******************************************************************************** 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/96/96.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42426 1.0000 500 9344 1.0000 500 53933 1.0000 500 42726 1.0000 500 42788 1.0000 500 51412 1.0000 500 32118 1.0000 500 43152 1.0000 500 36293 1.0000 500 46438 1.0000 500 54591 1.0000 500 13243 1.0000 500 46806 1.0000 500 54677 1.0000 500 51024 1.0000 500 28445 1.0000 500 37268 1.0000 500 47152 1.0000 500 37466 1.0000 500 47314 1.0000 500 28841 1.0000 500 21882 1.0000 500 38049 1.0000 500 47818 1.0000 500 47887 1.0000 500 48206 1.0000 500 14994 1.0000 500 605 1.0000 500 39306 1.0000 500 48795 1.0000 500 15472 1.0000 500 32554 1.0000 500 32557 1.0000 500 32786 1.0000 500 43664 1.0000 500 25506 1.0000 500 48955 1.0000 500 22921 1.0000 500 39978 1.0000 500 49526 1.0000 500 30461 1.0000 500 55090 1.0000 500 23423 1.0000 500 51230 1.0000 500 7784 1.0000 500 16286 1.0000 500 52678 1.0000 500 51279 1.0000 500 41356 1.0000 500 43936 1.0000 500 7646 1.0000 500 55197 1.0000 500 55198 1.0000 500 50463 1.0000 500 44338 1.0000 500 11490 1.0000 500 44850 1.0000 500 45071 1.0000 500 34976 1.0000 500 26948 1.0000 500 45434 1.0000 500 6554 1.0000 500 27246 1.0000 500 45690 1.0000 500 12310 1.0000 500 45915 1.0000 500 45997 1.0000 500 46001 1.0000 500 46020 1.0000 500 54534 1.0000 500 14988 1.0000 500 42680 1.0000 500 42697 1.0000 500 48481 1.0000 500 48488 1.0000 500 42793 1.0000 500 39115 1.0000 500 46925 1.0000 500 39307 1.0000 500 43037 1.0000 500 34908 1.0000 500 34931 1.0000 500 48921 1.0000 500 46446 1.0000 500 48923 1.0000 500 36771 1.0000 500 44821 1.0000 500 36907 1.0000 500 39827 1.0000 500 45334 1.0000 500 46003 1.0000 500 49604 1.0000 500 47134 1.0000 500 47159 1.0000 500 37740 1.0000 500 48150 1.0000 500 49527 1.0000 500 49976 1.0000 500 44724 1.0000 500 35545 1.0000 500 35859 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/96/96.seqs.fa -oc motifs/96 -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= 101 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= 50500 N= 101 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.247 G 0.234 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.247 G 0.234 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 30 llr = 315 E-value = 3.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::1a:4:::a32 pos.