTGGAG CACAGTTTGG 264306 143 3.88e-07 GCTACGTTTT ATAGTGGGGAGAAGCACACGG ATTACTATTG 270148 293 4.30e-07 GAGAGAGGCC GTGGAGGGACGAACGACAGAG AGATTTTGGT 21973 411 5.79e-07 TATTTTGGAC ATGGCGAGACGAGGGAGACGA GGAGTTGTAA 35087 344 7.03e-07 GTTGTTGTTC TGGGAGGAGGGGGGGAGGCTG TAGTAAATTC 23337 301 9.31e-07 GATAGGATTA GAGGTGAGAATAAGGAGAGGA ATGAACAAAT 32736 1 1.22e-06 . AGGATGAGAAGTAGGAAGGAA CATTGTCGTC 36979 99 1.33e-06 AGATATTTGA TGGGGGTGAAAAAGGCTGGGG GTAAAAGCAA 36334 164 1.33e-06 GCTGATGGGG AGGACGGAGATGAGGATGAAG TCTTTTACGG 268543 253 1.33e-06 TGATTTGAAG GTGGTGTGGTGGAGGCGAAGG AGCAATGTAT 21805 262 1.33e-06 GGTTCACAAC ATGGAGGTAGGAGGGACGAGG GACGAGTCGG 20742 203 1.33e-06 GATTTACAGT GTGGATGGAGAAAGGCGAGCG ATCGCCACCT 21368 128 1.45e-06 GGCATGTTGC TTGGCGGAAAGAGGACCAGGG GAGAGATTGC 20583 153 1.73e-06 GCACCCGGTG GGGGCGAGGAAGTGGGAAGAG GGGGCCCACA 15992 306 2.22e-06 GGTCGTTTGT TGAGAGAAGAGGTGGCGGGCG ACGGGCGGAA 40089 63 5.18e-06 AAGTACATTC TGAACGAAAAGGACGAAGATG GTAACGACAT 25222 102 5.18e-06 GAAGAGAGAT AGAATGCAAAGAAGCAGACAG GTATGCATGG 41038 379 1.41e-05 GTTTCGTGGG AGGGCTGGAGAATGGATGCGA CGGACGGACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22498 2.8e-08 326_[+2]_153 29144 3.7e-08 76_[+2]_403 22593 6.3e-08 27_[+2]_452 34533 9.1e-08 363_[+2]_116 20232 9.1e-08 363_[+2]_116 25767 2e-07 35_[+2]_444 261852 2.8e-07 378_[+2]_101 264306 3.9e-07 142_[+2]_337 270148 4.3e-07 292_[+2]_187 21973 5.8e-07 410_[+2]_69 35087 7e-07 343_[+2]_136 23337 9.3e-07 300_[+2]_179 32736 1.2e-06 [+2]_479 36979 1.3e-06 98_[+2]_381 36334 1.3e-06 163_[+2]_316 268543 1.3e-06 252_[+2]_227 21805 1.3e-06 261_[+2]_218 20742 1.3e-06 202_[+2]_277 21368 1.5e-06 127_[+2]_352 20583 1.7e-06 152_[+2]_327 15992 2.2e-06 305_[+2]_174 40089 5.2e-06 62_[+2]_417 25222 5.2e-06 101_[+2]_378 41038 1.4e-05 378_[+2]_101 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=24 22498 ( 327) AGAGAGTGAAGAAGGAAAGTG 1 29144 ( 77) GGGACGGGAAGGAGGGGAGCG 1 22593 ( 28) AGGAAGAAGAGGAGGAAGAGG 1 34533 ( 364) GTCGTGGGAAGAAGGCCACTG 1 20232 ( 364) GTCGTGGGAAGAAGGCCACTG 1 25767 ( 36) AAGACGAAAAGGAGGCGAATG 1 261852 ( 379) AGGAAGAGAGAGAGGCTGGAG 1 264306 ( 143) ATAGTGGGGAGAAGCACACGG 1 270148 ( 293) GTGGAGGGACGAACGACAGAG 1 21973 ( 411) ATGGCGAGACGAGGGAGACGA 1 35087 ( 344) TGGGAGGAGGGGGGGAGGCTG 1 23337 ( 301) GAGGTGAGAATAAGGAGAGGA 1 32736 ( 1) AGGATGAGAAGTAGGAAGGAA 1 36979 ( 99) TGGGGGTGAAAAAGGCTGGGG 1 36334 ( 