******************************************************************************** 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/453/453.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10006 1.0000 500 11441 1.0000 500 11915 1.0000 500 16440 1.0000 500 17841 1.0000 500 18089 1.0000 500 19136 1.0000 500 1914 1.0000 500 20223 1.0000 500 2050 1.0000 500 21869 1.0000 500 23310 1.0000 500 23626 1.0000 500 23825 1.0000 500 24130 1.0000 500 24142 1.0000 500 25014 1.0000 500 25030 1.0000 500 25048 1.0000 500 25492 1.0000 500 25658 1.0000 500 25831 1.0000 500 262025 1.0000 500 262907 1.0000 500 263108 1.0000 500 263184 1.0000 500 263198 1.0000 500 264208 1.0000 500 264371 1.0000 500 268044 1.0000 500 268845 1.0000 500 269257 1.0000 500 269858 1.0000 500 2912 1.0000 500 33182 1.0000 500 42283 1.0000 500 5809 1.0000 500 5854 1.0000 500 5944 1.0000 500 6284 1.0000 500 6591 1.0000 500 6628 1.0000 500 7376 1.0000 500 7404 1.0000 500 7982 1.0000 500 8092 1.0000 500 991 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/453/453.seqs.fa -oc motifs/453 -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= 47 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= 23500 N= 47 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.240 G 0.233 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.240 G 0.233 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 29 llr = 334 E-value = 9.3e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :47:175:7439775619638 pos.-specific C 732771191271332281261 probability G 1113223:12::::311:211 matrix T 121:::1:12:::::1::11: bits 2.1 1.9 1.7 * * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 * * ** ** (16.6 bits) 0.8 *** * **** ** * 0.6 * **** ** **** ** * 0.4 * ******* *********** 0.2 ********* *********** 0.0 --------------------- Multilevel CAACCAACAACAAAAACAACA consensus C GGGG CA CCGC GA sequence T T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25014 171 3.34e-10 ACTGCCTCTG CTACGAACAGCAAAAACAACA ATGGTATAGA 2050 458 4.22e-09 GAGAACAACA CTACCGACAACAACGACAAAA TCATTCAACA 263184 20 6.61e-09 CACCAAATAC CACCCAACAACAAAAACATAA AACACCAATA 11915 91 1.02e-08 TGACCGAGAC CAACCAACATGACAAACAACA TCCACCACTA 269858 163 1.18e-07 CCTCTTGACA CAACCAACACCAAAAAACAGA ATACAACACC 42283 7 1.87e-07 GCTGAT CAACCAGCCAAAAAGACACTA CTCAAAAAGC 991 146 4.96e-07 CAGCGTTAGG CAACGAGCTACAAAATCATCA GCTCACTTTC 263108 290 5.50e-07 GGGACGCATT CCTCCAGCACAACAACAAACA CAGACACGAG 5854 387 8.24e-07 ATCCTCATCA CTAGGCACATCAAAGCCAAAA TATTGCCCTG 23310 352 9.10e-07 AAACTGCGGA CGACGGACGGCAACAACAACA ACTCTCTTCA 19136 255 9.10e-07 CCATTCCCAC CCACCCACCGCAACCTCAACA ACAAGGCCGA 25831 414 1.34e-06 AGCTTCGTTT TCCCCATCATCACAACCACCA ATATACGGAA 25658 55 