-specific C 3:2:9:::3::1 probability G 1:7::1a:7:6: matrix T 69::14:a::16 bits 2.1 1.9 * ** * 1.7 * ** * 1.5 * ** ** * Relative 1.3 * ** ** * Entropy 1.0 **** **** (15.2 bits) 0.8 **** ***** 0.6 **** ****** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTGACAGTGAGT consensus C C T C AA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 45334 281 5.83e-08 CAAACTTTCG TTGACAGTGAGT AGCCGTCAGT 46020 146 1.18e-07 GGCACTAGCA TTGACTGTGAGT GATTATGTTT 41356 74 4.70e-07 AATAACATTG TTGACAGTGAAT ATCATTTCCT 7646 110 9.36e-07 AGGGTAGAGG TTGACAGTGAGC GAGAAACCAA 42788 219 9.36e-07 CTGCGGTTAG TTGACAGTGAGC GAATTTTATG 49976 425 1.22e-06 CCGACACTGA CTGACTGTGAGA GACACAACAG 46925 447 1.22e-06 CTCACATCTC CTGACAGTGAAT TTTCAGAAAG 35859 398 3.21e-06 GTGTCCCCAC GTGACTGTGAAT CTCCATACTG 46003 398 3.21e-06 GTGTCCCCAC GTGACTGTGAAT CTCCATACTG 38049 207 3.21e-06 GCTTATACGA TTGACGGTGAAT GACTCTATGC 35545 231 3.45e-06 CAATATGATA TTGACAGTGAAC AACAATTTTA 46001 184 3.80e-06 AAGTTTGTTA CTGACAGTGATT GTGTAATAGT 45997 353 3.80e-06 AAGATTGTTA CTGACAGTGATT GTGTAATAGC 43664 381 5.76e-06 CCAAACCCTT CTCACTGTCAGT CCGGACGCGC 49527 212 6.91e-06 GAATGTAGAC TTGACTGTTAGT TGTATTGGTA 44338 255 6.91e-06 ACAAACTTCG TTGATTGTGAGA AGGTGACGGT 48955 474 6.91e-06 TTGTTTCGAA TTCACAGTCAGA CGATCTACTC 37466 353 6.91e-06 TTTTAGGGGA TTCACAGTCAGA CAAAAAAAAG 49604 235 9.43e-06 GCTGGCTCCT TTGACTTTGAGT TCGACTTCCT 30461 236 1.01e-05 CGCGTCAAAC GTCACAGTCAGT AACTTTTTTC 32786 123 1.01e-05 TTCTGGTGTT TTGATGGTGAGT AGCAAGGACC 46438 327 1.16e-05 TGGGGAATTT GTGACCGTGAGT GGTTCCACTT 45690 127 1.36e-05 AACACACGTA CTGATTGTGAAT TGTTTTGCAG 54677 257 1.44e-05 CAATCCATAG CTAACAGTCAGT GTAACTTGTA 48206 226 1.69e-05 GGAGCATGAA TGGACTGTGAGA CTACATGCTG 22921 160 1.82e-05 CGAGTTTCCG TTGACGGTCATT TTAATTTGTT 42680 178 1.96e-05 GAATTCGGAA TTAACTGTCAGA TGCTCTATAC 48488 285 2.12e-05 ATTCGACAGT CTCACTGTCAGC ACCGTCTCCA 43152 99 2.28e-05 CTACAGCGAG TACACAGTGAGT CACTGTCTGT 11490 246 2.63e-05 TACCGAGGCG ATGACTGTGAAA TAACAATTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45334 5.8e-08 280_[+1]_208 46020 1.2e-07 145_[+1]_343 41356 4.7e-07 73_[+1]_415 7646 9.4e-07 109_[+1]_379 42788 9.4e-07 218_[+1]_270 49976 1.2e-06 424_[+1]_64 46925 1.2e-06 446_[+1]_42 35859 3.2e-06 397_[+1]_91 46003 3.2e-06 397_[+1]_91 38049 3.2e-06 206_[+1]_282 35545 3.4e-06 230_[+1]_258 46001 3.8e-06 183_[+1]_305 45997 3.8e-06 352_[+1]_136 43664 5.8e-06 380_[+1]_108 49527 6.9e-06 211_[+1]_277 44338 6.9e-06 254_[+1]_234 48955 6.9e-06 473_[+1]_15 37466 6.9e-06 352_[+1]_136 49604 9.4e-06 234_[+1]_254 30461 1e-05 235_[+1]_253 32786 1e-05 122_[+1]_366 46438 1.2e-05 326_[+1]_162 45690 1.4e-05 126_[+1]_362 54677 1.4e-05 256_[+1]_232 48206 1.7e-05 225_[+1]_263 22921 1.8e-05 159_[+1]_329 42680 2e-05 177_[+1]_311 48488 2.1e-05 284_[+1]_204 43152 2.3e-05 98_[+1]_390 11490 2.6e-05 245_[+1]_243 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=30 45334 ( 281) TTGACAGTGAGT 1 46020 ( 146) TTGACTGTGAGT 1 41356 ( 74) TTGACAGTGAAT 1 7646 ( 110) TTGACAGTGAGC 1 