******************************************************************************** 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/270/270.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10080 1.0000 500 11585 1.0000 500 1563 1.0000 500 16679 1.0000 500 18090 1.0000 500 21137 1.0000 500 21552 1.0000 500 2253 1.0000 500 22809 1.0000 500 23954 1.0000 500 24106 1.0000 500 25620 1.0000 500 25766 1.0000 500 261205 1.0000 500 261341 1.0000 500 261998 1.0000 500 262266 1.0000 500 263961 1.0000 500 264002 1.0000 500 264184 1.0000 500 264699 1.0000 500 26743 1.0000 500 268493 1.0000 500 2999 1.0000 500 32154 1.0000 500 36246 1.0000 500 37486 1.0000 500 4947 1.0000 500 6519 1.0000 500 6522 1.0000 500 7182 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/270/270.seqs.fa -oc motifs/270 -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= 31 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= 15500 N= 31 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.238 G 0.227 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.238 G 0.227 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 17 llr = 238 E-value = 6.9e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 14:2:::2:612::1::2:: pos.-specific C 116:21111:::1112:11: probability G 86:41961918286:6a249 matrix T 1:457:37:3162382:461 bits 2.1 * 1.9 * 1.7 * * * * 1.5 * * * * Relative 1.3 * * * * * Entropy 1.1 * * * * * * * (20.2 bits) 0.9 *** *** * * * * * ** 0.6 *** ************* ** 0.4 ***************** ** 0.2 ******************** 0.0 -------------------- Multilevel GGCTTGGTGAGTGGTGGTTG consensus ATGC T T G T C AG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 6519 112 8.81e-10 GGAGGGGGTC GACATGTTGAGTGGTGGTGG GCGTGGAGAG 18090 182 7.29e-09 TCCTTTTTCG GGCATGGTGAGAGTTTGTTG CTTGAAGTTT 25766 347 1.04e-08 GTGAGTGATG GGTGCGGAGAGTGTTGGGGG ATGTGTCCAA 263961 347 1.63e-08 AATTATCGGT GGCGCGGTGAGTCGTTGTTG ATTATCTTGC 21137 143 2.03e-08 GTTGTCAGAT GATTTGGTGTGAGTTCGGTG AGGTGAGTCA 264699 396 3.82e-08 AGTGCAGTTT GACATGTTGAGGTTTGGTTG CAGTTGAGCC 10080 49 6.28e-08 GACCTCAGGT GGCTTGTTGAGTTGTCGTTT GGTGAGTGGT 21552 218 7.61e-08 AGCATTTGAT GGCTTGTTGTGGTGAGGATG AGGAGGAGGA 2999 254 9.19e-08 TTGTATCAAG GCTTTGGTGTATGGTGGTGG CCTCTTGCAG 261998 412 1.89e-07 CACAATCTTT GATTCGGTGAGTGCTTGTCG TGCGAATTGC 26743 342 2.89e-07 TGCCGAAAAT TGTGTGGAGAGTGGAGGCTG TGGAAAATCG 262266 189 2.89e-07 AAGGACAACG CGCTTCGTGATTGGTGGAGG