1.34e-06 TCATTATGTA ACAGCAGCAACACAGTCACCA AGCGTCTTTC 8092 446 2.34e-06 TCTCCGCCCG CACCCGGCTTCAAACACCAAA CTTATCCACT 7376 133 2.55e-06 GACAACAAGA CATCCAACATCAAAACGCACC GTTTGTCAAA 25492 407 3.33e-06 TTGTCCACCA CCACCACCAGCACACGCAAAC CTCAACCACG 20223 288 3.33e-06 AGTATCCAAC CAGCCAATCACAAAAACAATA GACAACTAGG 6591 347 3.96e-06 CCTTTCAAAA GCACAAGCATAAACGCCAACG TGTTTAATCT 10006 101 4.31e-06 TGAGAGCACA CAAGGAGCACAAATAAGAGCA AGCGGCATAG 262907 183 4.69e-06 CGAGACAACG GAGCCGCCACCAAACACAGAA CCATAGCCGT 18089 321 4.69e-06 CAACAACAAC TAACAGAAAACAAAGACAGCA AAAGCAACAA 268044 29 5.10e-06 TCGTCGTCTC GTAGCAACAACAGCAGCAGCA GCAGCTCATC 25030 427 5.10e-06 CGCCTCCGCC CCACCGTCAACAACGACCAGG ATAGTACTAA 33182 130 8.33e-06 CGTTGCCGTA GCTGCATCACAACACACACCA GCCAACCAAC 25048 387 8.33e-06 AAACCGTACC CAACCAGCCCAAAACTAAGCC TTCTGGTTGT 23626 341 8.33e-06 TACTGATCGC TTCGCAGCACAAACTACAAAA GGAAGGGATA 24142 279 9.01e-06 GAACCACCTT CTAGCAACGGCCACAACAGCG TCTAATCAAT 7982 435 1.14e-05 CGTGGTACTA CTCCAAGCAAAACAGCCACAG TGACAACTAA 5944 186 1.33e-05 AAAAGAAAAC TGAGGAACAACCCAAAGAACA TCTCGGACGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25014 3.3e-10 170_[+1]_309 2050 4.2e-09 457_[+1]_22 263184 6.6e-09 19_[+1]_460 11915 1e-08 90_[+1]_389 269858 1.2e-07 162_[+1]_317 42283 1.9e-07 6_[+1]_473 991 5e-07 145_[+1]_334 263108 5.5e-07 289_[+1]_190 5854 8.2e-07 386_[+1]_93 23310 9.1e-07 351_[+1]_128 19136 9.1e-07 254_[+1]_225 25831 1.3e-06 413_[+1]_66 25658 1.3e-06 54_[+1]_425 8092 2.3e-06 445_[+1]_34 7376 2.6e-06 132_[+1]_347 25492 3.3e-06 406_[+1]_73 20223 3.3e-06 287_[+1]_192 6591 4e-06 346_[+1]_133 10006 4.3e-06 100_[+1]_379 262907 4.7e-06 182_[+1]_297 18089 4.7e-06 320_[+1]_159 268044 5.1e-06 28_[+1]_451 25030 5.1e-06 426_[+1]_53 33182 8.3e-06 129_[+1]_350 25048 8.3e-06 386_[+1]_93 23626 8.3e-06 340_[+1]_139 24142 9e-06 278_[+1]_201 7982 1.1e-05 434_[+1]_45 5944 1.3e-05 185_[+1]_294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=29 25014 ( 171) CTACGAACAGCAAAAACAACA 1 2050 ( 458) CTACCGACAACAACGACAAAA 1 263184 ( 20) CACCCAACAACAAAAACATAA 1 11915 ( 91) CAACCAACATGACAAACAACA 1 269858 ( 163) CAACCAACACCAAAAAACAGA 1 42283 ( 7) CAACCAGCCAAAAAGACACTA 1 991 ( 146) CAACGAGCTACAAAATCATCA 1 263108 ( 290) CCTCCAGCACAACAACAAACA 1 5854 ( 387) CTAGGCACATCAAAGCCAAAA 1 23310 ( 352) CGACGGACGGCAACAACAACA 1 19136 ( 255) CCACCCACCGCAACCTCAACA 1 25831 ( 414) TCCCCATCATCACAACCACCA 1 25658 ( 55) ACAGCAGCAACACAGTCACCA 1 8092 ( 446) CACCCGGCTTCAAACACCAAA 1 7376 ( 133) CATCCAACATCAAAACGCACC 1 25492 ( 407) CCACCACCAGCACACGCAAAC 1 20223 ( 288) CAGCCAATCACAAAAACAATA 1 6591 ( 347) GCACAAGCATAAACGCCAACG 1 10006 ( 101) CAAGGAGCACAAATAAGAGCA 1 262907 ( 183) GAGCCGCCACCAAACACAGAA 1 18089 ( 321) TAACAGAAAACAAAGACAGCA 