42788 ( 219) TTGACAGTGAGC 1 49976 ( 425) CTGACTGTGAGA 1 46925 ( 447) CTGACAGTGAAT 1 35859 ( 398) GTGACTGTGAAT 1 46003 ( 398) GTGACTGTGAAT 1 38049 ( 207) TTGACGGTGAAT 1 35545 ( 231) TTGACAGTGAAC 1 46001 ( 184) CTGACAGTGATT 1 45997 ( 353) CTGACAGTGATT 1 43664 ( 381) CTCACTGTCAGT 1 49527 ( 212) TTGACTGTTAGT 1 44338 ( 255) TTGATTGTGAGA 1 48955 ( 474) TTCACAGTCAGA 1 37466 ( 353) TTCACAGTCAGA 1 49604 ( 235) TTGACTTTGAGT 1 30461 ( 236) GTCACAGTCAGT 1 32786 ( 123) TTGATGGTGAGT 1 46438 ( 327) GTGACCGTGAGT 1 45690 ( 127) CTGATTGTGAAT 1 54677 ( 257) CTAACAGTCAGT 1 48206 ( 226) TGGACTGTGAGA 1 22921 ( 160) TTGACGGTCATT 1 42680 ( 178) TTAACTGTCAGA 1 48488 ( 285) CTCACTGTCAGC 1 43152 ( 99) TACACAGTGAGT 1 11490 ( 246) ATGACTGTGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 49389 bayes= 11.3587 E= 3.6e-005 -295 11 -81 112 -295 -1155 -281 184 -195 -31 165 -1155 196 -1155 -1155 -1155 -1155 186 -1155 -138 75 -289 -123 73 -1155 -1155 204 -297 -1155 -1155 -1155 194 -1155 11 158 -297 196 -1155 -1155 -1155 5 -1155 143 -138 -14 -89 -1155 128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 30 E= 3.6e-005 0.033333 0.266667 0.133333 0.566667 0.033333 0.000000 0.033333 0.933333 0.066667 0.200000 0.733333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.900000 0.000000 0.100000 0.433333 0.033333 0.100000 0.433333 0.000000 0.000000 0.966667 0.033333 0.000000 0.000000 0.000000 1.000000 0.000000 0.266667 0.700000 0.033333 1.000000 0.000000 0.000000 0.000000 0.266667 0.000000 0.633333 0.100000 0.233333 0.133333 0.000000 0.633333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TC]T[GC]AC[AT]GT[GC]A[GA][TA] -------------------------------------------------------------------------------- Time 70.46 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 31 llr = 314 E-value = 2.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 27::8:3a:443 pos.-specific C 23912a::9:36 probability G 5:19::7:163: matrix T 1::::::::::1 bits 2.1 1.9 * * 1.7 ** * * 1.5 ** * ** Relative 1.3 ******* Entropy 1.0 ********* (14.6 bits) 0.8 ********* 0.6 ********* * 0.4 ********** * 0.2 ************ 0.0 ------------ Multilevel GACGACGACGAC consensus C A ACA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 42793 140 4.87e-08 AAAGAGGAGG GACGACGACGAC CAACAAGAAA 9344 249 4.44e-07 CAACGACAAC GACGACAACGAC AATAACTTGG 51024 384 9.97e-07 CAACTTTAAG GACGACAACGGC AAACATCGCT 46001 15 1.50e-06 GACGAAAAAT GCCGACGACGAA CGGCGAATCC 45997 184 1.50e-06 GACGAAAAAT GCCGACGACGAA CGGCGAATCC 46438 403 2.53e-06 TACTCTCGGG GACGACGACGGT TGTCTGCTGA 32557 449 3.48e-06 GGTCTTTGTG TACGACGACGCC GGTATGTAAG 49976 65 4.00e-06 AAAGGAGTCG AACGACGACGCA TTGTGGGGGA 39306 200 4.00e-06 GAGTAGCGAT GACGACGACACT