******************************************************************************** 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/399/399.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1010 1.0000 500 10379 1.0000 500 10440 1.0000 500 10860 1.0000 500 10878 1.0000 500 11848 1.0000 500 14315 1.0000 500 1597 1.0000 500 1638 1.0000 500 1687 1.0000 500 16961 1.0000 500 20944 1.0000 500 2097 1.0000 500 21119 1.0000 500 2273 1.0000 500 24114 1.0000 500 25051 1.0000 500 25509 1.0000 500 260965 1.0000 500 261589 1.0000 500 31126 1.0000 500 3242 1.0000 500 3439 1.0000 500 34594 1.0000 500 36502 1.0000 500 4481 1.0000 500 4482 1.0000 500 4565 1.0000 500 5285 1.0000 500 7935 1.0000 500 8813 1.0000 500 9111 1.0000 500 9174 1.0000 500 9275 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/399/399.seqs.fa -oc motifs/399 -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= 34 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= 17000 N= 34 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.265 C 0.227 G 0.238 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.265 C 0.227 G 0.238 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 17 sites = 15 llr = 192 E-value = 3.9e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1::1:1:143:2::2:: pos.-specific C :3:::12:::22151:1 probability G :73:a3:93:8145:19 matrix T 9179:58:37:55:79: bits 2.1 * 1.9 * 1.7 * * 1.5 * * * * Relative 1.3 * ** ** * ** Entropy 1.1 * *** ** ** * ** (18.4 bits) 0.9 ***** ** ** * ** 0.6 ***** ** ** ***** 0.4 *********** ***** 0.2 ***************** 0.0 ----------------- Multilevel TGTTGTTGATGTTGTTG consensus CG GC TACAGCA sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------- 8813 219 1.87e-10 TGGGTAATAC TGTTGTTGATGTTGTTG ATATTTCTGT 25051 290 5.55e-10 TTTGATGATT TGTTGTTGTTGTTGTTG TAGTAGTTGT 10860 127 9.03e-10 ACTCTCTGGA TGTTGTTGGTGTTGTTG TCTGGTGTAT 25509 102 5.61e-08 CGTCTTGCGG TGTTGTTGTTGAGGATG CATCGGCGTT 10379 307 2.06e-07 CCTTTTATAT TGTTGCTGTTGCCGTTG AAAACCCTCT 7935 114 5.06e-07 ACCGTACAAC TCTTGTTGTAGCTCCTG AAACGGCATG 11848 140 5.56e-07 ACGGTATGTT TGTAGCTGGTGCTCTTG GCATTTGTGT 36502 170 7.24e-07 AAGACCCCAT TGTTGGCGAAGGGCTTG TTATCAAGCG 260965 205 1.01e-06 CGTGCGGTAT TGTTGTTGATGAGCATC ACCATTATCA 3242 202 2.16e-06 CCGTGGTACT TCTTGATGGTCTCCTTG ATGGTGTGTA 1010 294 2.16e-06 ATTTTGACCC TCGTGGTATTGTTCATG TGTATTCACT 3439 385 2.83e-06 CACTGAGTGT TCGTGGCGAAGTGCTGG TTGACTTGCG 2097 308 3.87e-06 GAAGAGGAGG AGGTGTTGAACAGGTTG TCTCCAATTG 10878 260 