******************************************************************************** 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/322/322.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11102 1.0000 500 11205 1.0000 500 1268 1.0000 500 13149 1.0000 500 1778 1.0000 500 20639 1.0000 500 21346 1.0000 500 22753 1.0000 500 23130 1.0000 500 24355 1.0000 500 25470 1.0000 500 261260 1.0000 500 262521 1.0000 500 263722 1.0000 500 264282 1.0000 500 268872 1.0000 500 2984 1.0000 500 31076 1.0000 500 32399 1.0000 500 3487 1.0000 500 35342 1.0000 500 3601 1.0000 500 36273 1.0000 500 36511 1.0000 500 3719 1.0000 500 4066 1.0000 500 4290 1.0000 500 4555 1.0000 500 4755 1.0000 500 5266 1.0000 500 6648 1.0000 500 9633 1.0000 500 bd1799 1.0000 500 bd1845 1.0000 500 bd857 1.0000 116 ******************************************************************************** ******************************************************************************** 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/322/322.seqs.fa -oc motifs/322 -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= 35 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= 17116 N= 35 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.250 C 0.236 G 0.252 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.250 C 0.236 G 0.252 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 24 llr = 286 E-value = 2.1e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :22322:2:::513252:425 pos.-specific C 92787:a551535583:a455 probability G 12::1::1213:::12:::2: matrix T :41::8:3381333:18:22: bits 2.1 1.9 * * 1.7 * * 1.5 * * * Relative 1.2 * * * ** Entropy 1.0 * * ** * * ** * (17.2 bits) 0.8 * ***** * * ** * 0.6 * ***** ** *** ** * 0.4 * ***** ******* *** * 0.2 * ******************* 0.0 --------------------- Multilevel CTCCCTCCCTCACCCATCACA consensus AAA A TT GTTA CA CAC sequence C C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 11205 229 5.61e-10 ATAGCTCTCT CTCCCTCTCTCACACGTCACA CGCCAGTACA 36273 455 1.12e-08 CGCCGTCCGT CCCCCTCCCTCTACCAACCCA CCCCGTCCCA 1268 301 3.09e-08 GCTTCGCTTG CTACCTCTTTCATTCCTCCCC ACCACCTACA 261260 12 6.01e-08 TCTCCTATTT CTCCGTCCCTCTCCGCTCCCC TCGCAGCTGC 262521 476 8.81e-08 CCTCCTCAAC CCCCCTCCGTGCCTCCTCATC GACC 36511 477 1.12e-07 CTCCTCCCTC CTCCCTCATTCAACCTTCAAC CGC 25470 480 1.12e-07 CTCTGAAGGT CGCCGACACTCACACATCACA 24355 424 1.26e-07 CTTCGTTGGC CACCCACACTCATCCGTCCTC TCGCCGGCTC 20639 480 2.02e-07 TTCCTCCTAC CTCCCTCCCTAACTCTACACC 11102 185 3.14e-07 TTGCTTTTCA CACACTCTCTCACAGATCCGA CTCAACAAAA 31076 435 4.31e-07 TCTTAACTAT CGCCCTGCTTGACTCATCCAC CAACCACATC 4555 425 8.69e-07 GCCTCTCAAC CACACACCCGCAACCCTCCCA AACTAATGGA 1778 418 8.69e-07 CAGCCGACCT CTACATCTGTGACCCATCTGA CACACACATC bd1799 