******************************************************************************** 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/242/242.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10517 1.0000 500 1069 1.0000 500 11342 1.0000 500 11626 1.0000 500 11934 1.0000 500 15114 1.0000 500 1907 1.0000 500 20747 1.0000 500 21281 1.0000 500 21770 1.0000 500 22302 1.0000 500 22621 1.0000 500 23144 1.0000 500 23332 1.0000 500 23622 1.0000 500 23667 1.0000 500 23969 1.0000 500 24216 1.0000 500 24345 1.0000 500 2452 1.0000 500 24598 1.0000 500 24790 1.0000 500 25142 1.0000 500 25311 1.0000 500 25906 1.0000 500 263785 1.0000 500 264498 1.0000 500 264548 1.0000 500 268352 1.0000 500 268655 1.0000 500 268859 1.0000 500 2897 1.0000 500 31007 1.0000 500 31932 1.0000 500 32229 1.0000 500 38509 1.0000 500 4019 1.0000 500 4712 1.0000 500 5007 1.0000 500 5313 1.0000 500 7066 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/242/242.seqs.fa -oc motifs/242 -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= 41 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= 20500 N= 41 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.240 G 0.238 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.240 G 0.238 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 29 llr = 353 E-value = 3.0e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :6326:463272433225228 pos.-specific C 9178:95268:853577:88: probability G 11::21::1::::21:13::2 matrix T 12::2::2::31:111:2::: bits 2.1 1.9 1.7 1.4 * Relative 1.2 * ** * * ** Entropy 1.0 * ** * * * *** (17.6 bits) 0.8 * ** * * ** ** *** 0.6 * ***** **** ** *** 0.4 ************* ****** 0.2 ********************* 0.0 --------------------- Multilevel CACCACCACCACCACCCACCA consensus TAAT ATAAT ACAAAGAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 24598 409 1.71e-09 TCCGACACCA CACCACAACCACAAGCCACAA CACCGCCTCC 2897 454 2.34e-09 AATCTCCTCA CACCACAAACACACCTCACCA CCTTCATATT 20747 388 5.89e-09 CTCTCACTCT CACCGCCATCACCACCCACCA CCACACGACT 264548 252 7.86e-09 GTCTGTCCAC CACCACCACCTCCTCTCACCA GCGCCCGACC 4019 159 2.03e-08 CACACAACGT CAACACATGCACACCCAACCA CTGTTGAGTA 24216 448 2.99e-08 TCCCCTTTTT CACAACCACAACCACACACAA GTCCGATCCT 31007 222 3.85e-08 CAAGCCATGC CACCGCCTCCTCAAACCGCCG TCAGATGCGT 24345 164 4.91e-08 ATGACAGATG CGCAACATCCTCCACCCGCCA GGATCATTTG 1069 363 7.00e-08 TCCACAACCA CACCACCACCGCCGCCATCCA TTTCCTCCTA 1907 289 8.82e-08 TCGAGAGGCC CACCAGCCACAACCACCACCA TCCCTCTATC 268352 436 1.38e-07 