******************************************************************************** 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/52/52.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1022 1.0000 500 13393 1.0000 500 14389 1.0000 500 15267 1.0000 500 17039 1.0000 500 17859 1.0000 500 1861 1.0000 500 20797 1.0000 500 20928 1.0000 500 20983 1.0000 500 21600 1.0000 500 21669 1.0000 500 2171 1.0000 500 22162 1.0000 500 22547 1.0000 500 2280 1.0000 500 25160 1.0000 500 25605 1.0000 500 25744 1.0000 500 262127 1.0000 500 263122 1.0000 500 26418 1.0000 500 268061 1.0000 500 268062 1.0000 500 268364 1.0000 500 26957 1.0000 500 270364 1.0000 500 27656 1.0000 500 34340 1.0000 500 34771 1.0000 500 35402 1.0000 500 35830 1.0000 500 36310 1.0000 500 4524 1.0000 500 4604 1.0000 500 55 1.0000 500 7996 1.0000 500 9466 1.0000 500 9787 1.0000 500 9921 1.0000 500 bd719 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/52/52.seqs.fa -oc motifs/52 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 41 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 20500 N= 41 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.234 G 0.237 T 0.262 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.234 G 0.237 T 0.262 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 24 llr = 317 E-value = 1.4e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :58:85:a5147:58153:: pos.-specific C 83:a:19:3531a3:93349 probability G :21::2::2131:2::2:3: matrix T 2:2:221::3:1::2::331 bits 2.1 * 1.9 * * 1.7 * ** * 1.5 * ** * * * Relative 1.3 * ** ** * ** * Entropy 1.0 * ** ** * ** * (19.1 bits) 0.8 * *** ** * ** * 0.6 * *** *** ** ** * 0.4 * *** *********** ** 0.2 ******************** 0.0 -------------------- Multilevel CAACAACAACAACAACAACC consensus C G CTC CT CTG sequence G G G G GCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 25744 478 2.58e-11 TTTATCAATA CAACAACAACAACAACAAGC AGA 22547 481 8.74e-10 CCAACTCCAA CAACAACAATCACCACCACC 4604 432 4.22e-09 GCTTCACCAA CAACAACAGCCACGACGACC CGGCCTCAGG 20797 481 6.71e-09 AATCACAAAT CATCATCAACAACAACAACC 268364 411 2.67e-08 GCAACAAAAC CAACAACAACGTCATCAACC ATCATCATCA 27656 449 6.19e-08 TTTCACTACG CGACACCACTAACAACACGC CTTCCCTCTT 268062 478 6.19e-08 ACAACTTCTA AAACAACAACCACCACACTC TAC 20928 179 7.76e-08 AGGGTGGAAG CAACAACAATGACGAAACTC GAAGAAGTGT 13393 102 7.76e-08 AGGGTGGAAG CAACAACAATGACGAAACTC GAAGAAGTGT 35402 159 1.20e-07 CAACTCCAAC CCACAACAACCACCTCCCGT ACGAGTGAGC bd719 321 2.67e-07 CGGGGTCGGC TGACAGCAAAGACAACCTGC TGTTTGATAT 26418 388 3.22e-07 CGCCGCCTCA CAACACCAACACCCACAGCC AACCCCCTCC 35830 109 5.03e-07 GTTTCACGTA