CACAGCGAAC 51412 357 4.52e-06 GCGTCCCACC GCCGACGACGAT GAGGATTCCC 49527 419 5.24e-06 CAACAACAGC AACGACAACAAC AGCGCTGTAT 48481 395 5.83e-06 GTATGGGAAG GAGGACGACGAC CTCAAACTCA 14994 120 5.83e-06 GGCGAGCATC GACGACGACGTC CGTGGCGGTG 23423 489 6.85e-06 AGACCCTTTC ACCGACGACACC 55090 489 6.85e-06 AGACCCTTTC ACCGACGACACC 52678 83 7.91e-06 TTCCTCCGCT CCCGACGACACC GATGCGGCAG 48955 194 8.71e-06 ATGGCTACGA TACGACGACAAA GCGTACCCAC 32786 200 1.13e-05 ACGGACACTG GACGCCAACAGC CACTAGGTGC 46806 1 1.24e-05 . CACGACAACGGA ATACACCGAG 7784 362 1.34e-05 TATCGGCCGT GACGATGACGAC AGTGATGGGC 44850 254 1.45e-05 GTAAAATAAA GACCACAACAAC AAGCACTGTC 45334 143 1.55e-05 AACTCATCCC GACGACGAGAGA GCGACGTCCT 11490 483 1.70e-05 GGCAGCCAAA AACGCCAACGAC GCAAAG 13243 216 1.70e-05 CGCACAGGAA GCCGCCAACGCC GCCAACAATC 605 195 2.01e-05 GTCGTATCAT CACCACGACGGC ATTGCCATTG 6554 408 2.10e-05 CGGCGATAGC TACGACGAGGAC TGGATCCGAA 25506 288 3.04e-05 CCCGACTCTT CCCGCCGACACC GGAAACGTTT 43037 346 3.31e-05 GGAGGAACGG CACGACGAGAAA GAAGTAAAGG 39307 84 3.31e-05 GACGGTCCCC AACCACGACGGA ATTGGCTCGG 45434 306 3.81e-05 ATTTAGATGC GCCGCCGACAGT CATCGAGGAA 42680 132 4.57e-05 GGAGGTCAAG GAGGACAACACA ACTTTCGCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42793 4.9e-08 139_[+2]_349 9344 4.4e-07 248_[+2]_240 51024 1e-06 383_[+2]_105 46001 1.5e-06 14_[+2]_474 45997 1.5e-06 183_[+2]_305 46438 2.5e-06 402_[+2]_86 32557 3.5e-06 448_[+2]_40 49976 4e-06 64_[+2]_424 39306 4e-06 199_[+2]_289 51412 4.5e-06 356_[+2]_132 49527 5.2e-06 418_[+2]_70 48481 5.8e-06 394_[+2]_94 14994 5.8e-06 119_[+2]_369 23423 6.9e-06 488_[+2] 55090 6.9e-06 488_[+2] 52678 7.9e-06 82_[+2]_406 48955 8.7e-06 193_[+2]_295 32786 1.1e-05 199_[+2]_289 46806 1.2e-05 [+2]_488 7784 1.3e-05 361_[+2]_127 44850 1.5e-05 253_[+2]_235 45334 1.5e-05 142_[+2]_346 11490 1.7e-05 482_[+2]_6 13243 1.7e-05 215_[+2]_273 605 2e-05 194_[+2]_294 6554 2.1e-05 407_[+2]_81 25506 3e-05 287_[+2]_201 43037 3.3e-05 345_[+2]_143 39307 3.3e-05 83_[+2]_405 45434 3.8e-05 305_[+2]_183 42680 4.6e-05 131_[+2]_357 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=31 42793 ( 140) GACGACGACGAC 1 9344 ( 249) GACGACAACGAC 1 51024 ( 384) GACGACAACGGC 1 46001 ( 15) GCCGACGACGAA 1 45997 ( 184) GCCGACGACGAA 1 46438 ( 403) GACGACGACGGT 1 32557 ( 449) TACGACGACGCC 1 49976 ( 65) AACGACGACGCA 1 39306 ( 200) GACGACGACACT 1 51412 ( 357) GCCGACGACGAT 1 49527 ( 419) AACGACAACAAC 1 48481 ( 395) GAGGACGACGAC 1 14994 ( 120) GACGACGACGTC 1 23423 ( 489) ACCGACGACACC 1 55090 ( 489) ACCGACGACACC 1 52678 ( 83) CCCGACGACACC 1 48955 ( 194) TACGACGACAAA 1 32786 ( 200) GACGCCAACAGC 1 46806 ( 1) CACGACAACGGA 1 7784 ( 362) GACGATGACGAC 1 44850 ( 254) GACCACAACAAC 1 45334 ( 143) GACGACGAGAGA 1 11490 ( 