AAAAACGCTT 1563 290 5.47e-07 TAACATCGAG GGCGGCGGGAGGGGTGGATG GATTGGCTAG 23954 86 5.91e-07 AACTGAGAGT GGTTCGGAGGGGGGCGGGGG ATACAATTTA 6522 214 9.23e-07 ACGTGCAATT AGCGTGTTCATTGTTGGGTG TTTGGGCTGT 268493 344 1.14e-06 AGCGTACGTA GATTTGCTGTGAGCTCGCTG TTTTCAAAGC 2253 451 1.61e-06 CAAGAAACAA AACGTGGCGTGTGGCCGAGG AGAGGGGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6519 8.8e-10 111_[+1]_369 18090 7.3e-09 181_[+1]_299 25766 1e-08 346_[+1]_134 263961 1.6e-08 346_[+1]_134 21137 2e-08 142_[+1]_338 264699 3.8e-08 395_[+1]_85 10080 6.3e-08 48_[+1]_432 21552 7.6e-08 217_[+1]_263 2999 9.2e-08 253_[+1]_227 261998 1.9e-07 411_[+1]_69 26743 2.9e-07 341_[+1]_139 262266 2.9e-07 188_[+1]_292 1563 5.5e-07 289_[+1]_191 23954 5.9e-07 85_[+1]_395 6522 9.2e-07 213_[+1]_267 268493 1.1e-06 343_[+1]_137 2253 1.6e-06 450_[+1]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=17 6519 ( 112) GACATGTTGAGTGGTGGTGG 1 18090 ( 182) GGCATGGTGAGAGTTTGTTG 1 25766 ( 347) GGTGCGGAGAGTGTTGGGGG 1 263961 ( 347) GGCGCGGTGAGTCGTTGTTG 1 21137 ( 143) GATTTGGTGTGAGTTCGGTG 1 264699 ( 396) GACATGTTGAGGTTTGGTTG 1 10080 ( 49) GGCTTGTTGAGTTGTCGTTT 1 21552 ( 218) GGCTTGTTGTGGTGAGGATG 1 2999 ( 254) GCTTTGGTGTATGGTGGTGG 1 261998 ( 412) GATTCGGTGAGTGCTTGTCG 1 26743 ( 342) TGTGTGGAGAGTGGAGGCTG 1 262266 ( 189) CGCTTCGTGATTGGTGGAGG 1 1563 ( 290) GGCGGCGGGAGGGGTGGATG 1 23954 ( 86) GGTTCGGAGGGGGGCGGGGG 1 6522 ( 214) AGCGTGTTCATTGTTGGGTG 1 268493 ( 344) GATTTGCTGTGAGCTCGCTG 1 2253 ( 451) AACGTGGCGTGTGGCCGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 14911 bayes= 10.5704 E= 6.9e-012 -123 -202 175 -214 36 -202 138 -1073 -1073 130 -1073 67 -64 -1073 64 86 -1073 -2 -194 144 -1073 -102 196 -1073 -1073 -202 151 18 -64 -202 -194 144 -1073 -202 205 -1073 123 -1073 -194 18 -223 -1073 186 -114 -64 -1073 5 118 -1073 -202 175 -55 -1073 -102 138 18 -123 -102 -1073 156 -1073 -2 138 -55 -1073 -1073 214 -1073 -23 -102 5 67 -1073 -202 64 118 -1073 -1073 205 -214 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 17 E= 6.9e-012 0.117647 0.058824 0.764706 0.058824 0.352941 0.058824 0.588235 0.000000 0.000000 0.588235 0.000000 0.411765 0.176471 0.000000 0.352941 0.470588 0.000000 0.235294 0.058824 0.705882 0.000000 0.117647 0.882353 0.000000 0.000000 0.058824 0.647059 0.294118 0.176471 0.058824 0.058824 0.705882 0.000000 0.058824 0.941176 0.000000 0.647059 0.000000 0.058824 0.294118 0.058824 0.000000 