164) AGGACGGAGATGAGGATGAAG 1 268543 ( 253) GTGGTGTGGTGGAGGCGAAGG 1 21805 ( 262) ATGGAGGTAGGAGGGACGAGG 1 20742 ( 203) GTGGATGGAGAAAGGCGAGCG 1 21368 ( 128) TTGGCGGAAAGAGGACCAGGG 1 20583 ( 153) GGGGCGAGGAAGTGGGAAGAG 1 15992 ( 306) TGAGAGAAGAGGTGGCGGGCG 1 40089 ( 63) TGAACGAAAAGGACGAAGATG 1 25222 ( 102) AGAATGCAAAGAAGCAGACAG 1 41038 ( 379) AGGGCTGGAGAATGGATGCGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20640 bayes= 11.6546 E= 5.5e-009 84 -1123 50 -37 -162 -1123 120 48 -30 -151 159 -1123 38 -1123 150 -1123 38 49 -250 12 -1123 -1123 196 -169 55 -251 96 -111 38 -1123 141 -269 146 -1123 31 -1123 138 -151 -18 -269 -30 -1123 159 -169 108 -1123 82 -269 146 -1123 -50 -111 -1123 -151 196 -1123 -262 -151 189 -1123 108 66 -150 -1123 -30 7 67 -69 118 -1123 82 -1123 -4 29 96 -1123 -4 -93 67 -11 -62 -1123 182 -1123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 5.5e-009 0.458333 0.000000 0.333333 0.208333 0.083333 0.000000 0.541667 0.375000 0.208333 0.083333 0.708333 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.333333 0.041667 0.291667 0.000000 0.000000 0.916667 0.083333 0.375000 0.041667 0.458333 0.125000 0.333333 0.000000 0.625000 0.041667 0.708333 0.000000 0.291667 0.000000 0.666667 0.083333 0.208333 0.041667 0.208333 0.000000 0.708333 0.083333 0.541667 0.000000 0.416667 0.041667 0.708333 0.000000 0.166667 0.125000 0.000000 0.083333 0.916667 0.000000 0.041667 0.083333 0.875000 0.000000 0.541667 0.375000 0.083333 0.000000 0.208333 0.250000 0.375000 0.166667 0.583333 0.000000 0.416667 0.000000 0.250000 0.291667 0.458333 0.000000 0.250000 0.125000 0.375000 0.250000 0.166667 0.000000 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AGT][GT][GA][GA][ACT]G[GA][GA][AG][AG][GA][AG]AGG[AC][GCA][AG][GCA][GAT]G -------------------------------------------------------------------------------- Time 31.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 26 llr = 267 E-value = 1.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::122:3::2:22::: pos.-specific C 1331212::32:1:21 probability G 7:56:81:a228:359 matrix T 2721615a:27:773: bits 2.1 * 1.9 * 1.7 ** * 1.5 ** * * Relative 1.3 * ** * * Entropy 1.0 ** * ** * * * (14.8 bits) 0.8 ** * ** *** * 0.6 ** ** ** **** * 0.4 ** *** ** ****** 0.2 ********* ****** 0.0 ---------------- Multilevel GTGGTGTTGCTGTTGG consensus CC A A GT sequence G