483) AACGCCAACGAC 1 13243 ( 216) GCCGCCAACGCC 1 605 ( 195) CACCACGACGGC 1 6554 ( 408) TACGACGAGGAC 1 25506 ( 288) CCCGCCGACACC 1 43037 ( 346) CACGACGAGAAA 1 39307 ( 84) AACCACGACGGA 1 45434 ( 306) GCCGCCGACAGT 1 42680 ( 132) GAGGACAACACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 49389 bayes= 11.9362 E= 2.0e-002 -41 -62 123 -143 146 23 -1160 -1160 -1160 192 -186 -1160 -1160 -135 195 -1160 170 -62 -1160 -1160 -1160 197 -1160 -301 17 -1160 160 -1160 196 -1160 -1160 -1160 -1160 187 -127 -1160 70 -1160 131 -1160 70 23 14 -301 17 123 -1160 -102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 31 E= 2.0e-002 0.193548 0.161290 0.548387 0.096774 0.709677 0.290323 0.000000 0.000000 0.000000 0.935484 0.064516 0.000000 0.000000 0.096774 0.903226 0.000000 0.838710 0.161290 0.000000 0.000000 0.000000 0.967742 0.000000 0.032258 0.290323 0.000000 0.709677 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.903226 0.096774 0.000000 0.419355 0.000000 0.580645 0.000000 0.419355 0.290323 0.258065 0.032258 0.290323 0.580645 0.000000 0.129032 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AC]CGAC[GA]AC[GA][ACG][CA] -------------------------------------------------------------------------------- Time 138.11 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 163 E-value = 2.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::3::6:::39:98:::: pos.-specific C :9:7:24:::366191::7:6 probability G :123:24:2:331:1:2:2a4 matrix T a:8:a21a2a31:::::a1:: bits 2.1 * 1.9 * * * * * * 1.7 * * * * * * 1.5 ** * * * *** * * Relative 1.3 *** * * * ***** * Entropy 1.0 ***** * * ***** ** (26.1 bits) 0.8 ***** * * ******** 0.6 ***** **** ********** 0.4 ***** *************** 0.2 ***** *************** 0.0 --------------------- Multilevel TCTCTACTATCCCACAATCGC consensus GG CG G GGA G G G sequence G T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6554 259 5.74e-12 AAAGCTTACC TCTCTACTATGGCACAATCGC AAGTAGTATG 46001 215 3.97e-11 TTCCACACTT TCTCTCCTATCCAACAATCGC TTGTCCTTTC 45997 384 3.97e-11 CTCCACACTT TCTCTCCTATCCAACAATCGC TTGTCCTTTC 35859 236 4.24e-10 TTTATGGGGT TCTGTAGTTTTGCACAATCGG GCGTTCGTAC 46003 236 4.24e-10 TTTATGGGGT TCTGTAGTTTTGCACAATCGG GCGTTCGTAC 43936 341 1.14e-08 GCGGCGCTGG TCGGTTCTATGCCACCATGGG GACGATACGG 43152 114 1.14e-08 AGTGAGTCAC TGTCTGTTATCCCACAGTCGG GGTACGCACA 48923 269 2.97e-08 GAGGATTTTC TCTCTTGTGTGCAAGAGTTGC CGCCGCCATC 48921 101 6.83e-08 AAGTCGATCT TCGCTGGTGTTTGCCAATGGC CGTTACATCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6554 5.7e-12 258_[+3]_221 46001 4e-11 214_[+3]_265 45997 4e-11 383_[+3]_96 35859 4.2e-10 235_[+3]_244 46003 4.2e-10 235_[+3]_244 43936 1.1e-08 340_[+3]_139 43152 1.1e-08 113_[+3]_366 48923 3e-08 268_[+3]_211 