213 1.81e-06 CCAAATTCAC CACCCTCGTTTACAAATCAGA TTCAATATTC 4755 327 2.16e-06 ATGTGGAGGT GCACCTCCTTGTTACATCTCC CGCCGTCTCT 3719 417 2.35e-06 TTATCTCTCT CGCCCTCCTCGTCCAAACTCA CGACACGCCA 3487 460 4.52e-06 TCAGTTTACG CCAACACACTGCTCCAACAAC CGCATCACCC 22753 144 5.28e-06 ACAAACAAAC CACAACCCCTCCCCAGTCACA GCCGCCGACC 9633 137 6.62e-06 TTTGGTAGTG CCAAAACCGTGTTCCATCCAA GTCCCGGGCC 268872 459 8.24e-06 CATAAAAGTC CGCCCTCTGTCCTCCCATATC CCCGTCCTCT 5266 350 1.17e-05 CAACACTCTT CGCACTCGCCTCCCAGTCACC CGAAGCAAAA 35342 252 1.43e-05 GCTTGGAGAG GTTCCTCCTTGCTTCCTCTTC GAAAAGTAAG 3601 457 1.74e-05 AGCCATTCCA TTCCGTCTCTTTCTCTTCCGA TCTCGTCCGT 13149 115 3.20e-05 CGAAGGCCGC CTTCATCTCGCTTACATCGAA CAAAAGCGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11205 5.6e-10 228_[+1]_251 36273 1.1e-08 454_[+1]_25 1268 3.1e-08 300_[+1]_179 261260 6e-08 11_[+1]_468 262521 8.8e-08 475_[+1]_4 36511 1.1e-07 476_[+1]_3 25470 1.1e-07 479_[+1] 24355 1.3e-07 423_[+1]_56 20639 2e-07 479_[+1] 11102 3.1e-07 184_[+1]_295 31076 4.3e-07 434_[+1]_45 4555 8.7e-07 424_[+1]_55 1778 8.7e-07 417_[+1]_62 bd1799 1.8e-06 212_[+1]_267 4755 2.2e-06 326_[+1]_153 3719 2.4e-06 416_[+1]_63 3487 4.5e-06 459_[+1]_20 22753 5.3e-06 143_[+1]_336 9633 6.6e-06 136_[+1]_343 268872 8.2e-06 458_[+1]_21 5266 1.2e-05 349_[+1]_130 35342 1.4e-05 251_[+1]_228 3601 1.7e-05 456_[+1]_23 13149 3.2e-05 114_[+1]_365 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=24 11205 ( 229) CTCCCTCTCTCACACGTCACA 1 36273 ( 455) CCCCCTCCCTCTACCAACCCA 1 1268 ( 301) CTACCTCTTTCATTCCTCCCC 1 261260 ( 12) CTCCGTCCCTCTCCGCTCCCC 1 262521 ( 476) CCCCCTCCGTGCCTCCTCATC 1 36511 ( 477) CTCCCTCATTCAACCTTCAAC 1 25470 ( 480) CGCCGACACTCACACATCACA 1 24355 ( 424) CACCCACACTCATCCGTCCTC 1 20639 ( 480) CTCCCTCCCTAACTCTACACC 1 11102 ( 185) CACACTCTCTCACAGATCCGA 1 31076 ( 435) CGCCCTGCTTGACTCATCCAC 1 4555 ( 425) CACACACCCGCAACCCTCCCA 1 1778 ( 418) CTACATCTGTGACCCATCTGA 1 bd1799 ( 213) CACCCTCGTTTACAAATCAGA 1 4755 ( 327) GCACCTCCTTGTTACATCTCC 1 3719 ( 417) CGCCCTCCTCGTCCAAACTCA 1 3487 ( 460) CCAACACACTGCTCCAACAAC 1 22753 ( 144) CACAACCCCTCCCCAGTCACA 1 9633 ( 137) CCAAAACCGTGTTCCATCCAA 1 268872 ( 459) CGCCCTCTGTCCTCCCATATC 1 5266 ( 350) CGCACTCGCCTCCCAGTCACC 1 35342 ( 252) GTTCCTCCTTGCTTCCTCTTC 1 3601 ( 457) TTCCGTCTCTTTCTCTTCCGA 1 13149 ( 115) CTTCATCTCGCTTACATCGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16416 bayes= 9.86376 E= 2.1e-009 -1123 189 -160 -265 -26 -18 -28 52 -26 158 -1123 -165 0 167 -1123 -1123 -58 158 -101 -1123 -26 -250 -1123 152 -1123 202 -260 -1123 -58 96 -160 16 -1123 120 -60 16 -1123 -150 -160 167 -258 108 40 -106 87 8 -1123 16 -100 120 -1123 35 0 108 -1123 -6 -58 167 -160 -1123 87 8 -60 -106 -26 -1123 -1123 160 -1123 202 -1123 -265 74 67 -260 -65 -26 96 -60 -65 100 108 -1123 -1123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 2.1e-009 0.000000 0.875000 0.083333 0.041667 0.208333 0.208333 0.208333 0.375000 0.208333 0.708333 0.000000 0.083333 0.250000 0.750000 0.000000 0.000000 0.166667 0.708333 0.125000 0.000000 0.208333 0.041667 0.000000 0.750000 0.000000 0.958333 0.041667 0.000000 0.166667 0.458333 0.083333 0.291667 0.000000 0.541667 0.166667 0.291667 0.000000 0.083333 0.083333 0.833333 0.041667 0.500000 0.333333 0.125000 0.458333 0.250000 0.000000 0.291667 0.125000 0.541667 0.000000 0.333333 0.250000 0.500000 0.000000 0.250000 0.166667 0.750000 0.083333 0.000000 0.458333 0.250000 0.166667 0.125000 0.208333 0.000000 0.000000 0.791667 0.000000 0.958333 0.000000 0.041667 0.416667 0.375000 0.041667 0.166667 0.208333 0.458333 0.166667 0.166667 0.500000 0.500000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[TACG][CA][CA]C[TA]C[CT][CT]T[CG][ATC][CT][CAT]C[AC][TA]C[AC][CA][AC] -------------------------------------------------------------------------------- Time 10.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 33 llr = 333 E-value = 5.3e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2121::1::311::8226325 pos.-specific C 1:2::3:2:1::1112:21:1 probability G 482385:67273491381372 matrix T 4156228234265::3:1222 bits 2.1 1.9 1.7 * 1.5 * Relative 1.2 * * * * * Entropy 1.0 * * * * ** * (14.5 bits) 0.8 * * * * * ** * * 0.6 * ****** * *** ** * 0.4 * ****** ***** ** * 0.2 *************** ***** 0.0 --------------------- Multilevel GGTTGGTGGTGTTGAGGAAGA consensus T GTC TTATGG TA G G sequence G A T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 20639 96 4.56e-08 TACCAGCTGA AGGTTGTGGTGTTGAGGAGGG ACAACTCGGT 3601 137 7.30e-08 GTTTAGGCGA GGTTGTTGTGGTGGACGAAGG TGAAGGAGCA 262521 238 2.03e-07 GTTGGTGTTT GGATGCTGGCGAGGAGGAAGA AGTCGCGTTG bd857 55 2.67e-07 GGCGTGATAT CGTTTGTGGAGTTGACAAAGA CGATATCGCA 23130 64 3.06e-07 GACAAGCGCT TGTTGTTTTTTGTGATGAAGA CGGTGACAGC 263722 172 3.49e-07 ACACGATGAC GGTTGCTGGTTGGGGAGAAGG AAAACTGGCG 36511 301 5.84e-07 CGGGCTTCGG TAGTTGTGGAGTGGAGGAGGA TCGACGAAGG 36273 204 6.62e-07 CCAACATGAC GGTAGCTGGCGTTGAAGACGA TGCCTTTGTC 4290 317 1.70e-06 GTCGGCTGGC TGTGGCTGTGGGGGCAGAGGG ATGGCGAGAG 25470 161 1.90e-06 ATGCCGTACG TGATGGTGTATTTGGTGATGT GTCGAGACGT 6648 32 3.62e-06 ATGATGATGA TGATGCTGTTGGCGATGATGC GTCAGTGAAA 32399 372 3.62e-06 ACCCCTGAAG TGACGGTGGTGGTGAGGCTGT GCCTGTGCGC 264282 201 4.01e-06 TAGGAGACAC GGGGGGTTGTGTTCAAGAGAA GCCGAAGAGA 11102 223 4.44e-06 AAAATGTTTC GGCGTCTCGGGTTGCGGAAGA TAAGATTCTC 4066 239 5.42e-06 AGCTCCTCAT GGTTGGATGGTTGGAGGAGTT GTTGTGAGGT 5266 71 6.60e-06 GATCCCTTGA GTGGTGTTGGGTGGATGATGA GGATGCGCGA 3719 237 6.60e-06 GATGGAGATG TACTGGTGGAGGTGATGTTGT ATTTCGATGG 