4.63e-06 AAAGAAGTAG TGGAGGTGGTGTGGCGG AAGTGGTCGC 10440 186 7.53e-06 ATATTCATTC TTTTGTCAAACTTGTTG ATTCAAAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8813 1.9e-10 218_[+1]_265 25051 5.5e-10 289_[+1]_194 10860 9e-10 126_[+1]_357 25509 5.6e-08 101_[+1]_382 10379 2.1e-07 306_[+1]_177 7935 5.1e-07 113_[+1]_370 11848 5.6e-07 139_[+1]_344 36502 7.2e-07 169_[+1]_314 260965 1e-06 204_[+1]_279 3242 2.2e-06 201_[+1]_282 1010 2.2e-06 293_[+1]_190 3439 2.8e-06 384_[+1]_99 2097 3.9e-06 307_[+1]_176 10878 4.6e-06 259_[+1]_224 10440 7.5e-06 185_[+1]_298 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=17 seqs=15 8813 ( 219) TGTTGTTGATGTTGTTG 1 25051 ( 290) TGTTGTTGTTGTTGTTG 1 10860 ( 127) TGTTGTTGGTGTTGTTG 1 25509 ( 102) TGTTGTTGTTGAGGATG 1 10379 ( 307) TGTTGCTGTTGCCGTTG 1 7935 ( 114) TCTTGTTGTAGCTCCTG 1 11848 ( 140) TGTAGCTGGTGCTCTTG 1 36502 ( 170) TGTTGGCGAAGGGCTTG 1 260965 ( 205) TGTTGTTGATGAGCATC 1 3242 ( 202) TCTTGATGGTCTCCTTG 1 1010 ( 294) TCGTGGTATTGTTCATG 1 3439 ( 385) TCGTGGCGAAGTGCTGG 1 2097 ( 308) AGGTGTTGAACAGGTTG 1 10878 ( 260) TGGAGGTGGTGTGGCGG 1 10440 ( 186) TTTTGTCAAACTTGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 17 n= 16456 bayes= 10.7728 E= 3.9e-003 -199 -1055 -1055 179 -1055 23 148 -201 -1055 -1055 16 144 -99 -1055 -1055 168 -1055 -1055 207 -1055 -199 -77 16 98 -1055 -18 -1055 157 -99 -1055 186 -1055 59 -1055 16 30 33 -1055 -1055 130 -1055 -18 175 -1055 -41 -18 -183 98 -1055 -77 75 79 -1055 104 116 -1055 -41 -77 -1055 130 -1055 -1055 -84 168 -1055 -177 197 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 17 nsites= 15 E= 3.9e-003 0.066667 0.000000 0.000000 0.933333 0.000000 0.266667 0.666667 0.066667 0.000000 0.000000 0.266667 0.733333 0.133333 0.000000 0.000000 0.866667 0.000000 0.000000 1.000000 0.000000 0.066667 0.133333 0.266667 0.533333 0.000000 0.200000 0.000000 0.800000 0.133333 0.000000 0.866667 0.000000 0.400000 0.000000 0.266667 0.333333 0.333333 0.000000 0.000000 0.666667 0.000000 0.200000 0.800000 0.000000 0.200000 0.200000 0.066667 0.533333 0.000000 0.133333 0.400000 0.466667 0.000000 0.466667 0.533333 0.000000 0.200000 0.133333 0.000000 0.666667 0.000000 0.000000 0.133333 0.866667 0.000000 0.066667 0.933333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[GC][TG]TG[TG][TC]G[ATG][TA][GC][TAC][TG][GC][TA]TG -------------------------------------------------------------------------------- Time 10.24 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 34 llr = 316 E-value = 1.