CCACTTCACGAACCACCTCC CGGTTGTCTG 15267 23 5.03e-07 TCGTCCCATG CCACTTCAGCAGCAACCACC GCGAGCTTAT 4524 218 7.07e-07 TGGAGGTCGT CGACAATAGAAACAACGTGC CAATGGATAA 270364 217 7.07e-07 TGGAGGTCGT CGACAATAGAAACAACGTGC CAATGGATAA 17039 406 7.68e-07 TCTTTGAGCA CATCATCAACAACATCACTT CTCGTCTCCT 22162 453 9.77e-07 GCCCGCCACG CCACTGCACCGCCGACGTGC TCGCTCCTCA 17859 413 1.54e-06 TCGCACCTCA CTGCAACAATCGCAACAACC GACGACGACG 25160 446 2.06e-06 CTGTGTTCAC TGACAGCACCATCATCATTC AACATTAGAG 21600 116 2.53e-06 GCCACTTCCA CCTCAACGCCGCCGACCACC ACACACATCA 2280 387 3.30e-06 CAATAACTCT TCACAACAAGCAACACCTTC ACGCCGACCG 34771 75 5.10e-06 CTCTTAAACT CCGCTGCACTCACCAACCCC ACAGTCTGTT 34340 366 7.22e-06 TTATCGGCCT TATCAGCAGCGACATCGTTT AACTTTCTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25744 2.6e-11 477_[+1]_3 22547 8.7e-10 480_[+1] 4604 4.2e-09 431_[+1]_49 20797 6.7e-09 480_[+1] 268364 2.7e-08 410_[+1]_70 27656 6.2e-08 448_[+1]_32 268062 6.2e-08 477_[+1]_3 20928 7.8e-08 178_[+1]_302 13393 7.8e-08 101_[+1]_379 35402 1.2e-07 158_[+1]_322 bd719 2.7e-07 320_[+1]_160 26418 3.2e-07 387_[+1]_93 35830 5e-07 108_[+1]_372 15267 5e-07 22_[+1]_458 4524 7.1e-07 217_[+1]_263 270364 7.1e-07 216_[+1]_264 17039 7.7e-07 405_[+1]_75 22162 9.8e-07 452_[+1]_28 17859 1.5e-06 412_[+1]_68 25160 2.1e-06 445_[+1]_35 21600 2.5e-06 115_[+1]_365 2280 3.3e-06 386_[+1]_94 34771 5.1e-06 74_[+1]_406 34340 7.2e-06 365_[+1]_115 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=24 25744 ( 478) CAACAACAACAACAACAAGC 1 22547 ( 481) CAACAACAATCACCACCACC 1 4604 ( 432) CAACAACAGCCACGACGACC 1 20797 ( 481) CATCATCAACAACAACAACC 1 268364 ( 411) CAACAACAACGTCATCAACC 1 27656 ( 449) CGACACCACTAACAACACGC 1 268062 ( 478) AAACAACAACCACCACACTC 1 20928 ( 179) CAACAACAATGACGAAACTC 1 13393 ( 102) CAACAACAATGACGAAACTC 1 35402 ( 159) CCACAACAACCACCTCCCGT 1 bd719 ( 321) TGACAGCAAAGACAACCTGC 1 26418 ( 388) CAACACCAACACCCACAGCC 1 35830 ( 109) CCACTTCACGAACCACCTCC 1 15267 ( 23) CCACTTCAGCAGCAACCACC 1 4524 ( 218) CGACAATAGAAACAACGTGC 1 270364 ( 217) CGACAATAGAAACAACGTGC 1 17039 ( 406) CATCATCAACAACATCACTT 1 22162 ( 453) CCACTGCACCGCCGACGTGC 1 17859 ( 413) CTGCAACAATCGCAACAACC 1 25160 ( 446) TGACAGCACCATCATCATTC 1 21600 ( 116) CCTCAACGCCGCCGACCACC 1 2280 ( 387) TCACAACAAGCAACACCTTC 1 34771 ( 75) CCGCTGCACTCACCAACCCC 1 34340 ( 366) TATCAGCAGCGACATCGTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 19721 bayes= 10.1287 E= 1.4e-022 -267 176 -1123 -65 78 32 -19 -265 149 -1123 -151 -65 -1123 209 -1123 -1123 164 -1123 -1123 -65 102 -149 -19 -65 -1123 197 -1123 -165 185 -1123 -251 -1123 102 10 -19 -1123 -109 121 -151 -7 64 32 30 -1123 141 -90 -151 -165 -267 203 -1123 -1123 91 32 -19 -1123 157 -1123 -1123 -33 -109 190 -1123 -1123 78 51 -19 -1123 32 32 -251 35 -1123 83 30 15 -1123 190 -1123 -107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 24 E= 1.4e-022 0.041667 0.791667 0.000000 0.166667 0.458333 0.291667 0.208333 0.041667 0.750000 0.000000 0.083333 0.166667 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.541667 0.083333 0.208333 0.166667 0.000000 0.916667 0.000000 0.083333 0.958333 0.000000 0.041667 0.000000 0.541667 0.250000 0.208333 0.000000 0.125000 0.541667 0.083333 0.250000 0.416667 0.291667 0.291667 0.000000 0.708333 0.125000 0.083333 0.083333 0.041667 0.958333 0.000000 0.000000 0.500000 0.291667 0.208333 0.000000 0.791667 0.000000 0.000000 0.208333 0.125000 0.875000 0.000000 0.000000 0.458333 0.333333 0.208333 0.000000 0.333333 0.291667 0.041667 0.333333 0.000000 0.416667 0.291667 0.291667 0.000000 0.875000 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[ACG]ACA[AG]CA[ACG][CT][ACG]AC[ACG][AT]C[ACG][ATC][CGT]C -------------------------------------------------------------------------------- Time 13.41 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 33 llr = 346 E-value = 3.3e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3152:::112::322 pos.-specific C 928:861a58:86337 probability G :2:1:2:::::1::21 matrix T 13:3:29:4181443: bits 2.1 1.9 * 1.7 * 1.5 * * ** Relative 1.3 * * * ** ** Entropy 1.0 * * * ** **** (15.1 bits) 0.8 * * * ** **** * 0.6 * * ********* * 0.4 * ************ * 0.2 * ************ * 0.0 ---------------- Multilevel CACACCTCCCTCCTTC consensus T T T T TAC sequence C CA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 26418 412 2.13e-08 ACAGCCAACC CCCTCCTCCCTCCTAC GCTCTCTCCT 25744 24 2.55e-08 AACGAAGTAG CACACCTCTCTCTCTC TCTTATCACA 4524 482 3.01e-08 TCCTTCCTTG CACACCTCCCTCTTGC ACC 270364 481 3.01e-08 TCCTTCCTTG CACACCTCCCTCTTGC ACCA 25605 481 7.06e-08 GTCAGTCGTC CACTCTTCTCTCCTCC GCCC 2280 442 7.06e-08 TGCTTGTGCA CCCTCCTCTCTCTCTC TTCAAAAGCA 22162 474 5.36e-07 CCGACGTGCT CGCTCCTCACTCCCAC AACAGAGTAC 268062 38 7.48e-07 ATATCTGAAG CTCACTTCTCTCCACG TACCACGCCA 268061 441 7.48e-07 ATATCTGAAG CTCACTTCTCTCCACG TACCACGCCA 17039 255 1.45e-06 TTATCCACGC TTCGCCTCCCTCCTCC TTTCAAACCT 26957 409 1.62e-06 AAAGAAACAC CCCACGTCTCTCCTGA GGGTTATCAA 9787 446 2.51e-06 AAGGTTCATT CTCAACTCTCACTTTC ACATTTCACA 9921 395 3.10e-06 TCGTAGCCCG CAAGCCTCCCTCCCAC GTGAGTGATT 35830 477 3.10e-06 ATGAATCTAG CCCAACTCCATCCAAC ACGAGACC 35402 97 3.10e-06 GCGAGCAAAT CGGACCTCCCTCCAAC CACTTTCCCC 1022 470 4.57e-06 TCTCGTCCAT TCCTCCTCCCTGCTTC ACTTAGTCTA 9466 