C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 32736 168 1.32e-08 GTTGATGTAT GTGGCGTTGGTGTTGG TTCTTTGATC 41419 15 4.40e-08 TGCTGCTGTT GTAGTGTTGCTGTTGG TCACTCGATA 22659 46 7.15e-07 GTTGGTTGAA GTTGTGCTGGTGATGG CCGCGACAGG 17292 176 1.04e-06 GGAAGAGGTC GCCATGTTGATGTGGG AGCAGGTGGG 35087 307 1.89e-06 CGGACGATTG GTAGAGCTGTTGTTGG GACGTGGCCA 1680 298 1.89e-06 TGAGCATGGT GTGGTTTTGGTGATTG ACCAAGACGA 264306 55 2.13e-06 TCTGGCTGGA GTGTTGATGGGGTTTG ACAAATCCTT 34533 235 2.37e-06 GCTCAGGTAT GTTGCGTTGTGGTTCG ACTACTGTTT 20232 235 2.37e-06 GCTCAGGTAT GTTGCGTTGTGGTTCG ACTACTGTTT 21805 84 2.96e-06 GTTGCGAGAC GTCGTCATGCTGTGTG AGATATGAGT 23079 220 3.29e-06 CGTTCTTTTC GCTGTGTTGCTGCTCG TGACGGCTCT 15336 398 4.05e-06 ACCCTGCTTC GTGGAGTTGACATTTG AGGTTGTCGA 15992 147 4.96e-06 GAGACGTTCG CTGATGATGCCGTTGG ATTCGATGAG 29144 137 5.47e-06 ACGAGTGGCT GCGACGATGATGTGTG GTTGTCAGGA 21374 277 7.29e-06 GGTTTGAAAG TCCATGATGTTGTTTG CGGTGTATTA 21368 25 8.78e-06 CGACCGACGG GTGGTGTTGCCGAGGC GTGAGTTGTT 23337 241 1.36e-05 TGCAAACGGG GTGGTGAGGCTGCTTG CTTGCCTGGA 20583 83 1.61e-05 TCTACTGCCA TTGTTGTTGTGGTGTG TATGGTGGGT 24545 478 1.75e-05 GAAGATAGAG GCTGTGATGATAATCG TCCTTGA 20742 75 2.22e-05 CGTTGCGATA TCCCCGATGGTGTTGG AAGGTTGATG 34661 9 2.78e-05 ACTATGCC GTCTTGGTGATATGGG GTACCTTGGA 21524 194 2.78e-05 AAACGGAAAC GTCCAGTTGGCATTGG ACTTTGCGTT 40089 373 2.99e-05 AGTCAAGTTT CTCGTTGTGTTGTTGG CAACCGACTC 36334 442 3.46e-05 ATCAAAGCTC GTGAAGCTGCCGAGCG TGCCGCTGAA 21973 343 3.46e-05 TCGGCGTAGG TCGGTTCTGATGTGCG AGGTGGCATT 264305 151 4.27e-05 ATCTTCTCTT TTGGACTTGCTGTTGC TTCGCAACAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32736 1.3e-08 167_[+3]_317 41419 4.4e-08 14_[+3]_470 22659 7.2e-07 45_[+3]_439 17292 1e-06 175_[+3]_309 35087 1.9e-06 306_[+3]_178 1680 1.9e-06 297_[+3]_187 264306 2.1e-06 54_[+3]_430 34533 2.4e-06 234_[+3]_250 20232 2.4e-06 234_[+3]_250 21805 3e-06 83_[+3]_401 23079 3.3e-06 219_[+3]_265 15336 4e-06 397_[+3]_87 15992 5e-06 146_[+3]_338 29144 5.5e-06 136_[+3]_348 21374 7.3e-06 276_[+3]_208 21368 8.8e-06 24_[+3]_460 23337 1.4e-05 240_[+3]_244 20583 1.6e-05 82_[+3]_402 24545 1.7e-05 477_[+3]_7 20742 2.2e-05 74_[+3]_410 34661 2.8e-05 8_[+3]_476 21524 2.8e-05 193_[+3]_291 40089 3e-05 372_[+3]_112 36334 3.5e-05 441_[+3]_43 21973 3.5e-05 342_[+3]_142 264305 4.3e-05 150_[+3]_334 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=26 32736 ( 168) GTGGCGTTGGTGTTGG 