3487 249 8.77e-06 AGTCGATAGT TGTTGGTGGCATTGGTGCCGA TGGTGGCGGT 1268 201 1.51e-05 CGAAGGGTGT TGTTGTAGGAAGCGAAGAAGA ACAGAAAGAT 4755 301 1.65e-05 GTCGACTATG AGTGGGTTGAGGTGAGATGTG GAGGTGCACC 24355 242 1.65e-05 GATTTGTTCC TGATGTTCGTTTGGAGGTTGC TATGAAACAA 1778 245 1.65e-05 CTCCCAACTT CGTGGCTCGTGGTGATGTGAT ACCAAAATTA 21346 45 1.79e-05 GCGTCTGATC GGATGGTTTGGATGAAAAGTA GCCAAACGGC 11205 23 1.79e-05 ACTCAGTTTG GGCGTGTGTGATGGACAAAGA CGATAGTTAA 2984 256 1.95e-05 CGTGTGCTGG TGTTGTTGTTTTGGGTGCGAT GCAAATGAAG 31076 105 2.51e-05 ATCTACGCGA GTGTTGTCGAGTTGAAGCGAA ATCCACTTTG 268872 375 2.72e-05 GCGCGCCGTC GGCTGCTTGTGGTCAGAAATG ACAGAAGTAG 22753 241 3.74e-05 GTCTTGAAGG AGCTGGACGTGTGGCTGAGAG TGTACTCTTC bd1845 392 4.03e-05 TTCATTACGT AGGTGCTGGTTTGGACAGAAT CAACCGATGT 35342 293 4.03e-05 AGGGCGAGTG TGTATCAGGAGTGGACAAAGC TCTTCATCGA 4555 2 4.35e-05 A GGTGGCTGTTGCTGCCGCCGA TCTTTTGGTT 13149 319 5.06e-05 AGAGATGAAG TGTGGTCGGATATGATGCTGA ATATGAGCTG 9633 351 6.30e-05 CAGTCAACAA ATTGGGTGGAGTTGAGAGTTG GTGCAAATAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20639 4.6e-08 95_[+2]_384 3601 7.3e-08 136_[+2]_343 262521 2e-07 237_[+2]_242 bd857 2.7e-07 54_[+2]_41 23130 3.1e-07 63_[+2]_416 263722 3.5e-07 171_[+2]_308 36511 5.8e-07 300_[+2]_179 36273 6.6e-07 203_[+2]_276 4290 1.7e-06 316_[+2]_163 25470 1.9e-06 160_[+2]_319 6648 3.6e-06 31_[+2]_448 32399 3.6e-06 371_[+2]_108 264282 4e-06 200_[+2]_279 11102 4.4e-06 222_[+2]_257 4066 5.4e-06 238_[+2]_241 5266 6.6e-06 70_[+2]_409 3719 6.6e-06 236_[+2]_243 3487 8.8e-06 248_[+2]_231 1268 1.5e-05 200_[+2]_279 4755 1.6e-05 300_[+2]_179 24355 1.6e-05 241_[+2]_238 1778 1.6e-05 244_[+2]_235 21346 1.8e-05 44_[+2]_435 11205 1.8e-05 22_[+2]_457 2984 2e-05 255_[+2]_224 31076 2.5e-05 104_[+2]_375 268872 2.7e-05 374_[+2]_105 22753 3.7e-05 240_[+2]_239 bd1845 4e-05 391_[+2]_88 35342 4e-05 292_[+2]_187 4555 4.4e-05 1_[+2]_478 13149 5.1e-05 318_[+2]_161 9633 6.3e-05 350_[+2]_129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=33 20639 ( 96) AGGTTGTGGTGTTGAGGAGGG 1 3601 ( 137) GGTTGTTGTGGTGGACGAAGG 1 262521 ( 238) GGATGCTGGCGAGGAGGAAGA 1 bd857 ( 55) CGTTTGTGGAGTTGACAAAGA 1 23130 ( 64) TGTTGTTTTTTGTGATGAAGA 1 263722 ( 172) GGTTGCTGGTTGGGGAGAAGG 1 36511 ( 301) TAGTTGTGGAGTGGAGGAGGA 1 36273 ( 204) GGTAGCTGGCGTTGAAGACGA 1 4290 ( 317) TGTGGCTGTGGGGGCAGAGGG 1 25470 ( 161) TGATGGTGTATTTGGTGATGT 1 6648 ( 32) TGATGCTGTTGGCGATGATGC 1 32399 ( 372) TGACGGTGGTGGTGAGGCTGT 1 264282 ( 201) GGGGGGTTGTGTTCAAGAGAA 1 11102 ( 223) GGCGTCTCGGGTTGCGGAAGA 1 4066 ( 239) GGTTGGATGGTTGGAGGAGTT 1 5266 ( 71) GTGGTGTTGGGTGGATGATGA 1 3719 ( 237) TACTGGTGGAGGTGATGTTGT 1 3487 ( 249) TGTTGGTGGCATTGGTGCCGA 1 1268 ( 201) TGTTGTAGGAAGCGAAGAAGA 1 4755 ( 301) AGTGGGTTGAGGTGAGATGTG 1 24355 ( 