373 5.00e-06 CTCCAGCTTC CACGCGTCCCTCCCTA ACTTATCTTC 20928 414 8.50e-06 CCGTCCGCTG CACTCGTCTAACCTTC CGCATGCGGA 13393 337 8.50e-06 CCGTCCGCTG CACTCGTCTAACCTTC CGCATGCGGA 268364 438 9.27e-06 ACCATCATCA TCAACCTCTCTCTACC AAATTGGCCT 34771 20 1.01e-05 GTCAAACTCA TCCTCCCCCCTCTTGC TTCTGGCCTT 20797 131 1.55e-05 CACAAACTTC CTCACCTCACTTTTCG ACAGTTCCAT 15267 451 1.55e-05 CGGGTTCTTT CACAACTCTCTTCACA CAACCCAGCC 27656 479 1.68e-05 CTTCCCTCTT CGCCACTCTCTCTATC TCGCAG 2171 19 1.68e-05 ACCATCTCCA CTCACCCCCCAGCAGC ACCCTTCTCT 21600 456 1.98e-05 GCGTCCTCCA CACACTTCCCACTTTT TTCATCTTCG 55 429 2.31e-05 TCACGTGATT CTTTCTTCACTCCCCC CCACTTCTTC 263122 277 3.10e-05 CGTCCTCACT CACACCTCCAAACACC AAGCATCCGT 21669 249 3.33e-05 ATCGTTGCGA CGCACTTCCTTCTCAA ACCTTCGTTT bd719 391 4.41e-05 TGACAGCGTC CTCTCTTCACTGCCGA CGAACGACCG 1861 456 5.07e-05 TTGAAGGCTT CGCTCTTCTTTTCAAC ACATCCGACC 4604 396 5.82e-05 TAATGGAGGT CTCAACCACCTCCAAC TGGAACTGAC 22547 409 9.72e-05 ACGGCACAAC CCAACGCCTCTCTCTG CGACTACACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 26418 2.1e-08 411_[+2]_73 25744 2.6e-08 23_[+2]_461 4524 3e-08 481_[+2]_3 270364 3e-08 480_[+2]_4 25605 7.1e-08 480_[+2]_4 2280 7.1e-08 441_[+2]_43 22162 5.4e-07 473_[+2]_11 268062 7.5e-07 37_[+2]_447 268061 7.5e-07 440_[+2]_44 17039 1.5e-06 254_[+2]_230 26957 1.6e-06 408_[+2]_76 9787 2.5e-06 445_[+2]_39 9921 3.1e-06 394_[+2]_90 35830 3.1e-06 476_[+2]_8 35402 3.1e-06 96_[+2]_388 1022 4.6e-06 469_[+2]_15 9466 5e-06 372_[+2]_112 20928 8.5e-06 413_[+2]_71 13393 8.5e-06 336_[+2]_148 268364 9.3e-06 437_[+2]_47 34771 1e-05 19_[+2]_465 20797 1.6e-05 130_[+2]_354 15267 1.6e-05 450_[+2]_34 27656 1.7e-05 478_[+2]_6 2171 1.7e-05 18_[+2]_466 21600 2e-05 455_[+2]_29 55 2.3e-05 428_[+2]_56 263122 3.1e-05 276_[+2]_208 21669 3.3e-05 248_[+2]_236 bd719 4.4e-05 390_[+2]_94 1861 5.1e-05 455_[+2]_29 4604 5.8e-05 395_[+2]_89 22547 9.7e-05 408_[+2]_76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=33 26418 ( 412) CCCTCCTCCCTCCTAC 1 25744 ( 24) CACACCTCTCTCTCTC 1 4524 ( 482) CACACCTCCCTCTTGC 1 270364 ( 481) CACACCTCCCTCTTGC 1 25605 ( 481) CACTCTTCTCTCCTCC 1 2280 ( 442) CCCTCCTCTCTCTCTC 1 22162 ( 474) CGCTCCTCACTCCCAC 1 268062 ( 38) CTCACTTCTCTCCACG 1 268061 ( 441) CTCACTTCTCTCCACG 1 17039 ( 255) TTCGCCTCCCTCCTCC 1 26957 ( 409) CCCACGTCTCTCCTGA 1 9787 ( 446) CTCAACTCTCACTTTC 1 9921 ( 395) CAAGCCTCCCTCCCAC 1 35830 ( 477) CCCAACTCCATCCAAC 1 35402 ( 97) CGGACCTCCCTCCAAC 1 1022 ( 470) TCCTCCTCCCTGCTTC 1 9466 ( 373) CACGCGTCCCTCCCTA 1 20928 ( 414) CACTCGTCTAACCTTC 1 13393 ( 337) CACTCGTCTAACCTTC 1 268364 ( 438) TCAACCTCTCTCTACC 1 34771 ( 20) TCCTCCCCCCTCTTGC 