1 268044 ( 29) GTAGCAACAACAGCAGCAGCA 1 25030 ( 427) CCACCGTCAACAACGACCAGG 1 33182 ( 130) GCTGCATCACAACACACACCA 1 25048 ( 387) CAACCAGCCCAAAACTAAGCC 1 23626 ( 341) TTCGCAGCACAAACTACAAAA 1 24142 ( 279) CTAGCAACGGCCACAACAGCG 1 7982 ( 435) CTCCAAGCAAAACAGCCACAG 1 5944 ( 186) TGAGGAACAACCCAAAGAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 22560 bayes= 10.8519 E= 9.3e-011 -291 152 -76 -95 67 20 -176 -14 133 -48 -176 -136 -1150 159 24 -1150 -133 152 -17 -1150 148 -180 -17 -1150 89 -180 57 -136 -291 195 -1150 -295 148 -80 -176 -195 54 1 -43 -37 8 152 -275 -1150 184 -180 -1150 -1150 141 20 -275 -1150 141 20 -1150 -295 89 -22 24 -295 117 -22 -176 -95 -133 172 -117 -1150 173 -80 -1150 -1150 108 -48 -17 -195 8 129 -176 -195 154 -122 -76 -1150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 29 E= 9.3e-011 0.034483 0.689655 0.137931 0.137931 0.413793 0.275862 0.068966 0.241379 0.655172 0.172414 0.068966 0.103448 0.000000 0.724138 0.275862 0.000000 0.103448 0.689655 0.206897 0.000000 0.724138 0.068966 0.206897 0.000000 0.482759 0.068966 0.344828 0.103448 0.034483 0.931034 0.000000 0.034483 0.724138 0.137931 0.068966 0.068966 0.379310 0.241379 0.172414 0.206897 0.275862 0.689655 0.034483 0.000000 0.931034 0.068966 0.000000 0.000000 0.689655 0.275862 0.034483 0.000000 0.689655 0.275862 0.000000 0.034483 0.482759 0.206897 0.275862 0.034483 0.586207 0.206897 0.068966 0.137931 0.103448 0.793103 0.103448 0.000000 0.862069 0.137931 0.000000 0.000000 0.551724 0.172414 0.206897 0.068966 0.275862 0.586207 0.068966 0.068966 0.758621 0.103448 0.137931 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[ACT]A[CG][CG][AG][AG]CA[ACT][CA]A[AC][AC][AGC][AC]CA[AG][CA]A -------------------------------------------------------------------------------- Time 16.45 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 25 llr = 277 E-value = 4.1e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :134:8:::4264:63 pos.-specific C 1122:::2:4::::1: probability G 4832a2489:844a27 matrix T 6132::6:12::2:1: 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 TGAAGATGGAGAAGAG consensus G GC GGC CAGG GA sequence TG T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 42283 108 2.96e-08 TGGATGTTGA TGAGGAGGGCGAGGAG GTGGACAAGC 17841 8 3.75e-08 TGTGAAA TGAGGATGGAGGGGAG GGAAGTGTCA 20223 432 1.17e-07 CTCATGTGGA TGGAGGTGGCGGAGAG GACGCCGACG 263184 210 1.39e-07 TGGACGAGGA GGATGAGGGAGAGGAG GGTGGACGGA 25831 258 1.65e-07 AGGACCATGA TGTCGAGGGAGAGGAA AGTTGAGATC 263198 190 3.39e-07 GGAGGGCTCC TGTAGAGGGTGAGGGG GGAAGCATTG 264371 341 5.69e-07 GGGGCGTGAT GGTGGATGGTGATGAG ATGGTTCACC 1914 48 7.31e-07 GCATCTTGCT TGAAGATGTCGAAGAG TTTTGCAATT 24130 4 1.31e-06 TCT TGGAGATGGCGGAGCA GCCCAAAGCT 