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3:41:391285741426336 pos.-specific C 23123:3:111::2::1::1: probability G 516:1a3:7615316641563 matrix T 34345:111:::1341222:2 bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * Entropy 1.1 * * (13.4 bits) 0.9 * * **** * 0.6 * * * ****** ** * * 0.4 * * * ****** ** **** 0.2 ************* ******* 0.0 --------------------- Multilevel GTGTTGCAGGAGAAGGGAGGA consensus TATAC A A AGTTAATAAG sequence C G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 16961 101 1.68e-11 TGATGGATTG GAGTTGGAGGAAAAGGGAGGA GGTGTACGAG 10860 396 2.64e-08 GGCGGTGGTG GTGTTGCAGGAGGAGGAGGGA AGCATGACGT 4565 399 5.40e-07 GTTCGTTGTT GCTTTGCAGCAAGAGAGAGAA GAATTGTCCC 9111 241 6.23e-07 GAAGGAGTAA CGGTCGCAGGAGACGAGAAGA CACAAGGCTT 4481 53 1.41e-06 GTGGTTCTGT GTGACGAAGGCGAAGACAGAA GCAATGTGCA 1010 51 2.63e-06 TTTGCACGGA GACTTGCAGGGAACTGGAGAG AGCACAACTA 31126 146 2.97e-06 ATCGTGGAGA TTGGAGCAGGAGATGGGATGA TGTAGACAAC 4482 267 6.61e-06 TCGACTGCGA GAGTTGTAGGGAAGGAGAGCG AACAACTTGG 260965 73 6.61e-06 AACTGCTTCC TTGACGTACGAAGAGGCAGGA TCATACCCTT 25051 197 6.61e-06 GTGACAGGTG GTGTTGGAGGGGAGAGAATGA AGGATGGATA 24114 309 6.61e-06 GAAAGGAACG TTGTCGAAGAAGAGGAGGAAA CCAACACAGC 3439 67 7.37e-06 AACTGTGGTG GCTTCGGAGGGAAAGACTGGG GGGTTGGACG 11848 101 7.37e-06 ATACTAGTTG GAGACGAAGGATATTGAAAGT GTGAGTGGAC 2097 181 8.20e-06 TATTGATGTG TTGATGAAGGAGGTTGTTTAG ATGCTTGGGT 8813 280 1.01e-05 TACCAAGCGT TTGATGGATCAAATTGGAAAG GGTTTTGCCA 7935 178 1.24e-05 TAGTATTGAT GCCATGGATGAGGTGGAATGG GTAGAGTGAA 21119 207 2.23e-05 ACTAAGAGGG CCGATGCATAAGATTGATTGA TATCTTGGCT 2273 396 2.69e-05 GCTTCCGTTC CAAAGGCAGGAGGTGGGAAGT ACTAATTATT 1687 455 2.69e-05 AATGTCGTCC GCTATGGAGAAAAAAAGAAAT ATAACACCAC 10878 350 2.69e-05 ATCTAAACAA GTGTTGTAGAAATCTAAAAGA CAAAACCACT 9275 110 2.94e-05 AAAAGTGGGT GGGCGGAAAGAGAGTAAAGGA GGCAGCATAT 34594 274 3.84e-05 ATTTTCTACA GCGACGCAAGAAACTTTGGGA CATTACGCTT 25509 236 4.19e-05 GCTTCTATTT TCTTTGATGAGGAATGGAGGG TGTGTTTTGT 1638 240 4.57e-05 CACTGAAAAG TACCAGCAGCAGATGGGTGGT GGCGCCTGGC 1597 431 4.57e-05 GGAGAAAGTG TAGCGGCAGCAGTAGGTAGAG CGAAGGAATT 3242 436 4.97e-05 CGTCCATTTT GACATGAAAGAAGAGACTGGT GTGAAATTTT 10440 306 4.97e-05 TAGTAGTTTA TTTAAGGACGAAACGGTAAGG GCTCGTCAAC 36502 340 5.87e-05 GGCAAGACAT CCTTTGAAGGTGAAGGCGGAA CTGACGCCGA 14315 275 5.87e-05 AACACCTCCC CATTGGTAGACAATGGGAAGA TTGATGTTGT 9174 200 7.48e-05 AAATCAGCGT GTGACGAATGAAGATGACGCA AGAAGTTCGT 10379 468 7.48e-05 AAGAGCAGAC TTTCGGGAGGAAAGTTTATGA GTGACGGCAG 261589 21 1.19e-04 