TTCGTCAACC TTCAACCACCACCACCCAACA TCTTGGAGGG 21281 478 4.35e-07 CTGTTTTTTG CCACACCACCACCACAGAACA AC 22302 353 5.30e-07 GCAGACGATC CACCGCACGCACCCGCATCCA CGTCGACAGT 25311 471 9.32e-07 CACATCAACA CACCTCACGCTCACACAGACA CCAACAAAC 5007 332 1.02e-06 GCGCTCCCCT CAAAACAACATCACTCCGCCG TCCTCCTCCT 264498 464 1.02e-06 CCTGACGGCA CTCCACTTCCACACAACGACA AAACGAGACT 263785 15 1.59e-06 CCGGTCGCTG CTCCTCCCCCTCCACCTGCAA ATAATGGTCA 15114 186 2.64e-06 ACAGAACACA CTCAACCACAACTTACAACCA ACATCATGAC 23332 367 3.94e-06 CACTTGGAAA CAACGCAGCCAACGCCCTCCG AGCCTCTGCG 11342 452 4.26e-06 TGCATCTCTC CTCCTCCTACACAGCACAAAG CCAGCCTCAA 7066 301 4.97e-06 AGCAACAGAG CCACAGAAACACATGCCGCCG TCTGGAACCA 38509 364 4.97e-06 CTGTTTGCTC CTCCACACAACACACACACCA ACCCCTTTCC 24790 145 4.97e-06 ATGAACCAAT GAACGCCAACAAACACCTCAA CTTTTTCAGC 32229 446 7.22e-06 CTGCTGCAGT GAACACAAGCAACTCACGCAA GGCGCTGAAA 23667 460 8.97e-06 CCACAACTCC CCCCTTCTCATCACACAACCA TCAATCGAGG 22621 447 9.63e-06 TCCAAAGTGT CAACAGCAACTTAGAACTCCA ACTTCGAGCA 11934 268 1.03e-05 GTTCATCAGT CGCCTCATCAACCGTCCATCA TCACCGTCGG 31932 158 1.45e-05 TAAACGTTTC CCCAACGACAACACACGGACA CAAGCTCGAT 23144 472 1.77e-05 CATCCAAGAA TACATCAAACATCATCCGCAA CAACCATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24598 1.7e-09 408_[+1]_71 2897 2.3e-09 453_[+1]_26 20747 5.9e-09 387_[+1]_92 264548 7.9e-09 251_[+1]_228 4019 2e-08 158_[+1]_321 24216 3e-08 447_[+1]_32 31007 3.8e-08 221_[+1]_258 24345 4.9e-08 163_[+1]_316 1069 7e-08 362_[+1]_117 1907 8.8e-08 288_[+1]_191 268352 1.4e-07 435_[+1]_44 21281 4.4e-07 477_[+1]_2 22302 5.3e-07 352_[+1]_127 25311 9.3e-07 470_[+1]_9 5007 1e-06 331_[+1]_148 264498 1e-06 463_[+1]_16 263785 1.6e-06 14_[+1]_465 15114 2.6e-06 185_[+1]_294 23332 3.9e-06 366_[+1]_113 11342 4.3e-06 451_[+1]_28 7066 5e-06 300_[+1]_179 38509 5e-06 363_[+1]_116 24790 5e-06 144_[+1]_335 32229 7.2e-06 445_[+1]_34 23667 9e-06 459_[+1]_20 22621 9.6e-06 446_[+1]_33 11934 1e-05 267_[+1]_212 31932 1.5e-05 157_[+1]_322 23144 1.8e-05 471_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=29 24598 ( 409) CACCACAACCACAAGCCACAA 1 2897 ( 454) CACCACAAACACACCTCACCA 1 20747 ( 388) CACCGCCATCACCACCCACCA 1 264548 ( 252) CACCACCACCTCCTCTCACCA 1 4019 ( 159) CAACACATGCACACCCAACCA 1 24216 ( 448) CACAACCACAACCACACACAA 1 31007 ( 222) CACCGCCTCCTCAAACCGCCG 1 24345 ( 164) CGCAACATCCTCCACCCGCCA 1 1069 ( 363) CACCACCACCGCCGCCATCCA 1 1907 ( 289) CACCAGCCACAACCACCACCA 1 268352 ( 436) TTCAACCACCACCACCCAACA 1 21281 ( 478) CCACACCACCACCACAGAACA 1 22302 ( 353) CACCGCACGCACCCGCATCCA 1 25311 ( 471) CACCTCACGCTCACACAGACA 1 5007 ( 332) CAAAACAACATCACTCCGCCG 1 264498 ( 464) CTCCACTTCCACACAACGACA 1 263785 ( 15) CTCCTCCCCCTCCACCTGCAA 1 15114 ( 186) CTCAACCACAACTTACAACCA 1 23332 ( 367) CAACGCAGCCAACGCCCTCCG 1 11342 ( 452) CTCCTCCTACACAGCACAAAG 1 7066 ( 301) CCACAGAAACACATGCCGCCG 1 38509 ( 364) CTCCACACAACACACACACCA 1 24790 ( 145) GAACGCCAACAAACACCTCAA 1 32229 ( 446) GAACACAAGCAACTCACGCAA 1 23667 ( 460) CCCCTTCTCATCACACAACCA 1 22621 ( 447) CAACAGCAACTTAGAACTCCA 1 11934 ( 268) CGCCTCATCAACCGTCCATCA 1 31932 ( 158) CCCAACGACAACACACGGACA 1 23144 ( 472) TACATCAAACATCATCCGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19680 bayes= 10.6547 E= 3.0e-020 -1150 185 -179 -191 116 -80 -179 -33 7 159 -1150 -1150 -12 166 -1150 -1150 124 -1150 -47 -33 -1150 185 -120 -291 77 101 -279 -291 107 -48 -279 -10 7 120 -79 -291 -12 166 -1150 -1150 132 -280 -279 9 -60 166 -1150 -191 77 111 -1150 -291 39 52 -47 -91 24 101 -120 -133 -12 152 -1150 -191 -34 152 -179 -291 88 -1150 53 -59 -34 166 -1150 -291 -12 166 -1150 -1150 166 -1150 -47 -1150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 29 E= 3.0e-020 0.000000 0.862069 0.068966 0.068966 0.586207 0.137931 0.068966 0.206897 0.275862 0.724138 0.000000 0.000000 0.241379 0.758621 0.000000 0.000000 0.620690 0.000000 0.172414 0.206897 0.000000 0.862069 0.103448 0.034483 0.448276 0.482759 0.034483 0.034483 0.551724 0.172414 0.034483 0.241379 0.275862 0.551724 0.137931 0.034483 0.241379 0.758621 0.000000 0.000000 0.655172 0.034483 0.034483 0.275862 0.172414 0.758621 0.000000 0.068966 0.448276 0.517241 0.000000 0.034483 0.344828 0.344828 0.172414 0.137931 0.310345 0.482759 0.103448 0.103448 0.241379 0.689655 0.000000 0.068966 0.206897 0.689655 0.068966 0.034483 0.482759 0.000000 0.344828 0.172414 0.206897 0.758621 0.000000 0.034483 0.241379 0.758621 0.000000 0.000000 0.827586 0.000000 0.172414 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AT][CA][CA][AT]C[CA][AT][CA][CA][AT]C[CA][AC][CA][CA][CA][AG][CA][CA]A -------------------------------------------------------------------------------- Time 14.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 31 llr = 338 E-value = 3.4e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:4:332:31131245:2:: pos.