1 20797 ( 131) CTCACCTCACTTTTCG 1 15267 ( 451) CACAACTCTCTTCACA 1 27656 ( 479) CGCCACTCTCTCTATC 1 2171 ( 19) CTCACCCCCCAGCAGC 1 21600 ( 456) CACACTTCCCACTTTT 1 55 ( 429) CTTTCTTCACTCCCCC 1 263122 ( 277) CACACCTCCAAACACC 1 21669 ( 249) CGCACTTCCTTCTCAA 1 bd719 ( 391) CTCTCTTCACTGCCGA 1 1861 ( 456) CGCTCTTCTTTTCAAC 1 4604 ( 396) CTCAACCACCTCCAAC 1 22547 ( 409) CCAACGCCTCTCTCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 19885 bayes= 10.578 E= 3.3e-019 -1169 191 -1169 -111 32 5 -65 6 -155 186 -297 -311 103 -295 -138 35 -81 186 -1169 -1169 -1169 137 -65 -11 -1169 -95 -1169 175 -313 205 -1169 -1169 -114 96 -1169 69 -114 181 -1169 -211 -55 -1169 -1169 164 -313 175 -138 -153 -1169 144 -1169 47 32 22 -1169 59 -14 22 -38 21 -81 157 -97 -311 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 33 E= 3.3e-019 0.000000 0.878788 0.000000 0.121212 0.333333 0.242424 0.151515 0.272727 0.090909 0.848485 0.030303 0.030303 0.545455 0.030303 0.090909 0.333333 0.151515 0.848485 0.000000 0.000000 0.000000 0.606061 0.151515 0.242424 0.000000 0.121212 0.000000 0.878788 0.030303 0.969697 0.000000 0.000000 0.121212 0.454545 0.000000 0.424242 0.121212 0.818182 0.000000 0.060606 0.181818 0.000000 0.000000 0.818182 0.030303 0.787879 0.090909 0.090909 0.000000 0.636364 0.000000 0.363636 0.333333 0.272727 0.000000 0.393939 0.242424 0.272727 0.181818 0.303030 0.151515 0.696970 0.121212 0.030303 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[ATC]C[AT]C[CT]TC[CT]CTC[CT][TAC][TCA]C -------------------------------------------------------------------------------- Time 26.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 31 llr = 342 E-value = 3.7e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3::3::15:31:54552:741 pos.-specific C 1::111:3::21:2::1:2:1 probability G 4192277:8519525148:47 matrix T 39148222225::2:442131 bits 2.1 1.9 1.7 1.5 ** * * * Relative 1.3 ** * * * Entropy 1.0 ** * * ** * (15.9 bits) 0.8 ** *** * ** * * 0.6 ** *** ** ** ** ** * 0.4 ** ****** ** ** **** 0.2 ************* ******* 0.0 --------------------- Multilevel GTGTTGGAGGTGAAGAGGAAG consensus A A C A GCATT G sequence T G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 262127 20 2.04e-09 CTCATAGTGT GTGATGGTGGTGATAATGAGG GAGGATGCGG 1861 122 8.53e-09 TCGTTGATGA ATGGTGGAGGCGACGATGATG GCTCCTGATT 9466 194 1.62e-08 CGCTGAGCCG ATGATGGATGCGAAGAGGAGG GTGAGCTTCA 35830 368 3.46e-08 GAGCTTCGTC ATGATGGAGATGAGAGTGAAG AGCAACCAGT 34771 339 4.01e-08 TCTCCCATGG TTGATGGAGGTGGTGTTTATG AAGATTTATT 34340 392 4.63e-08 GTTTAACTTT CTGTTGGAGATGGAAAAGAAG TTGGTGTAGA 2280 1 4.63e-08 . TTGTTCGAGATGAGGATGATG