GGCATTGGCT GAGTTGGAGAAGGTTCGTTCA GCAGCACCAC 20944 437 1.19e-04 AAAAACCGAA CAGCCGAAAGAGAATATTAAT AGGCCTTGAT 5285 358 2.38e-04 CTGAATCTCA TCTCTGCTGCAAACGATAACA CCCATCAAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16961 1.7e-11 100_[+2]_379 10860 2.6e-08 395_[+2]_84 4565 5.4e-07 398_[+2]_81 9111 6.2e-07 240_[+2]_239 4481 1.4e-06 52_[+2]_427 1010 2.6e-06 50_[+2]_429 31126 3e-06 145_[+2]_334 4482 6.6e-06 266_[+2]_213 260965 6.6e-06 72_[+2]_407 25051 6.6e-06 196_[+2]_283 24114 6.6e-06 308_[+2]_171 3439 7.4e-06 66_[+2]_413 11848 7.4e-06 100_[+2]_379 2097 8.2e-06 180_[+2]_299 8813 1e-05 279_[+2]_200 7935 1.2e-05 177_[+2]_302 21119 2.2e-05 206_[+2]_273 2273 2.7e-05 395_[+2]_84 1687 2.7e-05 454_[+2]_25 10878 2.7e-05 349_[+2]_130 9275 2.9e-05 109_[+2]_370 34594 3.8e-05 273_[+2]_206 25509 4.2e-05 235_[+2]_244 1638 4.6e-05 239_[+2]_240 1597 4.6e-05 430_[+2]_49 3242 5e-05 435_[+2]_44 10440 5e-05 305_[+2]_174 36502 5.9e-05 339_[+2]_140 14315 5.9e-05 274_[+2]_205 9174 7.5e-05 199_[+2]_280 10379 7.5e-05 467_[+2]_12 261589 0.00012 20_[+2]_459 20944 0.00012 436_[+2]_43 5285 0.00024 357_[+2]_122 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=34 16961 ( 101) GAGTTGGAGGAAAAGGGAGGA 1 10860 ( 396) GTGTTGCAGGAGGAGGAGGGA 1 4565 ( 399) GCTTTGCAGCAAGAGAGAGAA 1 9111 ( 241) CGGTCGCAGGAGACGAGAAGA 1 4481 ( 53) GTGACGAAGGCGAAGACAGAA 1 1010 ( 51) GACTTGCAGGGAACTGGAGAG 1 31126 ( 146) TTGGAGCAGGAGATGGGATGA 1 4482 ( 267) GAGTTGTAGGGAAGGAGAGCG 1 260965 ( 73) TTGACGTACGAAGAGGCAGGA 1 25051 ( 197) GTGTTGGAGGGGAGAGAATGA 1 24114 ( 309) TTGTCGAAGAAGAGGAGGAAA 1 3439 ( 67) GCTTCGGAGGGAAAGACTGGG 1 11848 ( 101) GAGACGAAGGATATTGAAAGT 1 2097 ( 181) TTGATGAAGGAGGTTGTTTAG 1 8813 ( 280) TTGATGGATCAAATTGGAAAG 1 7935 ( 178) GCCATGGATGAGGTGGAATGG 1 21119 ( 207) CCGATGCATAAGATTGATTGA 1 2273 ( 396) CAAAGGCAGGAGGTGGGAAGT 1 1687 ( 455) GCTATGGAGAAAAAAAGAAAT 1 10878 ( 350) GTGTTGTAGAAATCTAAAAGA 1 9275 ( 110) GGGCGGAAAGAGAGTAAAGGA 1 34594 ( 274) GCGACGCAAGAAACTTTGGGA 1 25509 ( 236) TCTTTGATGAGGAATGGAGGG 1 1638 ( 240) TACCAGCAGCAGATGGGTGGT 1 1597 ( 431) TAGCGGCAGCAGTAGGTAGAG 1 3242 ( 436) GACATGAAAGAAGAGACTGGT 1 10440 ( 306) TTTAAGGACGAAACGGTAAGG 1 36502 ( 340) CCTTTGAAGGTGAAGGCGGAA 1 14315 ( 275) CATTGGTAGACAATGGGAAGA 1 9174 ( 200) GTGACGAATGAAGATGACGCA 1 10379 ( 468) TTTCGGGAGGAAAGTTTATGA 1 261589 ( 21) GAGTTGGAGAAGGTTCGTTCA 1 20944 ( 437) CAGCCGAAAGAGAATATTAAT 1 5285 ( 358) TCTCTGCTGCAAACGATAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16320 bayes= 8.97356 E= 