0.823529 0.117647 0.176471 0.000000 0.235294 0.588235 0.000000 0.058824 0.764706 0.176471 0.000000 0.117647 0.588235 0.294118 0.117647 0.117647 0.000000 0.764706 0.000000 0.235294 0.588235 0.176471 0.000000 0.000000 1.000000 0.000000 0.235294 0.117647 0.235294 0.411765 0.000000 0.058824 0.352941 0.588235 0.000000 0.000000 0.941176 0.058824 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[GA][CT][TG][TC]G[GT]TG[AT]G[TG]G[GT]T[GC]G[TAG][TG]G -------------------------------------------------------------------------------- Time 7.97 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 31 llr = 306 E-value = 2.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 31614134:13:452532782 pos.-specific C 34174834761a457337327 probability G :41::11::1::1:::1:1:: matrix T 41223:32336:2::231::1 bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 * Entropy 1.1 * * * ** * (14.3 bits) 0.9 * * * * ** *** 0.6 * * **** ** **** 0.4 * **** ***** ** **** 0.2 ****** ********* **** 0.0 --------------------- Multilevel TCACACAACCTCACCATCAAC consensus AG TC CCTTA CAACAACC sequence C T TT TC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 261341 252 5.08e-08 TCCTTCTCTC CCACTCTCTCACAACATCAAC GTCGATAGCC 2253 415 7.08e-08 TTTGGCTGTG TAACACAACCACAACCACAAC GGCTCCAAGA 32154 479 1.54e-07 CTTCCACCAC AGACCCAACCCCCCCCTAAAC C 24106 60 1.54e-07 CTGAATCATT CCATACTTCTTCACCCTCAAC TTATTTTTCA 7182 80 2.76e-07 CTTCGCGTCT CCCCCCCCCCTCGCCTCCAAC TCAACTCCCA 264699 63 9.12e-07 GCGCTACACG CGACACCACCACCACCAAAAA CTACCGTCAC 21137 358 1.48e-06 TTTCCTCCCT CGTCACTTCCTCCCCTCCGAC GTCGGTCGCC 26743 68 1.67e-06 ATGAGGGGAG AGAATCTACCACCCCACCACC GCCGTCGACA 37486 146 1.87e-06 GTCCTTCGCT TCACTCATTCACACCCACCAA CATTCTTTAT 16679 335 1.87e-06 CACCTAAAAT TGACCCTCCTTCCAACCAACC ACTTTCCAAA 36246 467 4.06e-06 ATTTTAAATC TCCCACGCCGTCCCAACCAAC CGTCACACCA 261205 315 4.06e-06 CACACCGCCT TGACCACACAACAACAACAAC TATCACGAGG 25620 251 4.06e-06 CGCGCGCGGT TCACACCCTCCCCACTTCACA AGAAAAGCTC 21552 12 5.55e-06 TGCTCAGCGA AAACTCCCCCTCTCCATCGAA GATCAAACCT 264184 422 6.14e-06 GTTACAACTC TGACACACTCTCTCCGTACAC AGTCGATGCA 268493 479 9.10e-06 ACCTTCCGCT TGGCCAACCCACACCACCAAA C 2999 73 1.00e-05 CCACTCCCCG ACTTTCTCCGTCCACCACCAC TGCCGCGAGA 263961 451 1.21e-05 CGTTCATCTC TGATACAACTTCAAACACACA AACCGCACTC 6519 399 1.45e-05 TATCTTTTCT TCACACACGTTCCCCTTCCAT TCCTTCCCCT 262266 457 1.45e-05 CTAACCAACC ACCACCCTCTTCTACCACAAC TCAACGACGA 18090 