-specific C 1:12::::2:1::::11::2 probability G :a:2623a354547117117 matrix T 8:56155:344251532792 bits 2.1 * * 1.9 * * 1.7 * * * 1.4 * * * Relative 1.2 ** * * Entropy 1.0 ** * * (15.7 bits) 0.8 ** * * **** 0.6 ***** * * *** **** 0.4 ******** * ********* 0.2 ******** *********** 0.0 -------------------- Multilevel TGTTGTTGTGGGTGTAGTTG consensus AGAAG ATTAG AT A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 23622 170 5.01e-10 GCGATGATGT TGATATTGTGTGTGAAGTTG ATGGCTGTGA 25142 394 2.14e-09 GGGGACACGC TGTTGTTGTTGTTGTTGTTG GTCACCGCTG 1907 63 2.14e-09 CTGTCATGGT TGTTGTTGTTGTTGTTGTTG GAAGAGAGTG 21770 20 1.57e-07 ATTGATGCTC CGTTGTGGGTTGGGATGTTG CATTGGATGC 5007 16 1.80e-07 CACTGTGAGG TGAGGTAGGGGAGGGAGTTG AGGCATGTTG 264548 175 3.05e-07 ACTGACTTCT TGTTAATGGGGGTCAAGTTG TTTGGCTTTT 22621 234 3.93e-07 ATATTTGTGG TGTTGGTGCTCGTGTATTTG TTTTTATTGA 4019 417 1.13e-06 TGGAGTTTGC TGATGTGGTGTGTGGAGAGG TAAACGTTCT 7066 458 1.26e-06 CTGCATCGCT TGTGGCTGTGGTTGTGGTTG CTCGACGTAC 5313 439 1.56e-06 CGGTTGGAGC TGTGGTGGGTTGTTTAGTTT AGAATCAGGA 15114 71 1.92e-06 TGGTAGAGAT TGATTATGATAGTGTAGTTC ATTAATGGAA 264498 231 2.61e-06 GGTACCACGA CGATGAGGAGGAGGAAGGTG GAAGCCCTAG 22302 227 2.61e-06 GGCCTATTTG AGATAGAGAGTGTGTTGTTG TTGACATCGC 268859 166 2.88e-06 CGGACGAACA TGTTGATGGGTTGGTGTTTC GTCGATGAAG 38509 64 3.50e-06 TGGGAGTGGT TGCCATGGTAGGTGAAGTTT GCGAGCGGAA 11626 230 4.23e-06 ACAATCAGCT TGATGAGGTGTGGAACTTTG AGGAGGAGAG 263785 301 4.64e-06 GATGGCAGAG TGATAAGGATGTGGATGATC GTAGGAAGAT 11342 116 4.64e-06 ATCATGATTG TGATATAGGTCGAGAAGTTC TGTGTGTCCT 2452 405 5.09e-06 ACTATGGTGG CGACGTTGCTGGAGAGGTTG CTATCGATTC 24216 163 6.66e-06 CGGCTCCGTA TGTTGTTGTAAAGGACGTTT GGGTAGGAGG 23667 225 7.27e-06 GAGAGGAGAG TGCTGTTGCTTGGAGACTTG CACACCGATG 32229 17 9.39e-06 AACAGCAGAG TGTCATTGAAGATTTAGATG CGTTTGGATA 21281 26 1.02e-05 CCCGCTGCAC TGTCGTGGGTGAGATATGTG TTGGAATAGT 20747 4 1.11e-05 AAA TGAGGAAGCGAATGAACATG AACAACATGT 31007 425 1.20e-05 TCCGGTGAGT AGATGGTGATTGGATTGATG ATCAGATAAT 268655 385 1.53e-05 GGAGGTCGCC TGTTGGTGCGGGAGTTGGGG CAAGTTCTGG 10517 442 2.07e-05 TCAGATACCT TGTGTTTGTGTTTGTACATC GTAACATCAT 24790 13 2.40e-05 ATGAAGGCGA TGTCGATGAAAGTAGTGATG CTGCCAACAA 23144 307 2.40e-05 GAGACAAAAA TGACAAAGTGCCTGTGGTTG GTTCACCTCA 25906 340 2.57e-05 ATGATTTTTT TGTGCTGGGGTATGATTTTT GCTCGCGTGC 268352 346 4.44e-05 CTCAAGCGGG TGCGAGAGAGGAGGAACTTT CAAGTTCCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23622 5e-10 169_[+2]_311 25142 2.1e-09 393_[+2]_87 1907 2.1e-09 62_[+2]_418 21770 1.6e-07 19_[+2]_461 5007 1.8e-07 15_[+2]_465 264548 3.1e-07 174_[+2]_306 22621 3.9e-07 233_[+2]_247 4019 1.1e-06 416_[+2]_64 7066 1.3e-06 457_[+2]_23 5313 1.6e-06 438_[+2]_42 15114 1.9e-06 