1.6e-001 -1173 -36 107 26 29 22 -202 39 -317 -95 130 -3 53 -36 -301 61 -159 22 -70 89 -1173 -1173 207 -1173 15 51 15 -120 183 -1173 -1173 -220 -117 -195 157 -120 -36 -63 144 -1173 153 -195 -70 -319 83 -1173 107 -319 135 -1173 15 -220 53 -36 -70 12 -217 -1173 123 50 41 -295 123 -220 -17 -63 79 -39 129 -295 -102 -39 29 -1173 98 -39 15 -95 130 -1173 108 -1173 15 -61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 34 E= 1.6e-001 0.000000 0.176471 0.500000 0.323529 0.323529 0.264706 0.058824 0.352941 0.029412 0.117647 0.588235 0.264706 0.382353 0.176471 0.029412 0.411765 0.088235 0.264706 0.147059 0.500000 0.000000 0.000000 1.000000 0.000000 0.294118 0.323529 0.264706 0.117647 0.941176 0.000000 0.000000 0.058824 0.117647 0.058824 0.705882 0.117647 0.205882 0.147059 0.647059 0.000000 0.764706 0.058824 0.147059 0.029412 0.470588 0.000000 0.500000 0.029412 0.676471 0.000000 0.264706 0.058824 0.382353 0.176471 0.147059 0.294118 0.058824 0.000000 0.558824 0.382353 0.352941 0.029412 0.558824 0.058824 0.235294 0.147059 0.411765 0.205882 0.647059 0.029412 0.117647 0.205882 0.323529 0.000000 0.470588 0.205882 0.294118 0.117647 0.588235 0.000000 0.558824 0.000000 0.264706 0.176471 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][TAC][GT][TA][TC]G[CAG]AG[GA]A[GA][AG][AT][GT][GA][GAT][AT][GAT][GA][AG] -------------------------------------------------------------------------------- Time 20.07 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 34 llr = 317 E-value = 1.6e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 21463135143:442267:2 pos.-specific C 254317548358131842a2 probability G :2:1111:::1:::2::1:: matrix T 622:51111311534:1::6 bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * * * * (13.5 bits) 0.9 * * **** 0.6 * * ** * **** 0.4 **** ********* ***** 0.2 ******************** 0.0 -------------------- Multilevel TCAATCCACACCTATCAACT consensus ATCCA AC TA ATA CC A sequence T C CG C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 4565 103 2.67e-08 GTGGAGATGA TGCATCCACAACATGCAACT TTGAAGACGG 11848 419 8.15e-08 GACTATTGGT TCACTCAACAACTCACAACC TTGGGGGACA 2097 424 1.15e-07 TAATGTCGCC TCCCTCCCCACCGCTCCACT TCGAACACCT 10878 470 1.15e-07 CCCTGCCTAA TCCCACCACCACAATCACCC ACTGACCAAC 25051 7 2.21e-07 CCATCG TCCATTCCCACCCATCAACA ACCTCCGTAC 3439 241 4.07e-07 GGTTAGACAA ATCATCAACACCTTGCAACA CTTACTGGGC 24114 366 8.29e-07 AATCCAAGGC TCTGTCCACTCTTTTCAACT GTAGCATTAT 4482 406 1.24e-06 TTGTTTCCAT TTTATCACCCCCTTCCCACC TCACCGTAAG 