242) TGATGTTCGTTTGGAGGTTGC 1 1778 ( 245) CGTGGCTCGTGGTGATGTGAT 1 21346 ( 45) GGATGGTTTGGATGAAAAGTA 1 11205 ( 23) GGCGTGTGTGATGGACAAAGA 1 2984 ( 256) TGTTGTTGTTTTGGGTGCGAT 1 31076 ( 105) GTGTTGTCGAGTTGAAGCGAA 1 268872 ( 375) GGCTGCTTGTGGTCAGAAATG 1 22753 ( 241) AGCTGGACGTGTGGCTGAGAG 1 bd1845 ( 392) AGGTGCTGGTTTGGACAGAAT 1 35342 ( 293) TGTATCAGGAGTGGACAAAGC 1 4555 ( 2) GGTGGCTGTTGCTGCCGCCGA 1 13149 ( 319) TGTGGTCGGATATGATGCTGA 1 9633 ( 351) ATTGGGTGGAGTTGAGAGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16416 bayes= 8.99099 E= 5.3e-009 -72 -196 64 59 -204 -1169 175 -152 -46 -64 -47 89 -204 -296 26 121 -1169 -1169 159 -11 -1169 50 94 -52 -104 -296 -1169 170 -1169 -64 133 -30 -1169 -1169 153 6 28 -138 -25 59 -146 -1169 140 -11 -146 -296 26 114 -1169 -196 64 106 -1169 -196 190 -1169 160 -96 -106 -1169 -24 -38 26 21 -4 -1169 159 -1169 135 -38 -206 -111 41 -138 40 -11 -46 -1169 140 -79 86 -138 -6 -30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 33 E= 5.3e-009 0.151515 0.060606 0.393939 0.393939 0.060606 0.000000 0.848485 0.090909 0.181818 0.151515 0.181818 0.484848 0.060606 0.030303 0.303030 0.606061 0.000000 0.000000 0.757576 0.242424 0.000000 0.333333 0.484848 0.181818 0.121212 0.030303 0.000000 0.848485 0.000000 0.151515 0.636364 0.212121 0.000000 0.000000 0.727273 0.272727 0.303030 0.090909 0.212121 0.393939 0.090909 0.000000 0.666667 0.242424 0.090909 0.030303 0.303030 0.575758 0.000000 0.060606 0.393939 0.545455 0.000000 0.060606 0.939394 0.000000 0.757576 0.121212 0.121212 0.000000 0.212121 0.181818 0.303030 0.303030 0.242424 0.000000 0.757576 0.000000 0.636364 0.181818 0.060606 0.121212 0.333333 0.090909 0.333333 0.242424 0.181818 0.000000 0.666667 0.151515 0.454545 0.090909 0.242424 0.212121 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]GT[TG][GT][GC]T[GT][GT][TAG][GT][TG][TG]GA[GTA][GA]A[AGT]G[AGT] -------------------------------------------------------------------------------- Time 21.28 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 35 llr = 314 E-value = 5.1e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 255:584914631152311 pos.-specific C 1:111:::::2::6:23:5 probability G 6329326184244352223 matrix T 112:::::12:25::4371 bits 2.1 1.9 1.7 * 1.5 * * Relative 1.2 * * ** Entropy 1.0 * **** * (12.9 bits) 0.8 * **** ** * 0.6 ****** * *** * 0.4 ** ******** *** * 0.2 *************** ** 0.0 ------------------- Multilevel GAAGAAGAGGAGTCATATC consensus AGT GGA AGAGGGCTGG sequence TCT AC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 3719 77 3.53e-08 ATTCGTTCTT GGAGAAGAGACATCACTTC GAGGTTGCTA 11102 152 1.23e-07 AGTAGTAGGT GGAGCAGAGAATTCGTCTC CATCTTGCTT 21346 249 3.05e-07 CGCCCATTAG GATGGAGAGGGGTGATTTC CACGCTGCCG bd857 17 5.04e-07 