263108 52 2.46e-06 TGATGTATGT TGCAGATGACGAGGAG AACCGCTATG 25030 237 3.59e-06 CAGAAGCAGA GGAGGAGCGAGGAGGG GTGAGAGGTG 25658 342 3.94e-06 GTCTTGGAGT GGTAGGTGGTAGGGAG TAGGAAGCGG 25014 394 3.94e-06 GGTTTGATTG GAGGGATGGCGAAGGG TGGCATGTGG 264208 267 4.31e-06 GCAGTGACAA TGGTGGTGGAGGGGGA TGATCGGAGG 7404 48 4.71e-06 CATGATTGTG TGCTGAGGGTGATGGG GATGCTATTC 11441 220 5.14e-06 AATTGACGAC CGACGGTGGTGAAGAG AAAGTTGGCG 2050 141 7.77e-06 GTCAATGAAC GGCTGATCGAGATGAA GTATCGGATG 7982 40 9.09e-06 ATTGCTGTTG GGTCGAGGGCAGAGTG AGACCGCCAA 2912 119 9.09e-06 TTCTTACAGT GTGAGATGGAAATGAG AGTTGGTGCA 23626 378 9.09e-06 GATAGGCAGG CGTCGATCGAGGAGAA GCGAAGGCCT 268845 262 1.14e-05 AGCAGAGAGA GAGAGAGCGCGGGGAA GAAGAGAACT 33182 358 1.62e-05 GGGATAACGA TCACGATGGAGAAGCA TTGGAGATTG 25492 163 1.85e-05 TGATTCGTAC TTTAGATGGAAGTGAA CGAGGATTGT 11915 293 2.10e-05 GGCTCCCATT TGGAGGGGTCGAAGTG CTGTTGTTGT 269257 457 2.68e-05 ACCACTCCAG TCCCGAGCGCAAGGAG GGGGCTGTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42283 3e-08 107_[+2]_377 17841 3.8e-08 7_[+2]_477 20223 1.2e-07 431_[+2]_53 263184 1.4e-07 209_[+2]_275 25831 1.6e-07 257_[+2]_227 263198 3.4e-07 189_[+2]_295 264371 5.7e-07 340_[+2]_144 1914 7.3e-07 47_[+2]_437 24130 1.3e-06 3_[+2]_481 263108 2.5e-06 51_[+2]_433 25030 3.6e-06 236_[+2]_248 25658 3.9e-06 341_[+2]_143 25014 3.9e-06 393_[+2]_91 264208 4.3e-06 266_[+2]_218 7404 4.7e-06 47_[+2]_437 11441 5.1e-06 219_[+2]_265 2050 7.8e-06 140_[+2]_344 7982 9.1e-06 39_[+2]_445 2912 9.1e-06 118_[+2]_366 23626 9.1e-06 377_[+2]_107 268845 1.1e-05 261_[+2]_223 33182 1.6e-05 357_[+2]_127 25492 1.8e-05 162_[+2]_322 11915 2.1e-05 292_[+2]_192 269257 2.7e-05 456_[+2]_28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=25 42283 ( 108) TGAGGAGGGCGAGGAG 1 17841 ( 8) TGAGGATGGAGGGGAG 1 20223 ( 432) TGGAGGTGGCGGAGAG 1 263184 ( 210) GGATGAGGGAGAGGAG 1 25831 ( 258) TGTCGAGGGAGAGGAA 1 263198 ( 190) TGTAGAGGGTGAGGGG 1 264371 ( 341) GGTGGATGGTGATGAG 1 1914 ( 48) TGAAGATGTCGAAGAG 1 24130 ( 4) TGGAGATGGCGGAGCA 1 263108 ( 52) TGCAGATGACGAGGAG 1 25030 ( 237) GGAGGAGCGAGGAGGG 1 25658 ( 342) GGTAGGTGGTAGGGAG 1 25014 ( 394) GAGGGATGGCGAAGGG 1 264208 ( 267) TGGTGGTGGAGGGGGA 1 7404 ( 48) TGCTGAGGGTGATGGG 1 11441 ( 220) CGACGGTGGTGAAGAG 1 2050 ( 141) GGCTGATCGAGATGAA 1 7982 ( 40) GGTCGAGGGCAGAGTG 1 2912 ( 119) GTGAGATGGAAATGAG 1 23626 ( 378) CGTCGATCGAGGAGAA 1 268845 ( 262) GAGAGAGCGCGGGGAA 1 33182 ( 358) TCACGATGGAGAAGCA 1 25492 ( 163) TTTAGATGGAAGTGAA 1 11915 ( 293) TGGAGGGGTCGAAGTG 1 269257 ( 457) TCCCGAGCGCAAGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 22795 bayes= 10.9647 E= 4.1e-008 -1129 -159 63 107 -170 -159 171 -173 11 -59 26 7 62 0 -22 -74 -1129 -1129 210 -1129 162 -1129 -22 -1129 -1129 -1129 78 117 -1129 -26 178 -1129 -270 -1129 192 -173 62 73 -1129 -41 -38 -1129 178 -1129 121 -1129 78 -1129 62 -1129 78 -41 -1129 -1129 210 -1129 130 -159 -22 -173 30 -1129 154 -1129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 25 E= 4.1e-008 0.000000 0.080000 0.360000 0.560000 0.080000 0.080000 0.760000 0.080000 0.280000 0.160000 0.280000 0.280000 0.400000 0.240000 0.200000 0.160000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.200000 0.800000 0.000000 0.040000 0.000000 0.880000 0.080000 0.400000 0.400000 0.000000 0.200000 0.200000 0.000000 0.800000 0.000000 0.600000 0.000000 0.400000 0.000000 0.400000 0.000000 0.400000 0.200000 0.000000 0.000000 1.000000 0.000000 0.640000 0.080000 0.200000 0.080000 0.320000 0.000000 0.680000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG]G[AGT][ACG]G[AG][TG][GC]G[ACT][GA][AG][AGT]G[AG][GA] -------------------------------------------------------------------------------- Time 31.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 19 llr = 242 E-value = 1.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:1::2112:211:4::3:: pos.-specific C 223::::32:1:13::4::: probability G 6:3a:2923725654246:7 matrix T 183:a6:44364322831a3 bits 2.1 * 1.9 ** * * 1.7 ** * * 1.5 ** * * Relative 1.3 * ** * * * Entropy 1.1 * ** * * * ** (18.4 bits) 0.8 * ** * * * * *** 0.6 ** **** * ***** *** 0.4 ** **** *********** 0.2 ******** *********** 0.0 -------------------- Multilevel GTCGTTGTTGTGGGATCGTG consensus G G CGTGTTCGGGA T sequence T G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 20223 85 2.79e-08 GGATGCCGCT GTGGTGGCTGGTTGGTGGTG ATGGTACTTG 264371 319 4.30e-08 ATTTGTCGTA GTCGTAGTTTTGGGGGCGTG ATGGTGGATG 25030 7 7.32e-08 CACGTC GTTGTTGTCGAGGCATGGTT ACTGTATGGT 24142 36 8.31e-08 AGGGGGTACT GTTGTTGGTGTGCCATGGTG AAGCAGGATG 264208 424 1.20e-07 TGTATTGGTT GCGGTGGCGGTGGGAGGGTG TGAACACAAG 25048 410 1.91e-07 ACTAAGCCTT CTGGTTGTAGTTGGTTCATG TTCACTTCGT 10006 393 2.13e-07 TGTGTGTTCA GTGGTTGCGTTTTGATTATT AGTTTGGGGC 7376 278 2.38e-07 AAGGAGCAGT GCAGTTGTGGGTGGGTGGTG TGTTAGGCGG 263184 256 2.65e-07 GGTTCGAACC ATTGTTGTTTTGTTGTTGTG CCGGTGGAGG 269257 67 3.62e-07 TGTATGTCTC GTCGTGGGAGTTGTGTTGTT TGCATCGCTA 11915 311 3.62e-07 TCGAAGTGCT GTTGTTGTGGAGGTGTCTTG TGGTGCGCCG 24130 56 4.86e-07 GTTTGCCTTC GCGGTTGCTGCGGGTTCGTG TGCCTACGTC 2050 294 1.09e-06 TCGCGTCTCA ATCGTTGACTTGGCATCATG CAGTTTCGTG 11441 376 1.29e-06 TGACAAGGTG ATCGTTGTCGTTGCAGCATT TAACGACAGG 7982 3 1.51e-06 GT GTTGTGGAGGGAGGATCATG TTGAGTTATT 269858 263 1.51e-06 AATGATTCAT GTCGTAGGTGAGAGGTGATG TTGATGTCTG 5809 306 4.34e-06 ACGAACCGGA CTCGTAGCTTTGTTTTGGTT TTTCTTTCAG 268845 195 4.91e-06 CGCTCGGGGG CTGGTTGGGTGTTCGGTGTT GGGGTGCGCT 263108 146 5.21e-06 AAACTATTCT