70_[+2]_410 264498 2.6e-06 230_[+2]_250 22302 2.6e-06 226_[+2]_254 268859 2.9e-06 165_[+2]_315 38509 3.5e-06 63_[+2]_417 11626 4.2e-06 229_[+2]_251 263785 4.6e-06 300_[+2]_180 11342 4.6e-06 115_[+2]_365 2452 5.1e-06 404_[+2]_76 24216 6.7e-06 162_[+2]_318 23667 7.3e-06 224_[+2]_256 32229 9.4e-06 16_[+2]_464 21281 1e-05 25_[+2]_455 20747 1.1e-05 3_[+2]_477 31007 1.2e-05 424_[+2]_56 268655 1.5e-05 384_[+2]_96 10517 2.1e-05 441_[+2]_39 24790 2.4e-05 12_[+2]_468 23144 2.4e-05 306_[+2]_174 25906 2.6e-05 339_[+2]_141 268352 4.4e-05 345_[+2]_135 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=31 23622 ( 170) TGATATTGTGTGTGAAGTTG 1 25142 ( 394) TGTTGTTGTTGTTGTTGTTG 1 1907 ( 63) TGTTGTTGTTGTTGTTGTTG 1 21770 ( 20) CGTTGTGGGTTGGGATGTTG 1 5007 ( 16) TGAGGTAGGGGAGGGAGTTG 1 264548 ( 175) TGTTAATGGGGGTCAAGTTG 1 22621 ( 234) TGTTGGTGCTCGTGTATTTG 1 4019 ( 417) TGATGTGGTGTGTGGAGAGG 1 7066 ( 458) TGTGGCTGTGGTTGTGGTTG 1 5313 ( 439) TGTGGTGGGTTGTTTAGTTT 1 15114 ( 71) TGATTATGATAGTGTAGTTC 1 264498 ( 231) CGATGAGGAGGAGGAAGGTG 1 22302 ( 227) AGATAGAGAGTGTGTTGTTG 1 268859 ( 166) TGTTGATGGGTTGGTGTTTC 1 38509 ( 64) TGCCATGGTAGGTGAAGTTT 1 11626 ( 230) TGATGAGGTGTGGAACTTTG 1 263785 ( 301) TGATAAGGATGTGGATGATC 1 11342 ( 116) TGATATAGGTCGAGAAGTTC 1 2452 ( 405) CGACGTTGCTGGAGAGGTTG 1 24216 ( 163) TGTTGTTGTAAAGGACGTTT 1 23667 ( 225) TGCTGTTGCTTGGAGACTTG 1 32229 ( 17) TGTCATTGAAGATTTAGATG 1 21281 ( 26) TGTCGTGGGTGAGATATGTG 1 20747 ( 4) TGAGGAAGCGAATGAACATG 1 31007 ( 425) AGATGGTGATTGGATTGATG 1 268655 ( 385) TGTTGGTGCGGGAGTTGGGG 1 10517 ( 442) TGTGTTTGTGTTTGTACATC 1 24790 ( 13) TGTCGATGAAAGTAGTGATG 1 23144 ( 307) TGACAAAGTGCCTGTGGTTG 1 25906 ( 340) TGTGCTGGGGTATGATTTTT 1 268352 ( 346) TGCGAGAGAGGAGGAACTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 19721 bayes= 10.0181 E= 3.4e-012 -202 -131 -1160 169 -1160 -1160 207 -1160 68 -131 -1160 90 -1160 -31 -8 116 15 -289 136 -201 15 -289 -56 99 -44 -1160 28 99 -1160 -1160 207 -1160 -2 -57 11 31 -102 -1160 102 58 -102 -131 81 45 -2 -289 111 -42 -144 -1160 57 108 -70 -289 164 -201 68 -1160 -89 80 98 -189 -89 16 -1160 -89 157 -69 -22 -1160 -130 138 -1160 -1160 -188 185 -1160 -57 151 -69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 31 E= 3.4e-012 0.064516 0.096774 0.000000 0.838710 0.000000 0.000000 1.000000 0.000000 0.419355 0.096774 0.000000 0.483871 0.000000 0.193548 0.225806 0.580645 0.290323 0.032258 0.612903 0.064516 0.290323 0.032258 0.161290 0.516129 0.193548 0.000000 0.290323 0.516129 