GAGCTAACAG GAAGAAGAGGCAGCATCAC GTCAACCATG 6648 104 6.93e-07 TGATTGTTGA CATGGAGAGAAGGGATATC AATGCGAATA 36511 392 1.26e-06 GGGTGGGTTG AGAGGAGAGAGGGCGTCTG TGCTGGTCGG 3487 376 1.26e-06 GCGAGATGGA GGAGGAGAGGCGTCGATTT GATATTTTGT 4290 244 2.53e-06 GTAGCCCGAC GAAGGAAAGAAGTAAGATG GGAAATTTCA 24355 386 3.27e-06 AGATCTAACA AAGGGAGAGAAGTCACTTT CATCGAATCC 32399 61 3.72e-06 GTCATTTCAC GTTGAAGAGAAATGGTCTT TTTCGCCAAA 4066 443 4.76e-06 AATGTCGAGT GGAGAAAATTATGCATGTC GTCTTCCTCC 20639 195 7.62e-06 AGCATACGCT GTTGAAAAGGAATCACAAC GAATCCGTAA bd1845 142 9.54e-06 TTGATTTTCG GGGGAAGATGATGGGCTTC ATCTGATGAG 31076 14 1.32e-05 CGCAGGCCGC GATGCAGAGAGTGGAGGTC TTCATGGTTG 261260 192 1.32e-05 TGTCCTATCA CAAGAAGAATAAGCGCTTC TCCACATCGC 3601 203 1.62e-05 GACGAACGAC GAAGCGAAGGATTGATATT TTTGGTCGAG 5266 209 2.19e-05 TCATGTTGGA GAAGGAGAGGACGGGGATA TGGGAGGACA 4555 168 2.66e-05 ACGAGAAGTG AGGGGAGAGAGGGCGCAGG CGAGATTGTT 1268 259 2.66e-05 GTAAAATAAT CAACAAAAGGATTCATTTA TCCCCGTTCA 11205 115 2.92e-05 AGTTGCACTG GAACAAAAGACAACAGTTC ATTCTATCTC 264282 54 3.21e-05 GAGGCAATGA TAAGGGGAGAGAGCATGTG CGAGCAGCAC 22753 180 4.21e-05 CGACCGAGAG GAAGGAATGGAGGCACCGG CTGCTGCGTA 13149 445 4.21e-05 CTCACCACTG ACAGCAAAGAAGTCAGGTC GCTATCGCAG 35342 403 4.60e-05 GGTAGCCCCT GATGAAAATTCGTCAAATT AGTTTGTGGA 2984 295 5.02e-05 AGATACTGCA AGAGAGGGGGAAGGATGTC GTCGGAGAGT bd1799 182 5.95e-05 GCCCCATTTC GACGAGGAGCCAGCGTTTC CACCAAATTC 263722 139 6.46e-05 GAGGGTGAGG AGTGGAGAGGAGTGGAGAG GAGTACACGA 23130 229 9.63e-05 TTACGAAAAG CGAGAAAAATAGTGAAAGC GCTGAAATAA 1778 50 1.30e-04 CTCTGAACCA TTGCAAGAGTAATCGCATC AGCGTTCACT 36273 247 2.12e-04 GCCATGGTTG AGAGAGGATGGTGCGAAGG CCTGGGTGTT 268872 350 2.12e-04 GGGAGGCGAG TGCGAAGAGTGTTGGGCGC GCCGTCGGCT 262521 301 2.27e-04 GTTCCTGTCC GACGAGAGGGAGTCGACGG TAGTTCGTAG 25470 54 2.27e-04 TCTGGCGCTG GTGGAAAAGGCGACGGCGA AGGAGCGACG 4755 67 2.75e-04 TCTTGTCTCC GATGAGAAGAAGAAATTGA GTTGGATTTG 9633 239 6.14e-04 AATACGACAG CTGGCAGAGTGAGAGACTG TCTGTGAGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3719 3.5e-08 76_[+3]_405 11102 1.2e-07 151_[+3]_330 21346 3.1e-07 248_[+3]_233 bd857 5e-07 16_[+3]_81 6648 6.9e-07 103_[+3]_378 36511 1.3e-06 391_[+3]_90 3487 1.3e-06 375_[+3]_106 4290 2.5e-06 243_[+3]_238 24355 3.3e-06 385_[+3]_96 32399 3.7e-06 60_[+3]_421 4066 4.8e-06 442_[+3]_39 20639 7.6e-06 194_[+3]_287 bd1845 9.5e-06 141_[+3]_340 31076 1.3e-05 13_[+3]_468 261260 1.3e-05 191_[+3]_290 3601 1.6e-05 202_[+3]_279 5266 2.2e-05 208_[+3]_273 4555 2.7e-05 167_[+3]_314 1268 2.7e-05 258_[+3]_223 11205 2.9e-05 114_[+3]_367 264282 3.2e-05 53_[+3]_428 22753 4.2e-05 179_[+3]_302 13149 4.2e-05 444_[+3]_37 35342 4.6e-05 402_[+3]_79 2984 5e-05 294_[+3]_187 bd1799 5.9e-05 181_[+3]_300 263722 6.5e-05 138_[+3]_343 23130 9.6e-05 228_[+3]_253 