TTTGTTATAGTTTGATTGTG AAGCTAATGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20223 2.8e-08 84_[+3]_396 264371 4.3e-08 318_[+3]_162 25030 7.3e-08 6_[+3]_474 24142 8.3e-08 35_[+3]_445 264208 1.2e-07 423_[+3]_57 25048 1.9e-07 409_[+3]_71 10006 2.1e-07 392_[+3]_88 7376 2.4e-07 277_[+3]_203 263184 2.6e-07 255_[+3]_225 269257 3.6e-07 66_[+3]_414 11915 3.6e-07 310_[+3]_170 24130 4.9e-07 55_[+3]_425 2050 1.1e-06 293_[+3]_187 11441 1.3e-06 375_[+3]_105 7982 1.5e-06 2_[+3]_478 269858 1.5e-06 262_[+3]_218 5809 4.3e-06 305_[+3]_175 268845 4.9e-06 194_[+3]_286 263108 5.2e-06 145_[+3]_335 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=19 20223 ( 85) GTGGTGGCTGGTTGGTGGTG 1 264371 ( 319) GTCGTAGTTTTGGGGGCGTG 1 25030 ( 7) GTTGTTGTCGAGGCATGGTT 1 24142 ( 36) GTTGTTGGTGTGCCATGGTG 1 264208 ( 424) GCGGTGGCGGTGGGAGGGTG 1 25048 ( 410) CTGGTTGTAGTTGGTTCATG 1 10006 ( 393) GTGGTTGCGTTTTGATTATT 1 7376 ( 278) GCAGTTGTGGGTGGGTGGTG 1 263184 ( 256) ATTGTTGTTTTGTTGTTGTG 1 269257 ( 67) GTCGTGGGAGTTGTGTTGTT 1 11915 ( 311) GTTGTTGTGGAGGTGTCTTG 1 24130 ( 56) GCGGTTGCTGCGGGTTCGTG 1 2050 ( 294) ATCGTTGACTTGGCATCATG 1 11441 ( 376) ATCGTTGTCGTTGCAGCATT 1 7982 ( 3) GTTGTGGAGGGAGGATCATG 1 269858 ( 263) GTCGTAGGTGAGAGGTGATG 1 5809 ( 306) CTCGTAGCTTTGTTTTGGTT 1 268845 ( 195) CTGGTTGGGTGTTCGGTGTT 1 263108 ( 146) TTTGTTATAGTTTGATTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 22607 bayes= 11.6567 E= 1.6e-004 -72 -61 144 -234 -1089 -61 -1089 166 -230 39 44 24 -1089 -1089 210 -1089 -1089 -1089 -1089 191 -72 -1089 -15 124 -230 -1089 202 -1089 -130 13 -15 66 -72 -61 44 47 -1089 -1089 155 24 -72 -219 -15 112 -230 -1089 118 66 -230 -219 131 24 -1089 13 118 -34 69 -1089 85 -75 -1089 -1089 -15 157 -1089 62 66 -2 28 -1089 144 -234 -1089 -1089 -1089 191 -1089 -1089 155 24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 19 E= 1.6e-004 0.157895 0.157895 0.631579 0.052632 0.000000 0.157895 0.000000 0.842105 0.052632 0.315789 0.315789 0.315789 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.157895 0.000000 0.210526 0.631579 0.052632 0.000000 0.947368 0.000000 0.105263 0.263158 0.210526 0.421053 0.157895 0.157895 0.315789 0.368421 0.000000 0.000000 0.684211 0.315789 0.157895 0.052632 0.210526 0.578947 0.052632 0.000000 0.526316 0.421053 0.052632 0.052632 0.578947 0.315789 0.000000 0.263158 0.526316 0.210526 0.421053 0.000000 0.421053 0.157895 0.000000 0.000000 0.210526 0.789474 0.000000 0.368421 0.368421 0.263158 0.315789 0.000000 0.631579 0.052632 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.684211 0.315789 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GT[CGT]GT[TG]G[TCG][TG][GT][TG][GT][GT][GCT][AG][TG][CGT][GA]T[GT] -------------------------------------------------------------------------------- Time 