1 41419 ( 15) GTAGTGTTGCTGTTGG 1 22659 ( 46) GTTGTGCTGGTGATGG 1 17292 ( 176) GCCATGTTGATGTGGG 1 35087 ( 307) GTAGAGCTGTTGTTGG 1 1680 ( 298) GTGGTTTTGGTGATTG 1 264306 ( 55) GTGTTGATGGGGTTTG 1 34533 ( 235) GTTGCGTTGTGGTTCG 1 20232 ( 235) GTTGCGTTGTGGTTCG 1 21805 ( 84) GTCGTCATGCTGTGTG 1 23079 ( 220) GCTGTGTTGCTGCTCG 1 15336 ( 398) GTGGAGTTGACATTTG 1 15992 ( 147) CTGATGATGCCGTTGG 1 29144 ( 137) GCGACGATGATGTGTG 1 21374 ( 277) TCCATGATGTTGTTTG 1 21368 ( 25) GTGGTGTTGCCGAGGC 1 23337 ( 241) GTGGTGAGGCTGCTTG 1 20583 ( 83) TTGTTGTTGTGGTGTG 1 24545 ( 478) GCTGTGATGATAATCG 1 20742 ( 75) TCCCCGATGGTGTTGG 1 34661 ( 9) GTCTTGGTGATATGGG 1 21524 ( 194) GTCCAGTTGGCATTGG 1 40089 ( 373) CTCGTTGTGTTGTTGG 1 36334 ( 442) GTGAAGCTGCCGAGCG 1 21973 ( 343) TCGGTTCTGATGTGCG 1 264305 ( 151) TTGGACTTGCTGTTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 20855 bayes= 10.8113 E= 1.2e-002 -1134 -163 163 -49 -1134 18 -1134 144 -174 18 97 -49 -42 -163 138 -122 -42 -31 -1134 119 -1134 -163 178 -122 26 -63 -162 78 -1134 -1134 -261 184 -1134 -1134 208 -1134 -15 37 -3 -22 -1134 -31 -62 128 -74 -1134 184 -1134 -42 -163 -1134 144 -1134 -1134 38 136 -1134 -4 97 19 -1134 -163 197 -1134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 26 E= 1.2e-002 0.000000 0.076923 0.730769 0.192308 0.000000 0.269231 0.000000 0.730769 0.076923 0.269231 0.461538 0.192308 0.192308 0.076923 0.615385 0.115385 0.192308 0.192308 0.000000 0.615385 0.000000 0.076923 0.807692 0.115385 0.307692 0.153846 0.076923 0.461538 0.000000 0.000000 0.038462 0.961538 0.000000 0.000000 1.000000 0.000000 0.230769 0.307692 0.230769 0.230769 0.000000 0.192308 0.153846 0.653846 0.153846 0.000000 0.846154 0.000000 0.192308 0.076923 0.000000 0.730769 0.000000 0.000000 0.307692 0.692308 0.000000 0.230769 0.461538 0.307692 0.000000 0.076923 0.923077 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[TC][GC]GTG[TA]TG[CAGT]TGT[TG][GTC]G -------------------------------------------------------------------------------- Time 45.51 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15336 1.27e-03 190_[+1(4.83e-05)]_191_\ [+3(4.05e-06)]_87 15992 7.35e-06 146_[+3(4.96e-06)]_143_\ [+2(2.22e-06)]_79_[+1(3.72e-05)]_79 1680 2.19e-03 297_[+3(1.89e-06)]_187 17292 6.86e-04 175_[+3(1.04e-06)]_274_\ [+1(4.43e-05)]_19 20232 3.72e-09 234_[+3(2.37e-06)]_31_\ [+1(4.42e-07)]_66_[+2(9.10e-08)]_116 20583 