ATGTGCTCTC 26957 137 1.54e-07 ACTGCGAGGC GTGTGGGAGGCCGAGAGGAGG ACGAAATGGA 21600 232 4.06e-07 CATGAAAGCC ATTGTGGAGGAGGCAAGGAGG ACAAGAGAGA 9921 110 4.55e-07 GACGTTGTTT GTGCTGGCGTGGGCGAAGAGG CCGATAGGGT 15267 295 8.82e-07 AGAAGGGCGG TGGACGGAGGTGGCGTGGAAG GAAAGGGGGT 25160 56 1.48e-06 GACGGCGGCG ATGTGGTAGGCGAAGTTGAAA TAAAGTGGCG 14389 196 1.48e-06 GAGGCGTCGA GTGCTGACGAAGAAATTGAAG GAGATGAGAC 20928 205 1.64e-06 ACTCGAAGAA GTGTTCTTGGTGATATCGAAG AAGTACGTAT 13393 128 1.64e-06 ACTCGAAGAA GTGTTCTTGGTGATATCGAAG AAGTACGTAT 268061 234 2.42e-06 GACCACAACT TTGTTGGCGTTGAGGAATTGG AAGCACGATG 55 5 6.02e-06 GATA TTGCTGGAGAGGATAAGGCGA ATCCATTGGC 4604 102 7.77e-06 GTAGAGGATG ATTTGGGAGAGGAAGAGGAGA GCCGCAGTGA 21669 331 7.77e-06 AGGTTGTCTA CTGATGAAGGTGACGAGGTAC TAGTTCTCGG 4524 126 1.17e-05 TGCATCCTCG GTGGTTGTTGTGGAATTTCTG CGGGATATTT 270364 125 1.17e-05 TGCATCCTCG GTGGTTGTTGTGGAATTTCTG CGGGATATTT 268364 252 1.17e-05 GAAGTTCTTA GTGATGGATTCGGCCATGCTG CCAACACTGC 9787 103 1.60e-05 ACGAAGAGAA GCGAGGGCGAAGGAAACGAAG CATGAGTCAA 2171 268 1.73e-05 GTAAAAAACA GTGTGTGTGGGGAGGAGGTGT CCTCTGGGGA 1022 98 1.86e-05 GGCGGTGGAT GTGGCCGCTGTGGAGAAGAGT GTGAAAGTGG 20983 29 2.33e-05 GAGGTGCTGG ATAGTGACGTTGGAGTGGCGG TCCTTGTGTA 7996 54 2.50e-05 TGACCCATGA TGGTTTGCGGCGGTGGTGAAT GTGTTGATCT 26418 43 2.50e-05 GTCGGTGATC TTGTTGAAGTTAGCGTGGATA AGGTTGTGCA 25605 204 2.50e-05 TAGCATTGTG ATGATTGAGTTGAGAGGTATC GAGAGACGTC 36310 43 2.69e-05 TGGATGACGA TTGTTGTCGGAGAGAGAGGAG GCAGCTCAGG 20797 325 4.99e-05 TGGAACATCG GTTATGTCGATCGGATGGAAT GTATGCAACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262127 2e-09 19_[+3]_460 1861 8.5e-09 121_[+3]_358 9466 1.6e-08 193_[+3]_286 35830 3.5e-08 367_[+3]_112 34771 4e-08 338_[+3]_141 34340 4.6e-08 391_[+3]_88 2280 4.6e-08 [+3]_479 26957 1.5e-07 136_[+3]_343 21600 4.1e-07 231_[+3]_248 9921 4.6e-07 109_[+3]_370 15267 8.8e-07 294_[+3]_185 25160 1.5e-06 55_[+3]_424 14389 1.5e-06 195_[+3]_284 20928 1.6e-06 204_[+3]_275 13393 1.6e-06 127_[+3]_352 268061 2.4e-06 233_[+3]_246 55 6e-06 4_[+3]_475 4604 7.8e-06 101_[+3]_378 21669 7.8e-06 330_[+3]_149 4524 1.2e-05 125_[+3]_354 270364 1.2e-05 124_[+3]_355 268364 1.2e-05 251_[+3]_228 9787 1.6e-05 102_[+3]_377 2171 1.7e-05 267_[+3]_212 1022 1.9e-05 97_[+3]_382 20983 2.3e-05 28_[+3]_451 7996 2.5e-05 53_[+3]_426 26418 2.5e-05 42_[+3]_437 25605 2.5e-05 203_[+3]_276 36310 2.7e-05 42_[+3]_437 20797 5e-05 324_[+3]_155 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=31 262127 ( 20) GTGATGGTGGTGATAATGAGG 1 1861 ( 122) ATGGTGGAGGCGACGATGATG 1 9466 ( 194) ATGATGGATGCGAAGAGGAGG 1 35830 ( 368) ATGATGGAGATGAGAGTGAAG 1 34771 ( 