46.99 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10006 2.72e-06 100_[+1(4.31e-06)]_271_\ [+3(2.13e-07)]_88 11441 6.80e-05 219_[+2(5.14e-06)]_140_\ [+3(1.29e-06)]_105 11915 3.04e-09 16_[+3(5.26e-05)]_54_[+1(1.02e-08)]_\ 92_[+1(3.60e-05)]_68_[+2(2.10e-05)]_2_[+3(3.62e-07)]_15_[+3(4.83e-05)]_135 16440 4.58e-02 174_[+3(8.65e-05)]_306 17841 1.44e-04 7_[+2(3.75e-08)]_477 18089 4.01e-02 320_[+1(4.69e-06)]_159 19136 1.47e-02 222_[+1(3.14e-05)]_11_\ [+1(9.10e-07)]_225 1914 5.73e-03 47_[+2(7.31e-07)]_437 20223 4.93e-10 84_[+3(2.79e-08)]_183_\ [+1(3.33e-06)]_123_[+2(1.17e-07)]_53 2050 1.49e-09 140_[+2(7.77e-06)]_137_\ [+3(1.09e-06)]_144_[+1(4.22e-09)]_22 21869 3.80e-01 500 23310 1.49e-02 351_[+1(9.10e-07)]_128 23626 1.14e-03 340_[+1(8.33e-06)]_16_\ [+2(9.09e-06)]_107 23825 5.89e-01 500 24130 1.59e-05 3_[+2(1.31e-06)]_36_[+3(4.86e-07)]_\ 425 24142 1.57e-06 35_[+3(8.31e-08)]_223_\ [+1(9.01e-06)]_21_[+2(9.99e-05)]_164 25014 2.81e-08 170_[+1(3.34e-10)]_57_\ [+1(3.85e-05)]_124_[+2(3.94e-06)]_91 25030 4.19e-08 6_[+3(7.32e-08)]_5_[+3(9.20e-05)]_\ 185_[+2(3.59e-06)]_174_[+1(5.10e-06)]_53 25048 4.57e-05 386_[+1(8.33e-06)]_2_[+3(1.91e-07)]_\ 71 25492 2.30e-04 162_[+2(1.85e-05)]_228_\ [+1(3.33e-06)]_73 25658 6.77e-05 54_[+1(1.34e-06)]_266_\ [+2(3.94e-06)]_143 25831 4.53e-06 257_[+2(1.65e-07)]_140_\ [+1(1.34e-06)]_66 262025 1.47e-01 41_[+3(3.82e-05)]_439 262907 4.90e-02 182_[+1(4.69e-06)]_297 263108 1.90e-07 51_[+2(2.46e-06)]_78_[+3(5.21e-06)]_\ 124_[+1(5.50e-07)]_190 263184 1.42e-11 19_[+1(6.61e-09)]_169_\ [+2(1.39e-07)]_30_[+3(2.65e-07)]_225 263198 4.27e-03 189_[+2(3.39e-07)]_295 264208 1.74e-05 201_[+3(7.90e-05)]_45_\ [+2(4.31e-06)]_105_[+3(5.12e-05)]_16_[+3(1.20e-07)]_57 264371 2.99e-07 151_[+3(8.14e-05)]_147_\ [+3(4.30e-08)]_2_[+2(5.69e-07)]_144 268044 3.69e-02 28_[+1(5.10e-06)]_451 268845 2.80e-04 194_[+3(4.91e-06)]_47_\ [+2(1.14e-05)]_223 269257 7.94e-05 66_[+3(3.62e-07)]_370_\ [+2(2.68e-05)]_28 269858 3.61e-06 162_[+1(1.18e-07)]_79_\ [+3(1.51e-06)]_218 2912 6.01e-02 118_[+2(9.09e-06)]_366 33182 2.95e-04 129_[+1(8.33e-06)]_207_\ [+2(1.62e-05)]_127 42283 2.07e-07 6_[+1(1.87e-07)]_80_[+2(2.96e-08)]_\ 40_[+2(6.59e-05)]_321 5809 4.88e-02 305_[+3(4.34e-06)]_175 5854 2.27e-03 386_[+1(8.24e-07)]_93 5944 2.22e-02 185_[+1(1.33e-05)]_294 6284 2.05e-01 500 6591 4.08e-02 346_[+1(3.96e-06)]_133 6628 4.11e-01 500 7376 8.24e-06 132_[+1(2.55e-06)]_124_\ [+3(2.38e-07)]_203 7404 2.75e-03 47_[+2(4.71e-06)]_437 7982 3.11e-06 2_[+3(1.51e-06)]_17_[+2(9.09e-06)]_\ 379_[+1(1.14e-05)]_45 8092 4.39e-03 445_[+1(2.34e-06)]_34 991 5.66e-03 145_[+1(4.96e-07)]_334 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************