39 1.74e-05 ATCGTCACAA CCACTCGATTTCAAAACACAC CGCCACTACG 261998 75 1.90e-05 GCAATACTGC ATACTCACCTTCTCCTGCAAT GTTTCAACTC 4947 477 2.25e-05 GCTCCACAAC CAGCCACTCTTCAACATCAAC ACC 1563 480 2.67e-05 TCATTCAAAC CCCTCCCCTCTCCCCAAGACC 10080 466 3.15e-05 CGTAATTTGT TGATTCTACAACACATACACC GTCATTGACA 6522 305 4.01e-05 TGGCTTGGTT ACTCCCAACCTCTCGTTTAAC AGCATATTGT 11585 258 4.01e-05 ACATTCCTCT AAACAGTACCTCCACAGCCAT TCGTCTACAG 23954 479 8.44e-05 GAACGGACAG ACTTCGCTCCTCGACACACAC C 25766 389 1.11e-04 GTGGACAAAT TTTCCCAATTCCACCATTACC TACTATTTTC 22809 305 1.19e-04 CTTCACAGGG TGACACGTTCTTCAAAGCCAC CCAAAGCAAA 264002 359 2.36e-04 CGATCAACAC ATTTTGCATCACACAACAAAC AAAACAGTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261341 5.1e-08 251_[+2]_228 2253 7.1e-08 414_[+2]_65 32154 1.5e-07 478_[+2]_1 24106 1.5e-07 59_[+2]_420 7182 2.8e-07 79_[+2]_400 264699 9.1e-07 62_[+2]_417 21137 1.5e-06 357_[+2]_122 26743 1.7e-06 67_[+2]_412 37486 1.9e-06 145_[+2]_334 16679 1.9e-06 334_[+2]_145 36246 4.1e-06 466_[+2]_13 261205 4.1e-06 314_[+2]_165 25620 4.1e-06 250_[+2]_229 21552 5.5e-06 11_[+2]_468 264184 6.1e-06 421_[+2]_58 268493 9.1e-06 478_[+2]_1 2999 1e-05 72_[+2]_407 263961 1.2e-05 450_[+2]_29 6519 1.5e-05 398_[+2]_81 262266 1.5e-05 456_[+2]_23 18090 1.7e-05 38_[+2]_441 261998 1.9e-05 74_[+2]_405 4947 2.3e-05 476_[+2]_3 1563 2.7e-05 479_[+2] 10080 3.1e-05 465_[+2]_14 6522 4e-05 304_[+2]_175 11585 4e-05 257_[+2]_222 23954 8.4e-05 478_[+2]_1 25766 0.00011 388_[+2]_91 22809 0.00012 304_[+2]_175 264002 0.00024 358_[+2]_121 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=31 261341 ( 252) CCACTCTCTCACAACATCAAC 1 2253 ( 415) TAACACAACCACAACCACAAC 1 32154 ( 479) AGACCCAACCCCCCCCTAAAC 1 24106 ( 60) CCATACTTCTTCACCCTCAAC 1 7182 ( 80) CCCCCCCCCCTCGCCTCCAAC 1 264699 ( 63) CGACACCACCACCACCAAAAA 1 21137 ( 358) CGTCACTTCCTCCCCTCCGAC 1 26743 ( 68) AGAATCTACCACCCCACCACC 1 37486 ( 146) TCACTCATTCACACCCACCAA 1 16679 ( 335) TGACCCTCCTTCCAACCAACC 1 36246 ( 467) TCCCACGCCGTCCCAACCAAC 1 261205 ( 315) TGACCACACAACAACAACAAC 1 25620 ( 251) TCACACCCTCCCCACTTCACA 1 21552 ( 12) AAACTCCCCCTCTCCATCGAA 1 264184 ( 422) TGACACACTCTCTCCGTACAC 1 268493 ( 479) TGGCCAACCCACACCACCAAA 1 2999 ( 73) ACTTTCTCCGTCCACCACCAC 1 263961 ( 451) TGATACAACTTCAAACACACA 1 6519 ( 399) TCACACACGTTCCCCTTCCAT 1 262266 ( 457) ACCACCCTCTTCTACCACAAC 1 18090 ( 39) CCACTCGATTTCAAAACACAC 1 261998 ( 75) ATACTCACCTTCTCCTGCAAT 1 4947 ( 477) CAGCCACTCTTCAACATCAAC 1 1563 ( 480) CCCTCCCCTCTCCCCAAGACC 1 10080 ( 466) TGATTCTACAACACATACACC 1 6522 ( 305) ACTCCCAACCTCTCGTTTAAC 1 11585 ( 258) AAACAGTACCTCCACAGCCAT 1 23954 ( 479) ACTTCGCTCCTCGACACACAC 1 25766 ( 389) TTTCCCAATTCCACCATTACC 1 22809 ( 305) TGACACGTTCTTCAAAGCCAC 1 264002 ( 359) ATTTTGCATCACACAACAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 8.90388 E= 2.6e-005 23 11 -1160 69 -110 82 65 -142 115 -88 -181 -42 -209 157 -1160 -20 36 57 -1160 16 -151 176 -123 -1160 23 44 -123 -1 49 70 -1160 -20 -1160 151 -281 16 -209 128 -181 16 7 -130 -1160 124 -1160 202 -1160 -300 49 70 -181 -68 71 120 -1160 -1160 -29 164 -281 -1160 71 28 -281 -20 7 28 -123 32 -29 151 -281 -201 130 11 -181 -1160 149 -8 -1160 -1160 -51 157 -1160 -142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 31 E= 2.6e-005 0.322581 0.258065 0.000000 0.419355 0.129032 0.419355 0.354839 0.096774 0.612903 0.129032 0.064516 0.193548 0.064516 0.709677 0.000000 0.225806 0.354839 0.354839 0.000000 0.290323 0.096774 0.806452 0.096774 0.000000 0.322581 0.322581 0.096774 0.258065 0.387097 0.387097 0.000000 0.225806 0.000000 0.677419 0.032258 0.290323 0.064516 0.580645 0.064516 0.290323 0.290323 0.096774 0.000000 0.612903 0.000000 0.967742 0.000000 0.032258 0.387097 0.387097 0.064516 0.161290 0.451613 0.548387 0.000000 0.000000 0.225806 0.741935 0.032258 0.000000 0.451613 0.290323 0.032258 0.225806 0.290323 0.290323 0.096774 0.322581 0.225806 0.677419 0.032258 0.064516 0.677419 0.258065 0.064516 0.000000 0.774194 0.225806 0.000000 0.000000 0.193548 0.709677 0.000000 0.096774 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TAC][CG]A[CT][ACT]C[ACT][ACT][CT][CT][TA]C[AC][CA][CA][ACT][TAC][CA][AC][AC]C -------------------------------------------------------------------------------- Time 16.63 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 31 llr = 277 E-value = 3.6e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :39:6:252:44233: pos.-specific C 2::::2:2::::2222 probability G 871747733a346436 matrix T :::211::5:32:122 bits 2.1 1.9 * 1.7 * 1.5 * * * Relative 1.3 * * * Entropy 1.1 **** * * (12.9 bits) 0.9 **** ** * 0.6 ******* * * * 0.4 ********** ** * 0.2 ************** * 0.0 ---------------- Multilevel GGAGAGGATGAAGGAG consensus A TG AGG GGAAG sequence CA TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 6519 136 1.68e-07 TGGTGGGCGT GGAGAGGAGGGAGGGT