1778 0.00013 49_[+3]_432 36273 0.00021 246_[+3]_235 268872 0.00021 349_[+3]_132 262521 0.00023 300_[+3]_181 25470 0.00023 53_[+3]_428 4755 0.00027 66_[+3]_415 9633 0.00061 238_[+3]_243 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=35 3719 ( 77) GGAGAAGAGACATCACTTC 1 11102 ( 152) GGAGCAGAGAATTCGTCTC 1 21346 ( 249) GATGGAGAGGGGTGATTTC 1 bd857 ( 17) GAAGAAGAGGCAGCATCAC 1 6648 ( 104) CATGGAGAGAAGGGATATC 1 36511 ( 392) AGAGGAGAGAGGGCGTCTG 1 3487 ( 376) GGAGGAGAGGCGTCGATTT 1 4290 ( 244) GAAGGAAAGAAGTAAGATG 1 24355 ( 386) AAGGGAGAGAAGTCACTTT 1 32399 ( 61) GTTGAAGAGAAATGGTCTT 1 4066 ( 443) GGAGAAAATTATGCATGTC 1 20639 ( 195) GTTGAAAAGGAATCACAAC 1 bd1845 ( 142) GGGGAAGATGATGGGCTTC 1 31076 ( 14) GATGCAGAGAGTGGAGGTC 1 261260 ( 192) CAAGAAGAATAAGCGCTTC 1 3601 ( 203) GAAGCGAAGGATTGATATT 1 5266 ( 209) GAAGGAGAGGACGGGGATA 1 4555 ( 168) AGGGGAGAGAGGGCGCAGG 1 1268 ( 259) CAACAAAAGGATTCATTTA 1 11205 ( 115) GAACAAAAGACAACAGTTC 1 264282 ( 54) TAAGGGGAGAGAGCATGTG 1 22753 ( 180) GAAGGAATGGAGGCACCGG 1 13149 ( 445) ACAGCAAAGAAGTCAGGTC 1 35342 ( 403) GATGAAAATTCGTCAAATT 1 2984 ( 295) AGAGAGGGGGAAGGATGTC 1 bd1799 ( 182) GACGAGGAGCCAGCGTTTC 1 263722 ( 139) AGTGGAGAGGAGTGGAGAG 1 23130 ( 229) CGAGAAAAATAGTGAAAGC 1 1778 ( 50) TTGCAAGAGTAATCGCATC 1 36273 ( 247) AGAGAGGATGGTGCGAAGG 1 268872 ( 350) TGCGAAGAGTGTTGGGCGC 1 262521 ( 301) GACGAGAGGGAGTCGACGG 1 25470 ( 54) GTGGAAAAGGCGACGGCGA 1 4755 ( 67) GATGAGAAGAAGAAATTGA 1 9633 ( 239) CTGGCAGAGTGAGAGACTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 16486 bayes= 8.8766 E= 5.1e-003 -32 -72 118 -161 96 -304 44 -87 104 -146 -56 -19 -1177 -146 186 -1177 112 -72 32 -1177 168 -1177 -34 -1177 57 -1177 132 -1177 187 -1177 -214 -319 -213 -1177 171 -119 57 -304 66 -39 119 -24 -14 -1177 33 -304 76 -19 -154 -1177 76 89 -154 134 32 -1177 112 -1177 86 -1177 -32 -5 -34 51 19 12 -56 13 -154 -1177 -14 139 -113 104 3 -87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 35 E= 5.1e-003 0.200000 0.142857 0.571429 0.085714 0.485714 0.028571 0.342857 0.142857 0.514286 0.085714 0.171429 0.228571 0.000000 0.085714 0.914286 0.000000 0.542857 0.142857 0.314286 0.000000 0.800000 0.000000 0.200000 0.000000 0.371429 0.000000 0.628571 0.000000 0.914286 0.000000 0.057143 0.028571 0.057143 0.000000 0.828571 0.114286 0.371429 0.028571 0.400000 0.200000 0.571429 0.200000 0.228571 0.000000 0.314286 0.028571 0.428571 0.228571 0.085714 0.000000 0.428571 0.485714 0.085714 0.600000 0.314286 0.000000 0.542857 0.000000 0.457143 0.000000 0.200000 0.228571 0.200000 0.371429 0.285714 0.257143 0.171429 0.285714 0.085714 0.000000 0.228571 0.685714 0.114286 0.485714 0.257143 