2.50e-06 82_[+3(1.61e-05)]_54_[+2(1.73e-06)]_\ 38_[+2(3.31e-05)]_102_[+1(4.38e-06)]_150 20742 4.39e-06 74_[+3(2.22e-05)]_112_\ [+2(1.33e-06)]_224_[+1(7.74e-06)]_37 21368 4.77e-05 24_[+3(8.78e-06)]_87_[+2(1.45e-06)]_\ 352 21374 1.38e-03 276_[+3(7.29e-06)]_208 21524 4.23e-04 193_[+3(2.78e-05)]_229_\ [+1(7.99e-07)]_46 21805 6.55e-07 83_[+3(2.96e-06)]_162_\ [+2(1.33e-06)]_175_[+1(6.94e-06)]_27 21973 1.56e-05 10_[+1(4.83e-05)]_316_\ [+3(3.46e-05)]_52_[+2(5.79e-07)]_69 22498 1.43e-07 170_[+1(1.66e-07)]_140_\ [+2(2.82e-08)]_153 22593 1.12e-06 27_[+2(6.26e-08)]_421_\ [+1(5.14e-07)]_15 22659 1.32e-04 45_[+3(7.15e-07)]_391_\ [+1(1.77e-05)]_32 23079 5.30e-04 140_[+1(6.21e-05)]_63_\ [+3(3.29e-06)]_265 23337 2.09e-05 134_[+2(1.60e-05)]_85_\ [+3(1.36e-05)]_44_[+2(9.31e-07)]_179 24545 1.64e-02 477_[+3(1.75e-05)]_7 24750 5.72e-02 464_[+1(5.53e-06)]_20 25222 5.91e-05 101_[+2(5.18e-06)]_313_\ [+1(3.06e-06)]_49 25767 6.75e-05 35_[+2(2.05e-07)]_444 25905 6.29e-02 337_[+1(2.36e-05)]_147 261270 2.22e-01 84_[+1(4.83e-05)]_400 261852 4.05e-03 378_[+2(2.84e-07)]_101 264305 3.84e-04 150_[+3(4.27e-05)]_179_\ [+1(4.42e-07)]_139 264306 2.54e-06 54_[+3(2.13e-06)]_72_[+2(3.88e-07)]_\ 337 268543 1.26e-05 252_[+2(1.33e-06)]_156_\ [+1(1.77e-05)]_16_[+1(4.38e-06)]_23 270148 4.16e-05 292_[+2(4.30e-07)]_118_\ [+1(1.95e-05)]_53 29144 4.86e-08 76_[+2(3.71e-08)]_20_[+3(3.22e-05)]_\ 3_[+3(5.47e-06)]_297_[+1(7.74e-06)]_35 32325 7.58e-03 178_[+1(2.38e-06)]_306 32736 1.88e-10 [+2(1.22e-06)]_146_[+3(1.32e-08)]_\ 214_[+1(2.36e-07)]_39_[+1(1.18e-05)]_32 34533 3.72e-09 234_[+3(2.37e-06)]_31_\ [+1(4.42e-07)]_66_[+2(9.10e-08)]_116 34661 7.20e-03 8_[+3(2.78e-05)]_476 34729 8.71e-04 355_[+1(2.64e-08)]_69_\ [+1(8.55e-05)]_44 35087 1.61e-07 306_[+3(1.89e-06)]_21_\ [+2(7.03e-07)]_66_[+1(4.38e-06)]_54 36322 3.14e-02 76_[+1(2.85e-05)]_408 36334 1.31e-04 73_[+2(4.70e-05)]_24_[+2(9.03e-06)]_\ 24_[+2(1.33e-06)]_257_[+3(3.46e-05)]_43 36979 7.89e-04 98_[+2(1.33e-06)]_339_\ [+1(6.74e-05)]_26 39286 2.74e-03 423_[+1(2.10e-06)]_61 40089 5.35e-06 62_[+2(5.18e-06)]_115_\ [+2(5.42e-05)]_153_[+3(2.99e-05)]_62_[+1(1.84e-06)]_15_[+1(3.06e-06)]_3 41038 2.50e-03 378_[+2(1.41e-05)]_60_\ [+1(2.85e-05)]_25 41419 4.54e-06 14_[+3(4.40e-08)]_228_\ [+1(2.70e-06)]_150_[+1(8.55e-05)]_60 9040 4.79e-02 271_[+1(4.43e-05)]_213 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************