AGGAACGGAA 1563 325 2.12e-07 GCTAGTGTGA GGAGAGGAGGAGAAGG AGACAAAAGG 25766 177 4.50e-07 GATTGTCGGT GGAGACGATGGTGGAG AGATGGTAGA 23954 33 1.40e-06 TGATTGATAA GGATGGGGTGAGGACG CTTAGTTATG 18090 435 2.18e-06 ACTCCGACAG GGAGACGATGAAAAAG ATCTCCACAA 11585 136 2.18e-06 TGGACGAGGA GAAGGGGAGGTGGGGC CGAATGTCAT 32154 323 2.51e-06 AATCTCTGGG GGAGAGAGAGTTGGGG ACCAAGTGTA 264699 248 3.76e-06 AAGTGTGAGC GGAGGGAGTGTGGTGG CTGGTTGGTG 4947 271 4.87e-06 GATAGCCTCA GAAGAGACTGGAGGTG TTGTCGGAGG 268493 89 5.53e-06 TACTGTTTGG CAAGAGGATGAGGATG CAGATGGAGG 264002 209 7.94e-06 GAATTCAAAT GGAGATGCTGATGCAG ATGAATACCC 6522 124 1.55e-05 ATCACTTCTT GGAGAGGATGCACCCG CCGACGTCGA 37486 93 1.91e-05 TACTACTGGA GGAGACGGGGGAAAGC AATATTGAAG 264184 76 1.91e-05 TCGCTGCAGA CGAGAGGCGGAGGCAC TGCTGACTCC 2999 305 2.84e-05 ACAGGAAAGG GAAGGCGGTGAAAACG TTGGTGTTGT 21552 240 2.84e-05 TGAGGATGAG GAGGAGGATGAGGACT GACTCAAAAA 10080 1 2.84e-05 . GGATAGGCAGGAATAG TGTACAGTAC 21137 99 3.43e-05 TTGGGATGAT GAATGGAGTGTAGGTG CAGTAGAGGC 261998 298 4.92e-05 TACTGTATTT GAAGTGGAGGATAAAG GCCGTACCTT 261341 11 4.92e-05 CGAACACATA CGAGGGGGGGGGGCTT AAATTCAGCG 16679 84 5.37e-05 TGAATGTCAG GGAAAGGAAGAGGGCT ACAGCGAGAG 22809 100 5.84e-05 TATAGCACCA GGATGGGCTGGAGAAA GCTAGGTCGT 25620 473 6.36e-05 CACGTCGTGC GGAGATACGGGTCGAG TGGAACAATA 263961 321 7.49e-05 GACAGAATTT GGGGGTGAAGGAGCCG AATTATCGGT 36246 185 8.11e-05 GCTGCTCCTT GCAGGGGAAGAACGGC CGCCAGTTGC 26743 413 8.11e-05 AATGTAACTT CAATAGAAAGTAGGGG ATAATATTTG 2253 476 8.11e-05 CGAGGAGAGG GGAGAGAAAGTTCTGC CACAACACA 7182 6 1.19e-04 GCTGT GGGTGCGAGGGGCGAG GAGCAAAGTC 261205 57 1.19e-04 AAGGATAGTT GGATTGGGTGTACGAT GCAACAATGT 24106 112 2.08e-04 CGCGCGTCTT GGAGATGGTAATGTGG TTGATGAATT 262266 235 1.13e-03 CAGATTTGAA CAAGGGTCTGTGAATC ATCATTCCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6519 1.7e-07 135_[+3]_349 1563 2.1e-07 324_[+3]_160 25766 4.5e-07 176_[+3]_308 23954 1.4e-06 32_[+3]_452 18090 2.2e-06 434_[+3]_50 11585 2.2e-06 135_[+3]_349 32154 2.5e-06 322_[+3]_162 264699 3.8e-06 247_[+3]_237 4947 4.9e-06 270_[+3]_214 268493 5.5e-06 88_[+3]_396 264002 7.9e-06 208_[+3]_276 6522 1.6e-05 123_[+3]_361 37486 1.9e-05 92_[+3]_392 264184 1.9e-05 75_[+3]_409 2999 2.8e-05 304_[+3]_180 21552 2.8e-05 239_[+3]_245 10080 2.8e-05 [+3]_484 21137 3.4e-05 98_[+3]_386 261998 4.9e-05 297_[+3]_187 261341 4.9e-05 10_[+3]_474 16679 5.4e-05 83_[+3]_401 22809 5.8e-05 99_[+3]_385 25620 6.4e-05 472_[+3]_12 