339) TTGATGGAGGTGGTGTTTATG 1 34340 ( 392) CTGTTGGAGATGGAAAAGAAG 1 2280 ( 1) TTGTTCGAGATGAGGATGATG 1 26957 ( 137) GTGTGGGAGGCCGAGAGGAGG 1 21600 ( 232) ATTGTGGAGGAGGCAAGGAGG 1 9921 ( 110) GTGCTGGCGTGGGCGAAGAGG 1 15267 ( 295) TGGACGGAGGTGGCGTGGAAG 1 25160 ( 56) ATGTGGTAGGCGAAGTTGAAA 1 14389 ( 196) GTGCTGACGAAGAAATTGAAG 1 20928 ( 205) GTGTTCTTGGTGATATCGAAG 1 13393 ( 128) GTGTTCTTGGTGATATCGAAG 1 268061 ( 234) TTGTTGGCGTTGAGGAATTGG 1 55 ( 5) TTGCTGGAGAGGATAAGGCGA 1 4604 ( 102) ATTTGGGAGAGGAAGAGGAGA 1 21669 ( 331) CTGATGAAGGTGACGAGGTAC 1 4524 ( 126) GTGGTTGTTGTGGAATTTCTG 1 270364 ( 125) GTGGTTGTTGTGGAATTTCTG 1 268364 ( 252) GTGATGGATTCGGCCATGCTG 1 9787 ( 103) GCGAGGGCGAAGGAAACGAAG 1 2171 ( 268) GTGTGTGTGGGGAGGAGGTGT 1 1022 ( 98) GTGGCCGCTGTGGAGAAGAGT 1 20983 ( 29) ATAGTGACGTTGGAGTGGCGG 1 7996 ( 54) TGGTTTGCGGCGGTGGTGAAT 1 26418 ( 43) TTGTTGAAGTTAGCGTGGATA 1 25605 ( 204) ATGATTGAGTTGAGAGGTATC 1 36310 ( 43) TTGTTGTCGGAGAGAGAGGAG 1 20797 ( 325) GTTATGTCGATCGGATGGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19680 bayes= 10.0151 E= 3.7e-012 -5 -186 82 -2 -1160 -286 -188 178 -304 -1160 187 -144 28 -127 -29 56 -1160 -186 -56 156 -1160 -86 158 -70 -105 -1160 158 -70 95 31 -1160 -44 -1160 -1160 182 -70 -5 -1160 121 -44 -105 -27 -88 107 -304 -186 193 -1160 95 -1160 103 -1160 41 -5 -7 -44 76 -286 112 -1160 95 -1160 -88 44 -72 -127 71 44 -1160 -1160 182 -70 141 -54 -288 -144 54 -1160 58 -2 -105 -186 151 -102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 31 E= 3.7e-012 0.258065 0.064516 0.419355 0.258065 0.000000 0.032258 0.064516 0.903226 0.032258 0.000000 0.870968 0.096774 0.322581 0.096774 0.193548 0.387097 0.000000 0.064516 0.161290 0.774194 0.000000 0.129032 0.709677 0.161290 0.129032 0.000000 0.709677 0.161290 0.516129 0.290323 0.000000 0.193548 0.000000 0.000000 0.838710 0.161290 0.258065 0.000000 0.548387 0.193548 0.129032 0.193548 0.129032 0.548387 0.032258 0.064516 0.903226 0.000000 0.516129 0.000000 0.483871 0.000000 0.354839 0.225806 0.225806 0.193548 0.451613 0.032258 0.516129 0.000000 0.516129 0.000000 0.129032 0.354839 0.161290 0.096774 0.387097 0.354839 0.000000 0.000000 0.838710 0.161290 0.709677 0.161290 0.032258 0.096774 0.387097 0.000000 0.354839 0.258065 0.129032 0.064516 0.677419 0.129032 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GAT]TG[TA]TGG[AC]G[GA]TG[AG][ACG][GA][AT][GT]GA[AGT]G -------------------------------------------------------------------------------- Time 37.98 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1022 1.35e-03 97_[+3(1.86e-05)]_351_\ [+2(4.57e-06)]_15 13393 3.43e-08 