48921 6.8e-08 100_[+3]_379 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 6554 ( 259) TCTCTACTATGGCACAATCGC 1 46001 ( 215) TCTCTCCTATCCAACAATCGC 1 45997 ( 384) TCTCTCCTATCCAACAATCGC 1 35859 ( 236) TCTGTAGTTTTGCACAATCGG 1 46003 ( 236) TCTGTAGTTTTGCACAATCGG 1 43936 ( 341) TCGGTTCTATGCCACCATGGG 1 43152 ( 114) TGTCTGTTATCCCACAGTCGG 1 48923 ( 269) TCTCTTGTGTGCAAGAGTTGC 1 48921 ( 101) TCGCTGGTGTTTGCCAATGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 48480 bayes= 12.5292 E= 2.0e-001 -982 -982 -982 194 -982 184 -107 -982 -982 -982 -8 157 -982 143 51 -982 -982 -982 -982 194 37 -16 -8 -23 -982 84 92 -123 -982 -982 -982 194 111 -982 -8 -23 -982 -982 -982 194 -982 43 51 35 -982 117 51 -123 37 117 -107 -982 179 -115 -982 -982 -982 184 -107 -982 179 -115 -982 -982 160 -982 -8 -982 -982 -982 -982 194 -982 143 -8 -123 -982 -982 209 -982 -982 117 92 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 2.0e-001 0.000000 0.000000 0.000000 1.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.222222 0.777778 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.222222 0.222222 0.222222 0.000000 0.444444 0.444444 0.111111 0.000000 0.000000 0.000000 1.000000 0.555556 0.000000 0.222222 0.222222 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.555556 0.333333 0.111111 0.333333 0.555556 0.111111 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.888889 0.111111 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.222222 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 0.555556 0.444444 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TC[TG][CG]T[ACGT][CG]T[AGT]T[CGT][CG][CA]ACA[AG]T[CG]G[CG] -------------------------------------------------------------------------------- Time 208.61 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42426 5.62e-01 500 9344 5.04e-03 88_[+2(5.78e-05)]_148_\ [+2(4.44e-07)]_107_[+2(9.75e-05)]_121 53933 7.03e-01 500 42726 1.65e-01 38_[+3(4.54e-05)]_441 42788 1.19e-02 218_[+1(9.36e-07)]_270 51412 5.69e-03 356_[+2(4.52e-06)]_132 32118 8.82e-01 500 43152 5.00e-06 98_[+1(2.28e-05)]_3_[+3(1.14e-08)]_\ 366 36293 1.91e-01 500 46438 1.13e-04 326_[+1(1.16e-05)]_64_\ [+2(2.53e-06)]_86 54591 7.37e-02 342_[+2(8.40e-05)]_146 13243 2.70e-02 215_[+2(1.70e-05)]_273 46806 2.59e-02 [+2(1.24e-05)]_488 54677 2.87e-02 256_[+1(1.44e-05)]_232 51024 1.15e-03 383_[+2(9.97e-07)]_105 28445 6.19e-01 500 37268 3.61e-01 500 47152 7.54e-01 500 37466 2.77e-02 352_[+1(6.91e-06)]_136 47314 3.88e-01 500 28841 8.22e-02 500 21882 2.37e-01 500 38049 1.24e-02 206_[+1(3.21e-06)]_282 47818 1.89e-01 221_[+3(6.77e-05)]_258 47887 7.77e-01 500 48206 3.98e-02 225_[+1(1.69e-05)]_263 14994 6.66e-03 119_[+2(5.83e-06)]_369 605 3.10e-02 