36502 104 1.41e-06 CCTCCTTTGG TCCCTGCCCTCCAATACACT TCTGTGACAT 260965 479 2.07e-06 GCAAGCTACA CCACACCACCGCTATCAACA TC 31126 271 3.78e-06 TCGGACGGGA ACAACCGTCACCTTTCAACT CCACACGACG 14315 252 5.95e-06 ACAGAATGGC TGCCGCCTCTCCAAACACCT CCCCATTGGT 10440 468 6.64e-06 AGCACACACC CCACAAAACACCCAACAACT CGAAACGAAC 1010 431 7.40e-06 AAGCCAAGGA ACACACAACCACTCTACACA TTATAGATTT 9275 295 8.24e-06 AATAACAAAA ACAAACGACACTTCTCCCCT GCTCCCTCCT 21119 376 8.24e-06 TTTGCCACCC CGCAGCACCTCCTCGCCCCT TACCTTCGCC 20944 476 8.24e-06 ATAAATGCAT TGAAACACCTCTCATCAACC TCACA 9111 466 1.02e-05 ACAGAACAAC TCCAAGCTTCACAATCAACT CGCAAACAAT 10379 167 1.25e-05 CTCGACACGA TTTAGCCACTGCTTCCAACT TGTCAACCCG 10860 166 1.85e-05 TTTGATGCCA CAAATCCATCACCATCCACT GAACGGTATG 8813 43 2.24e-05 GTTTCTGGAG ATCATTATCATCATTCCACT CGCTTGGTTT 3242 92 2.70e-05 TCCCGATGGC TCCATCAATACCACACTGCT TAAGGGTCAA 261589 264 3.24e-05 AAAAATGCCC TCTATTATCTACTAAACACT ATAATGGCCT 16961 160 4.60e-05 CTGGATACTT TTCAACCCTTCATATCAACA AAGGAGATTG 1597 185 6.95e-05 TAGTTCTAAA TCTGACCACAATTTGCCGCC GAGGCGTTGG 5285 323 8.15e-05 AACGTAACAG CCACACCAAATCAATACACC CTCCCCTGAA 4481 368 9.52e-05 TCGGTCTTCG GTACTCTCCCTCTCGCCACT CGCCACTCGC 9174 349 1.19e-04 GTCTCACCGT CGTACACACATCATCCAACT TTCGTCACTC 2273 449 1.28e-04 TGGTGACAAG TAAATCTCCCCCATCCTCCT TTGACCTTCA 1638 465 1.83e-04 GCGACGATGT TGTGTTGCCTACACACACCT CATAAAACGA 25509 466 1.96e-04 CCACACGCTC ACCATGACCACCCCAAAGCA GCAGCAACAA 34594 83 2.89e-04 ACGATGGCGC ACAGGCTACAACAAACACCG ACGAAGCATC 1687 476 3.69e-04 AAAAAGAAAT ATAACACCACACTAGCAACA TCGAC 7935 285 7.16e-04 CTCAGGCTAA TTTCTCCCTTTTTTGACCCC CCTAGAGGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4565 2.7e-08 102_[+3]_378 11848 8.1e-08 418_[+3]_62 2097 1.1e-07 423_[+3]_57 10878 1.1e-07 469_[+3]_11 25051 2.2e-07 6_[+3]_474 3439 4.1e-07 240_[+3]_240 24114 8.3e-07 365_[+3]_115 4482 1.2e-06 405_[+3]_75 36502 1.4e-06 103_[+3]_377 260965 2.1e-06 478_[+3]_2 31126 3.8e-06 270_[+3]_210 14315 6e-06 251_[+3]_229 10440 6.6e-06 467_[+3]_13 1010 7.4e-06 430_[+3]_50 9275 8.2e-06 294_[+3]_186 21119 8.2e-06 375_[+3]_105 20944 8.2e-06 475_[+3]_5 9111 1e-05 465_[+3]_15 10379 1.2e-05 166_[+3]_314 10860 1.9e-05 165_[+3]_315 8813 2.2e-05 42_[+3]_438 3242 2.7e-05 91_[+3]_389 261589 3.2e-05 263_[+3]_217 16961 4.6e-05 159_[+3]_321 1597 7e-05 184_[+3]_296 5285 8.2e-05 322_[+3]_158 4481 9.5e-05 367_[+3]_113 9174 0.00012 348_[+3]_132 2273 0.00013 448_[+3]_32 1638 0.00018 464_[+3]_16 25509 0.0002 465_[+3]_15 34594 0.00029 82_[+3]_398 1687 