263961 7.5e-05 320_[+3]_164 36246 8.1e-05 184_[+3]_300 26743 8.1e-05 412_[+3]_72 2253 8.1e-05 475_[+3]_9 7182 0.00012 5_[+3]_479 261205 0.00012 56_[+3]_428 24106 0.00021 111_[+3]_373 262266 0.0011 234_[+3]_250 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=31 6519 ( 136) GGAGAGGAGGGAGGGT 1 1563 ( 325) GGAGAGGAGGAGAAGG 1 25766 ( 177) GGAGACGATGGTGGAG 1 23954 ( 33) GGATGGGGTGAGGACG 1 18090 ( 435) GGAGACGATGAAAAAG 1 11585 ( 136) GAAGGGGAGGTGGGGC 1 32154 ( 323) GGAGAGAGAGTTGGGG 1 264699 ( 248) GGAGGGAGTGTGGTGG 1 4947 ( 271) GAAGAGACTGGAGGTG 1 268493 ( 89) CAAGAGGATGAGGATG 1 264002 ( 209) GGAGATGCTGATGCAG 1 6522 ( 124) GGAGAGGATGCACCCG 1 37486 ( 93) GGAGACGGGGGAAAGC 1 264184 ( 76) CGAGAGGCGGAGGCAC 1 2999 ( 305) GAAGGCGGTGAAAACG 1 21552 ( 240) GAGGAGGATGAGGACT 1 10080 ( 1) GGATAGGCAGGAATAG 1 21137 ( 99) GAATGGAGTGTAGGTG 1 261998 ( 298) GAAGTGGAGGATAAAG 1 261341 ( 11) CGAGGGGGGGGGGCTT 1 16679 ( 84) GGAAAGGAAGAGGGCT 1 22809 ( 100) GGATGGGCTGGAGAAA 1 25620 ( 473) GGAGATACGGGTCGAG 1 263961 ( 321) GGGGGTGAAGGAGCCG 1 36246 ( 185) GCAGGGGAAGAACGGC 1 26743 ( 413) CAATAGAAAGTAGGGG 1 2253 ( 476) GGAGAGAAAGTTCTGC 1 7182 ( 6) GGGTGCGAGGGGCGAG 1 261205 ( 57) GGATTGGGTGTACGAT 1 24106 ( 112) GGAGATGGTAATGTGG 1 262266 ( 235) CAAGGGTCTGTGAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15035 bayes= 8.91886 E= 3.6e-003 -1160 -56 189 -1160 7 -288 158 -1160 171 -1160 -123 -1160 -309 -1160 171 -20 107 -1160 65 -201 -1160 -56 165 -101 -29 -1160 171 -300 81 -8 36 -1160 -29 -1160 36 90 -309 -1160 209 -1160 49 -288 51 -1 60 -1160 65 -20 -29 -30 136 -1160 23 -56 77 -101 23 -30 51 -68 -309 -30 144 -68 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 31 E= 3.6e-003 0.000000 0.161290 0.838710 0.000000 0.290323 0.032258 0.677419 0.000000 0.903226 0.000000 0.096774 0.000000 0.032258 0.000000 0.741935 0.225806 0.580645 0.000000 0.354839 0.064516 0.000000 0.161290 0.709677 0.129032 0.225806 0.000000 0.741935 0.032258 0.483871 0.225806 0.290323 0.000000 0.225806 0.000000 0.290323 0.483871 0.032258 0.000000 0.967742 0.000000 0.387097 0.032258 0.322581 0.258065 0.419355 0.000000 0.354839 0.225806 0.225806 0.193548 0.580645 0.000000 0.322581 0.161290 0.387097 0.129032 0.322581 0.193548 0.322581 0.161290 0.032258 0.193548 0.612903 0.161290 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[GA]A[GT][AG]G[GA][AGC][TGA]G[AGT][AGT][GA][GA][AG]G -------------------------------------------------------------------------------- Time 24.36 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10080 1.23e-06 [+3(2.84e-05)]_32_[+1(6.28e-08)]_\ 397_[+2(3.15e-05)]_14 11585 1.99e-04 135_[+3(2.18e-06)]_106_\ [+2(4.01e-05)]_222 1563 8.97e-08 289_[+1(5.47e-07)]_15_\ [+3(2.12e-07)]_139_[+2(2.67e-05)] 16679 8.52e-05 11_[+1(6.79e-05)]_52_[+3(5.37e-05)]_\ 235_[+2(1.87e-06)]_145 18090 9.77e-09 38_[+2(1.74e-05)]_28_[+2(7.32e-05)]_\ 73_[+1(7.29e-09)]_233_[+3(2.18e-06)]_50 21137 3.28e-08 98_[+3(3.43e-05)]_28_[+1(2.03e-08)]_\ 195_[+2(1.48e-06)]_122 21552 1.19e-07 11_[+2(5.55e-06)]_185_\ [+1(7.61e-08)]_2_[+3(2.84e-05)]_132_[+2(2.25e-05)]_92 2253 2.40e-07 414_[+2(7.08e-08)]_15_\ [+1(1.61e-06)]_5_[+3(8.11e-05)]_9 22809 1.95e-02 99_[+3(5.84e-05)]_385 23954 1.49e-06 32_[+3(1.40e-06)]_37_[+1(5.91e-07)]_\ 373_[+2(8.44e-05)]_1 24106 3.77e-04 59_[+2(1.54e-07)]_398_\ [+2(4.01e-05)]_1 25620 1.19e-03 250_[+2(4.06e-06)]_201_\ [+3(6.36e-05)]_12 25766 1.71e-08 176_[+3(4.50e-07)]_34_\ [+1(1.55e-05)]_100_[+1(1.04e-08)]_134 261205 4.11e-03 314_[+2(4.06e-06)]_165 261341 2.36e-05 10_[+3(4.92e-05)]_225_\ [+2(5.08e-08)]_228 261998 3.43e-06 74_[+2(1.90e-05)]_202_\ [+3(4.92e-05)]_98_[+1(1.89e-07)]_69 262266 5.04e-05 188_[+1(2.89e-07)]_248_\ [+2(1.45e-05)]_23 263961 3.66e-07 12_[+1(9.62e-05)]_288_\ [+3(7.49e-05)]_10_[+1(1.63e-08)]_84_[+2(1.21e-05)]_29 264002 1.42e-02 174_[+3(9.49e-05)]_18_\ [+3(7.94e-06)]_276 264184 1.59e-03 75_[+3(1.91e-05)]_330_\ [+2(6.14e-06)]_58 264699 4.94e-09 62_[+2(9.12e-07)]_105_\ [+3(2.34e-05)]_43_[+3(3.76e-06)]_132_[+1(3.82e-08)]_85 26743 8.84e-07 67_[+2(1.67e-06)]_253_\ [+1(2.89e-07)]_23_[+2(9.06e-05)]_7_[+3(8.11e-05)]_35_[+2(1.00e-05)]_16 268493 1.27e-06 88_[+3(5.53e-06)]_239_\ [+1(1.14e-06)]_115_[+2(9.10e-06)]_1 2999 6.20e-07 72_[+2(1.00e-05)]_133_\ [+1(8.98e-05)]_7_[+1(9.19e-08)]_31_[+3(2.84e-05)]_158_[+2(8.44e-05)]_1 32154 1.22e-06 322_[+3(2.51e-06)]_140_\ [+2(1.54e-07)]_1 36246 6.60e-04 184_[+3(8.11e-05)]_266_\ [+2(4.06e-06)]_13 37486 3.92e-04 28_[+3(9.49e-05)]_48_[+3(1.91e-05)]_\ 37_[+2(1.87e-06)]_334 4947 5.73e-04 270_[+3(4.87e-06)]_190_\ [+2(2.25e-05)]_3 6519 1.09e-10 111_[+1(8.81e-10)]_4_[+3(1.68e-07)]_\ 247_[+2(1.45e-05)]_81 6522 9.82e-06 123_[+3(1.55e-05)]_74_\ [+1(9.23e-07)]_71_[+2(4.01e-05)]_175 7182 3.82e-04 79_[+2(2.76e-07)]_347_\ [+2(2.45e-05)]_32 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************