0.000000 0.000000 1.000000 0.000000 0.258065 0.161290 0.258065 0.322581 0.129032 0.000000 0.483871 0.387097 0.129032 0.096774 0.419355 0.354839 0.258065 0.032258 0.516129 0.193548 0.096774 0.000000 0.354839 0.548387 0.161290 0.032258 0.741935 0.064516 0.419355 0.000000 0.129032 0.451613 0.516129 0.064516 0.129032 0.290323 0.000000 0.129032 0.709677 0.161290 0.225806 0.000000 0.096774 0.677419 0.000000 0.000000 0.064516 0.935484 0.000000 0.161290 0.677419 0.161290 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TG[TA][TG][GA][TA][TG]G[TAG][GT][GT][GA][TG]G[TA][AT]G[TA]TG -------------------------------------------------------------------------------- Time 28.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 23 llr = 227 E-value = 8.5e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 618::3:24::1 pos.-specific C :2:::6::5::3 probability G 45:aa:a8:8a2 matrix T :22::1::12:4 bits 2.1 * * 1.9 ** * * 1.7 ** * * 1.4 ** ** * Relative 1.2 *** ** * Entropy 1.0 * *** ** ** (14.2 bits) 0.8 * *** ** ** 0.6 * ********* 0.4 * ********* 0.2 ************ 0.0 ------------ Multilevel AGAGGCGGCGGT consensus G T A A C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 38509 1 1.26e-07 . GGAGGCGGCGGT TGTTTCAGCG 268352 149 4.18e-07 AAGAATCAGA GGAGGCGGCGGG AGGGGGAAAG 23332 226 9.52e-07 GAGATTCACC AGAGGAGGAGGT GACTTGATGG 23969 261 1.40e-06 TGAGCAGGCG GCAGGCGGCGGC GCCGTGTCAC 268655 454 2.07e-06 AGGCTGTGGT GAAGGCGGCGGT TTTGCCGTTT 25906 283 2.07e-06 CTTCTGGGGC GGTGGCGGCGGC GTTTCGATCG 2897 57 3.68e-06 TCACTTTTTG GGTGGCGGAGGC CGATTTGTGA 23667 261 5.84e-06 GATGCAAGAG ATAGGAGGAGGT TTGAGGGTAT 263785 259 8.71e-06 TGCAACAGCA GCAGGCGGCTGT TCATCAGGGA 22302 47 9.69e-06 GCTATTTGTG GTAGGCGGCTGT GTCAGCGGCA 1907 12 9.69e-06 GGGAGGTTAG GAAGGAGGAGGT GAAGTTTGTT 11626 315 1.23e-05 GCTAGTTTCA AGAGGAGACGGG ACAGGAAGCT 25142 217 1.39e-05 ACCTCTCAAA ACAGGCGGTGGC AGTGTTTTGT 5313 395 1.54e-05 CCTTGGGGTG AGAGGCGGCGAC GGCGGAAGGC 24790 55 1.54e-05 AATGGTTTAC AAAGGAGGAGGG CATCCTTGAT 10517 359 1.71e-05 GACGGTGATG AGTGGTGGAGGC GCAACAATGA 25311 121 2.17e-05 GATGGTCGTC AGAAGCGGCGGG CGACAGGACC 23144 154 2.32e-05 GAGCATGGAC AGAGGTGACGGG TATTGACTTT 1069 468 2.75e-05 CTCTCTCTTG ATAGGCGGCCGT CGCTACTGAA 24345 465 3.92e-05 AGAGTTGCGG AGAGGAGAAGGA AAAAGCTAGG 2452 3 4.97e-05 GA ATAGGCGAAGGA TGGTGCGGTT 21281 133 5.75e-05 GTTGAGGTGA AGTGGTGGATGC TTTGCCTTTC 4712 300 1.05e-04 CATTGAATAG GCTGGCGGTTGT CGCAATGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38509 1.3e-07 [+3]_488 268352 4.2e-07 148_[+3]_340 23332 9.5e-07 225_[+3]_263 23969 1.4e-06 260_[+3]_228 268655 2.1e-06 453_[+3]_35 25906 2.1e-06 282_[+3]_206 2897 3.7e-06 56_[+3]_432 23667 5.8e-06 260_[+3]_228 263785 8.7e-06 258_[+3]_230 22302 9.7e-06 46_[+3]_442 1907 9.7e-06 11_[+3]_477 11626 1.2e-05 314_[+3]_174 25142 1.4e-05 216_[+3]_272 5313 1.5e-05 394_[+3]_94 24790 1.5e-05 54_[+3]_434 10517 1.7e-05 358_[+3]_130 25311 2.2e-05 120_[+3]_368 23144 2.3e-05 153_[+3]_335 1069 2.8e-05 467_[+3]_21 24345 3.9e-05 464_[+3]_24 2452 5e-05 2_[+3]_486 21281 5.7e-05 132_[+3]_356 4712 0.0001 299_[+3]_189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=23 38509 ( 1) GGAGGCGGCGGT 1 268352 ( 149) GGAGGCGGCGGG 1 23332 ( 226) AGAGGAGGAGGT 1 23969 ( 261) GCAGGCGGCGGC 1 268655 ( 454) GAAGGCGGCGGT 1 25906 ( 283) GGTGGCGGCGGC 1 2897 ( 57) GGTGGCGGAGGC 1 23667 ( 261) ATAGGAGGAGGT 1 263785 ( 259) GCAGGCGGCTGT 1 22302 ( 47) GTAGGCGGCTGT 1 1907 ( 12) GAAGGAGGAGGT 1 11626 ( 315) AGAGGAGACGGG 1 25142 ( 217) ACAGGCGGTGGC 1 5313 ( 395) AGAGGCGGCGAC 1 24790 ( 55) AAAGGAGGAGGG 1 10517 ( 359) AGTGGTGGAGGC 1 25311 ( 121) AGAAGCGGCGGG 1 23144 ( 154) AGAGGTGACGGG 1 1069 ( 468) ATAGGCGGCCGT 1 24345 ( 465) AGAGGAGAAGGA 1 2452 ( 3) ATAGGCGAAGGA 1 21281 ( 133) AGTGGTGGATGC 1 4712 ( 300) GCTGGCGGTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 20049 bayes= 11.3272 E= 8.5e-003 111 -1117 87 -1117 -101 -46 113 -58 158 -1117 -1117 -26 -259 -1117 200 -1117 -1117 -1117 207 -1117 -1 134 -1117 -99 -1117 -1117 207 -1117 -59 -1117 179 -1117 58 112 -1117 -158 -1117 -246 171 -58 -259 -1117 200 -1117 -159 34 -13 59 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 23 E= 8.5e-003 0.565217 0.000000 0.434783 0.000000 0.130435 0.173913 0.521739 0.173913 0.782609 0.000000 0.000000 0.217391 0.043478 0.000000 0.956522 0.000000 0.000000 0.000000 1.000000 0.000000 0.260870 0.608696 0.000000 0.130435 0.000000 0.000000 1.000000 0.000000 0.173913 0.000000 0.826087 0.000000 0.391304 0.521739 0.000000 0.086957 0.000000 0.043478 0.782609 0.173913 0.043478 0.000000 0.956522 0.000000 0.086957 0.304348 0.217391 0.391304 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG]G[AT]GG[CA]GG[CA]GG[TCG] -------------------------------------------------------------------------------- Time 41.