0.00037 475_[+3]_5 7935 0.00072 284_[+3]_196 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=34 4565 ( 103) TGCATCCACAACATGCAACT 1 11848 ( 419) TCACTCAACAACTCACAACC 1 2097 ( 424) TCCCTCCCCACCGCTCCACT 1 10878 ( 470) TCCCACCACCACAATCACCC 1 25051 ( 7) TCCATTCCCACCCATCAACA 1 3439 ( 241) ATCATCAACACCTTGCAACA 1 24114 ( 366) TCTGTCCACTCTTTTCAACT 1 4482 ( 406) TTTATCACCCCCTTCCCACC 1 36502 ( 104) TCCCTGCCCTCCAATACACT 1 260965 ( 479) CCACACCACCGCTATCAACA 1 31126 ( 271) ACAACCGTCACCTTTCAACT 1 14315 ( 252) TGCCGCCTCTCCAAACACCT 1 10440 ( 468) CCACAAAACACCCAACAACT 1 1010 ( 431) ACACACAACCACTCTACACA 1 9275 ( 295) ACAAACGACACTTCTCCCCT 1 21119 ( 376) CGCAGCACCTCCTCGCCCCT 1 20944 ( 476) TGAAACACCTCTCATCAACC 1 9111 ( 466) TCCAAGCTTCACAATCAACT 1 10379 ( 167) TTTAGCCACTGCTTCCAACT 1 10860 ( 166) CAAATCCATCACCATCCACT 1 8813 ( 43) ATCATTATCATCATTCCACT 1 3242 ( 92) TCCATCAATACCACACTGCT 1 261589 ( 264) TCTATTATCTACTAAACACT 1 16961 ( 160) TTCAACCCTTCATATCAACA 1 1597 ( 185) TCTGACCACAATTTGCCGCC 1 5285 ( 323) CCACACCAAATCAATACACC 1 4481 ( 368) GTACTCTCCCTCTCGCCACT 1 9174 ( 349) CGTACACACATCATCCAACT 1 2273 ( 449) TAAATCTCCCCCATCCTCCT 1 1638 ( 465) TGTGTTGCCTACACACACCT 1 25509 ( 466) ACCATGACCACCCCAAAGCA 1 34594 ( 83) ACAGGCTACAACAAACACCG 1 1687 ( 476) ATAACACCACACTAGCAACA 1 7935 ( 285) TTTCTCCCTTTTTTGACCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 16354 bayes= 8.97657 E= 1.6e-003 -17 -36 -301 105 -217 122 -43 -20 53 75 -1173 -20 108 51 -102 -1173 15 -136 -102 89 -159 164 -143 -120 29 114 -143 -161 83 75 -1173 -88 -217 181 -1173 -88 74 22 -1173 12 29 105 -202 -88 -317 186 -1173 -88 41 -63 -301 80 64 22 -1173 26 -17 -95 -21 71 -59 186 -1173 -1173 108 75 -1173 -220 135 5 -143 -1173 -1173 214 -1173 -1173 -36 -14 -301 105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 34 E= 1.6e-003 0.235294 0.176471 0.029412 0.558824 0.058824 0.529412 0.176471 0.235294 0.382353 0.382353 0.000000 0.235294 0.558824 0.323529 0.117647 0.000000 0.294118 0.088235 0.117647 0.500000 0.088235 0.705882 0.088235 0.117647 0.323529 0.500000 0.088235 0.088235 0.470588 0.382353 0.000000 0.147059 0.058824 0.794118 0.000000 0.147059 0.441176 0.264706 0.000000 0.294118 0.323529 0.470588 0.058824 0.147059 0.029412 0.823529 0.000000 0.147059 0.352941 0.147059 0.029412 0.470588 0.411765 0.264706 0.000000 0.323529 0.235294 0.117647 0.205882 0.441176 0.176471 0.823529 0.000000 0.000000 0.558824 0.382353 0.000000 0.058824 0.676471 0.235294 0.088235 0.000000 0.000000 1.000000 