194_[+2(2.01e-05)]_294 39306 3.14e-03 199_[+2(4.00e-06)]_289 48795 5.51e-01 500 15472 3.34e-02 500 32554 3.10e-01 500 32557 2.64e-03 57_[+3(8.40e-05)]_179_\ [+3(7.99e-05)]_170_[+2(3.48e-06)]_40 32786 1.22e-03 122_[+1(1.01e-05)]_65_\ [+2(1.13e-05)]_289 43664 3.00e-02 380_[+1(5.76e-06)]_108 25506 1.85e-02 287_[+2(3.04e-05)]_201 48955 3.29e-04 193_[+2(8.71e-06)]_268_\ [+1(6.91e-06)]_15 22921 4.22e-02 159_[+1(1.82e-05)]_329 39978 4.52e-01 500 49526 5.62e-01 500 30461 2.02e-02 235_[+1(1.01e-05)]_77_\ [+1(1.96e-05)]_164 55090 1.37e-02 488_[+2(6.85e-06)] 23423 8.66e-03 488_[+2(6.85e-06)] 51230 9.83e-01 500 7784 6.48e-02 361_[+2(1.34e-05)]_37_\ [+2(3.99e-05)]_78 16286 5.46e-01 500 52678 4.37e-02 82_[+2(7.91e-06)]_406 51279 5.35e-01 500 41356 4.99e-04 73_[+1(4.70e-07)]_415 43936 3.64e-04 340_[+3(1.14e-08)]_139 7646 2.59e-03 109_[+1(9.36e-07)]_379 55197 3.74e-01 500 55198 4.19e-01 500 50463 2.69e-01 500 44338 3.04e-02 254_[+1(6.91e-06)]_234 11490 3.14e-03 245_[+1(2.63e-05)]_225_\ [+2(1.70e-05)]_6 44850 3.45e-03 253_[+2(1.45e-05)]_235 45071 5.82e-01 500 34976 2.17e-01 500 26948 1.91e-01 500 45434 7.37e-02 305_[+2(3.81e-05)]_183 6554 6.88e-09 149_[+3(3.90e-05)]_88_\ [+3(5.74e-12)]_128_[+2(2.10e-05)]_81 27246 9.03e-01 500 45690 1.43e-02 126_[+1(1.36e-05)]_362 12310 9.14e-01 500 45915 7.15e-01 500 45997 1.36e-11 183_[+2(1.50e-06)]_157_\ [+1(3.80e-06)]_19_[+3(3.97e-11)]_96 46001 1.36e-11 14_[+2(1.50e-06)]_157_\ [+1(3.80e-06)]_19_[+3(3.97e-11)]_265 46020 8.47e-04 145_[+1(1.18e-07)]_343 54534 2.67e-01 500 14988 9.61e-02 500 42680 2.48e-03 131_[+2(4.57e-05)]_34_\ [+1(1.96e-05)]_311 42697 5.37e-01 500 48481 4.37e-03 394_[+2(5.83e-06)]_6_[+1(7.29e-05)]_\ 76 48488 9.04e-02 284_[+1(2.12e-05)]_204 42793 3.89e-04 139_[+2(4.87e-08)]_349 39115 7.29e-01 500 46925 1.36e-02 446_[+1(1.22e-06)]_42 39307 2.69e-02 83_[+2(3.31e-05)]_405 43037 1.29e-01 345_[+2(3.31e-05)]_143 34908 8.34e-01 500 34931 2.89e-01 500 48921 6.30e-04 100_[+3(6.83e-08)]_379 46446 3.50e-01 500 48923 9.51e-06 111_[+2(8.74e-05)]_145_\ [+3(2.97e-08)]_211 36771 9.37e-01 500 44821 4.40e-01 500 36907 1.32e-01 500 39827 1.99e-01 500 45334 2.51e-05 142_[+2(1.55e-05)]_126_\ [+1(5.83e-08)]_208 46003 3.97e-08 235_[+3(4.24e-10)]_85_\ [+3(3.75e-05)]_35_[+1(3.21e-06)]_91 49604 2.50e-02 234_[+1(9.43e-06)]_254 47134 4.81e-01 500 47159 4.25e-01 500 37740 2.72e-01 500 48150 5.51e-01 500 49527 6.82e-04 211_[+1(6.91e-06)]_195_\ [+2(5.24e-06)]_70 49976 1.19e-04 64_[+2(4.00e-06)]_348_\ [+1(1.22e-06)]_64 44724 2.90e-01 500 35545 5.56e-03 230_[+1(3.45e-06)]_48_\ [+1(8.59e-05)]_198 35859 3.97e-08 235_[+3(4.24e-10)]_85_\ [+3(3.75e-05)]_35_[+1(3.21e-06)]_91 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************