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][AG][AT]G[AG][AG][GA]AG[GAT][AGC][GAT][TG][CG][AG][TCAG][ATC][TG][CG] -------------------------------------------------------------------------------- Time 31.99 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11102 6.27e-09 151_[+3(1.23e-07)]_14_\ [+1(3.14e-07)]_17_[+2(4.44e-06)]_257 11205 1.02e-08 22_[+2(1.79e-05)]_71_[+3(2.92e-05)]_\ 95_[+1(5.61e-10)]_251 1268 3.14e-07 200_[+2(1.51e-05)]_37_\ [+3(2.66e-05)]_23_[+1(3.09e-08)]_115_[+1(4.23e-05)]_43 13149 6.07e-04 114_[+1(3.20e-05)]_183_\ [+2(5.06e-05)]_105_[+3(4.21e-05)]_37 1778 2.70e-05 244_[+2(1.65e-05)]_152_\ [+1(8.69e-07)]_62 20639 2.75e-09 95_[+2(4.56e-08)]_78_[+3(7.62e-06)]_\ 238_[+1(6.45e-05)]_7_[+1(2.02e-07)] 21346 6.74e-05 44_[+2(1.79e-05)]_183_\ [+3(3.05e-07)]_233 22753 1.01e-04 143_[+1(5.28e-06)]_15_\ [+3(4.21e-05)]_42_[+2(3.74e-05)]_239 23130 3.68e-05 63_[+2(3.06e-07)]_144_\ [+3(9.63e-05)]_44_[+1(9.06e-05)]_188 24355 1.83e-07 241_[+2(1.65e-05)]_123_\ [+3(3.27e-06)]_19_[+1(1.26e-07)]_56 25470 1.03e-06 160_[+2(1.90e-06)]_298_\ [+1(1.12e-07)] 261260 1.57e-05 11_[+1(6.01e-08)]_159_\ [+3(1.32e-05)]_290 262521 1.09e-07 237_[+2(2.03e-07)]_181_\ [+1(6.78e-05)]_15_[+1(8.81e-08)]_4 263722 4.30e-04 138_[+3(6.46e-05)]_14_\ [+2(3.49e-07)]_28_[+2(7.25e-05)]_259 264282 9.30e-04 53_[+3(3.21e-05)]_128_\ [+2(4.01e-06)]_279 268872 4.37e-04 374_[+2(2.72e-05)]_63_\ [+1(8.24e-06)]_21 2984 5.90e-03 255_[+2(1.95e-05)]_18_\ [+3(5.02e-05)]_187 31076 2.83e-06 13_[+3(1.32e-05)]_72_[+2(2.51e-05)]_\ 309_[+1(4.31e-07)]_45 32399 6.88e-05 60_[+3(3.72e-06)]_292_\ [+2(3.62e-06)]_108 3487 1.11e-06 248_[+2(8.77e-06)]_[+2(8.33e-05)]_\ 30_[+2(4.70e-05)]_34_[+3(1.26e-06)]_65_[+1(4.52e-06)]_20 35342 2.74e-04 251_[+1(1.43e-05)]_20_\ [+2(4.03e-05)]_89_[+3(4.60e-05)]_79 3601 4.97e-07 136_[+2(7.30e-08)]_63_\ [+2(1.51e-05)]_215_[+1(1.74e-05)]_23 36273 4.59e-08 203_[+2(6.62e-07)]_230_\ [+1(1.12e-08)]_[+1(6.13e-05)]_4 36511 3.21e-09 300_[+2(5.84e-07)]_70_\ [+3(1.26e-06)]_66_[+1(1.12e-07)]_3 3719 1.83e-08 76_[+3(3.53e-08)]_122_\ [+3(7.61e-05)]_[+2(6.60e-06)]_159_[+1(2.35e-06)]_63 4066 4.40e-04 238_[+2(5.42e-06)]_183_\ [+3(4.76e-06)]_39 4290 8.48e-05 243_[+3(2.53e-06)]_54_\ [+2(1.70e-06)]_26_[+2(1.65e-05)]_52_[+2(7.78e-05)]_43 4555 1.60e-05 1_[+2(4.35e-05)]_145_[+3(2.66e-05)]_\ 238_[+1(8.69e-07)]_55 4755 1.11e-04 300_[+2(1.65e-05)]_5_[+1(2.16e-06)]_\ 153 5266 2.54e-05 70_[+2(6.60e-06)]_117_\ [+3(2.19e-05)]_122_[+1(1.17e-05)]_130 6648 4.64e-05 31_[+2(3.62e-06)]_51_[+3(6.93e-07)]_\ 378 9633 1.65e-03 136_[+1(6.62e-06)]_193_\ [+2(6.30e-05)]_129 bd1799 1.67e-03 181_[+3(5.95e-05)]_12_\ [+1(1.81e-06)]_267 bd1845 4.36e-03 141_[+3(9.54e-06)]_231_\ [+2(4.03e-05)]_88 bd857 1.64e-07 16_[+3(5.04e-07)]_19_[+2(2.67e-07)]_\ 41 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************