101_[+1(7.76e-08)]_6_[+3(1.64e-06)]_\ 188_[+2(8.50e-06)]_54_[+1(4.80e-06)]_34_[+1(7.99e-05)]_20 14389 1.80e-02 195_[+3(1.48e-06)]_284 15267 1.86e-07 22_[+1(5.03e-07)]_252_\ [+3(8.82e-07)]_135_[+2(1.55e-05)]_8_[+1(6.53e-05)]_6 17039 2.40e-05 254_[+2(1.45e-06)]_135_\ [+1(7.68e-07)]_75 17859 3.74e-05 412_[+1(1.54e-06)]_68 1861 5.63e-06 121_[+3(8.53e-09)]_313_\ [+2(5.07e-05)]_29 20797 1.42e-07 130_[+2(1.55e-05)]_178_\ [+3(4.99e-05)]_135_[+1(6.71e-09)] 20928 3.43e-08 178_[+1(7.76e-08)]_6_[+3(1.64e-06)]_\ 188_[+2(8.50e-06)]_71 20983 7.59e-02 28_[+3(2.33e-05)]_451 21600 4.95e-07 115_[+1(2.53e-06)]_96_\ [+3(4.06e-07)]_51_[+3(1.48e-05)]_131_[+2(1.98e-05)]_29 21669 5.14e-04 248_[+2(3.33e-05)]_66_\ [+3(7.77e-06)]_149 2171 2.04e-03 18_[+2(1.68e-05)]_233_\ [+3(1.73e-05)]_212 22162 2.73e-06 452_[+1(9.77e-07)]_1_[+2(5.36e-07)]_\ 11 22547 2.29e-06 408_[+2(9.72e-05)]_56_\ [+1(8.74e-10)] 2280 4.88e-10 [+3(4.63e-08)]_365_[+1(3.30e-06)]_\ 35_[+2(7.06e-08)]_43 25160 5.75e-05 55_[+3(1.48e-06)]_313_\ [+1(4.76e-05)]_36_[+1(2.06e-06)]_35 25605 2.28e-05 203_[+3(2.50e-05)]_256_\ [+2(7.06e-08)]_4 25744 1.24e-11 23_[+2(2.55e-08)]_438_\ [+1(2.58e-11)]_3 262127 1.98e-06 19_[+3(2.04e-09)]_423_\ [+1(4.59e-05)]_17 263122 6.39e-02 276_[+2(3.10e-05)]_208 26418 6.29e-09 42_[+3(2.50e-05)]_324_\ [+1(3.22e-07)]_4_[+2(2.13e-08)]_73 268061 3.87e-05 233_[+3(2.42e-06)]_186_\ [+2(7.48e-07)]_44 268062 2.00e-06 37_[+2(7.48e-07)]_174_\ [+1(1.92e-06)]_230_[+1(6.19e-08)]_3 268364 8.46e-08 251_[+3(1.17e-05)]_138_\ [+1(2.67e-08)]_7_[+2(9.27e-06)]_47 26957 2.68e-06 136_[+3(1.54e-07)]_251_\ [+2(1.62e-06)]_76 270364 8.90e-09 124_[+3(1.17e-05)]_71_\ [+1(7.07e-07)]_244_[+2(3.01e-08)]_4 27656 6.85e-06 448_[+1(6.19e-08)]_10_\ [+2(1.68e-05)]_6 34340 8.42e-06 365_[+1(7.22e-06)]_6_[+3(4.63e-08)]_\ 88 34771 6.22e-08 19_[+2(1.01e-05)]_39_[+1(5.10e-06)]_\ 244_[+3(4.01e-08)]_8_[+3(2.20e-06)]_112 35402 1.13e-05 96_[+2(3.10e-06)]_46_[+1(1.20e-07)]_\ 322 35830 2.18e-09 58_[+3(1.48e-05)]_29_[+1(5.03e-07)]_\ 209_[+3(2.01e-05)]_9_[+3(3.46e-08)]_88_[+2(3.10e-06)]_8 36310 1.10e-01 42_[+3(2.69e-05)]_437 4524 8.90e-09 125_[+3(1.17e-05)]_71_\ [+1(7.07e-07)]_244_[+2(3.01e-08)]_3 4604 5.71e-08 101_[+3(7.77e-06)]_273_\ [+2(5.82e-05)]_20_[+1(4.22e-09)]_49 55 9.43e-04 4_[+3(6.02e-06)]_403_[+2(2.31e-05)]_\ 56 7996 1.23e-01 53_[+3(2.50e-05)]_426 9466 1.50e-06 193_[+3(1.62e-08)]_158_\ [+2(5.00e-06)]_112 9787 2.66e-04 102_[+3(1.60e-05)]_322_\ [+2(2.51e-06)]_39 9921 1.69e-05 109_[+3(4.55e-07)]_264_\ [+2(3.10e-06)]_90 bd719 2.33e-04 320_[+1(2.67e-07)]_50_\ [+2(4.41e-05)]_94 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************