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10517 4.00e-03 358_[+3(1.71e-05)]_71_\ [+2(2.07e-05)]_39 1069 6.30e-06 362_[+1(7.00e-08)]_41_\ [+3(9.94e-05)]_31_[+3(2.75e-05)]_21 11342 2.90e-04 115_[+2(4.64e-06)]_316_\ [+1(4.26e-06)]_28 11626 5.66e-04 229_[+2(4.23e-06)]_65_\ [+3(1.23e-05)]_174 11934 5.61e-02 267_[+1(1.03e-05)]_212 15114 5.02e-05 70_[+2(1.92e-06)]_95_[+1(2.64e-06)]_\ 294 1907 9.41e-11 11_[+3(9.69e-06)]_10_[+2(6.66e-06)]_\ 9_[+2(2.14e-09)]_13_[+2(2.23e-05)]_173_[+1(8.82e-08)]_119_[+1(9.37e-05)]_\ 51 20747 4.45e-07 3_[+2(1.11e-05)]_316_[+1(4.96e-05)]_\ 27_[+1(5.89e-09)]_92 21281 4.81e-06 25_[+2(1.02e-05)]_87_[+3(5.75e-05)]_\ 333_[+1(4.35e-07)]_2 21770 2.47e-04 19_[+2(1.57e-07)]_461 22302 3.43e-07 46_[+3(9.69e-06)]_168_\ [+2(2.61e-06)]_106_[+1(5.30e-07)]_127 22621 7.52e-05 233_[+2(3.93e-07)]_49_\ [+2(5.72e-05)]_124_[+1(9.63e-06)]_33 23144 1.19e-04 153_[+3(2.32e-05)]_141_\ [+2(2.40e-05)]_145_[+1(1.77e-05)]_8 23332 7.29e-05 225_[+3(9.52e-07)]_129_\ [+1(3.94e-06)]_113 23622 5.70e-06 169_[+2(5.01e-10)]_311 23667 6.93e-06 224_[+2(7.27e-06)]_16_\ [+3(5.84e-06)]_187_[+1(8.97e-06)]_20 23969 2.65e-03 260_[+3(1.40e-06)]_228 24216 1.14e-06 162_[+2(6.66e-06)]_265_\ [+1(2.99e-08)]_32 24345 4.74e-05 163_[+1(4.91e-08)]_280_\ [+3(3.92e-05)]_24 2452 3.09e-03 2_[+3(4.97e-05)]_390_[+2(5.09e-06)]_\ 76 24598 4.19e-05 408_[+1(1.71e-09)]_[+1(6.18e-05)]_\ 50 24790 2.77e-05 12_[+2(2.40e-05)]_22_[+3(1.54e-05)]_\ 78_[+1(4.97e-06)]_335 25142 1.03e-06 216_[+3(1.39e-05)]_10_\ [+2(7.71e-05)]_135_[+2(2.14e-09)]_87 25311 1.65e-04 120_[+3(2.17e-05)]_154_\ [+1(6.87e-05)]_163_[+1(9.32e-07)]_9 25906 5.49e-04 282_[+3(2.07e-06)]_45_\ [+2(2.57e-05)]_141 263785 1.41e-06 14_[+1(1.59e-06)]_223_\ [+3(8.71e-06)]_30_[+2(4.64e-06)]_180 264498 1.09e-05 176_[+2(1.20e-05)]_34_\ [+2(2.61e-06)]_213_[+1(1.02e-06)]_16 264548 9.48e-08 174_[+2(3.05e-07)]_57_\ [+1(7.86e-09)]_228 268352 7.59e-08 148_[+3(4.18e-07)]_185_\ [+2(4.44e-05)]_70_[+1(1.38e-07)]_44 268655 3.53e-04 384_[+2(1.53e-05)]_49_\ [+3(2.07e-06)]_35 268859 9.18e-03 165_[+2(2.88e-06)]_2_[+2(7.27e-05)]_\ 293 2897 7.95e-08 56_[+3(3.68e-06)]_385_\ [+1(2.34e-09)]_26 31007 3.02e-06 221_[+1(3.85e-08)]_182_\ [+2(1.20e-05)]_56 31932 7.53e-03 157_[+1(1.45e-05)]_322 32229 7.06e-04 16_[+2(9.39e-06)]_409_\ [+1(7.22e-06)]_34 38509 6.59e-08 [+3(1.26e-07)]_51_[+2(3.50e-06)]_\ 280_[+1(4.97e-06)]_116 4019 8.33e-07 158_[+1(2.03e-08)]_237_\ [+2(1.13e-06)]_64 4712 3.15e-01 500 5007 6.19e-07 15_[+2(1.80e-07)]_296_\ [+1(1.02e-06)]_148 5313 4.82e-04 394_[+3(1.54e-05)]_32_\ [+2(1.56e-06)]_42 7066 1.04e-04 300_[+1(4.97e-06)]_136_\ [+2(1.26e-06)]_23 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************