0.000000 0.000000 0.205882 0.205882 0.029412 0.558824 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA][CT][ACT][AC][TA]C[CA][AC]C[ATC][CA]C[TA][ATC][TAG]C[AC][AC]C[TAC] -------------------------------------------------------------------------------- Time 29.46 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1010 9.56e-07 50_[+2(2.63e-06)]_222_\ [+1(2.16e-06)]_120_[+3(7.40e-06)]_50 10379 3.68e-06 166_[+3(1.25e-05)]_120_\ [+1(2.06e-07)]_144_[+2(7.48e-05)]_12 10440 3.57e-05 185_[+1(7.53e-06)]_103_\ [+2(4.97e-05)]_141_[+3(6.64e-06)]_13 10860 2.46e-11 126_[+1(9.03e-10)]_22_\ [+3(1.85e-05)]_210_[+2(2.64e-08)]_84 10878 3.59e-07 259_[+1(4.63e-06)]_73_\ [+2(2.69e-05)]_99_[+3(1.15e-07)]_11 11848 1.17e-08 100_[+2(7.37e-06)]_18_\ [+1(5.56e-07)]_139_[+2(6.91e-05)]_102_[+3(8.15e-08)]_62 14315 3.11e-03 251_[+3(5.95e-06)]_3_[+2(5.87e-05)]_\ 205 1597 9.27e-03 184_[+3(6.95e-05)]_226_\ [+2(4.57e-05)]_49 1638 2.45e-02 239_[+2(4.57e-05)]_240 1687 3.31e-02 454_[+2(2.69e-05)]_25 16961 1.00e-08 100_[+2(1.68e-11)]_38_\ [+3(4.60e-05)]_321 20944 5.72e-03 475_[+3(8.24e-06)]_5 2097 1.04e-07 113_[+2(9.46e-05)]_46_\ [+2(8.20e-06)]_106_[+1(3.87e-06)]_99_[+3(1.15e-07)]_4_[+3(4.22e-05)]_33 21119 1.80e-04 206_[+2(2.23e-05)]_2_[+1(8.85e-05)]_\ 129_[+3(8.24e-06)]_105 2273 2.00e-02 395_[+2(2.69e-05)]_84 24114 6.97e-05 308_[+2(6.61e-06)]_36_\ [+3(8.29e-07)]_115 25051 4.35e-11 6_[+3(2.21e-07)]_170_[+2(6.61e-06)]_\ 72_[+1(5.55e-10)]_7_[+1(2.07e-05)]_170 25509 7.76e-06 101_[+1(5.61e-08)]_117_\ [+2(4.19e-05)]_14_[+1(4.63e-06)]_213 260965 3.52e-07 72_[+2(6.61e-06)]_111_\ [+1(1.01e-06)]_257_[+3(2.07e-06)]_2 261589 1.42e-02 263_[+3(3.24e-05)]_217 31126 1.02e-04 145_[+2(2.97e-06)]_104_\ [+3(3.78e-06)]_210 3242 4.06e-05 91_[+3(2.70e-05)]_90_[+1(2.16e-06)]_\ 217_[+2(4.97e-05)]_44 3439 2.24e-07 66_[+2(7.37e-06)]_153_\ [+3(4.07e-07)]_124_[+1(2.83e-06)]_99 34594 3.03e-02 273_[+2(3.84e-05)]_206 36502 1.31e-06 103_[+3(1.41e-06)]_46_\ [+1(7.24e-07)]_153_[+2(5.87e-05)]_140 4481 1.73e-03 52_[+2(1.41e-06)]_294_\ [+3(9.52e-05)]_113 4482 7.29e-05 266_[+2(6.61e-06)]_11_\ [+2(3.84e-05)]_86_[+3(1.24e-06)]_75 4565 6.78e-07 102_[+3(2.67e-08)]_276_\ [+2(5.40e-07)]_81 5285 8.87e-02 322_[+3(8.15e-05)]_158 7935 5.24e-05 113_[+1(5.06e-07)]_47_\ [+2(1.24e-05)]_302 8813 1.72e-09 42_[+3(2.24e-05)]_156_\ [+1(1.87e-10)]_44_[+2(1.01e-05)]_200 9111 1.31e-04 240_[+2(6.23e-07)]_204_\ [+3(1.02e-05)]_15 9174 8.72e-03 199_[+2(7.48e-05)]_280 9275 3.15e-03 109_[+2(2.94e-05)]_164_\ [+3(8.24e-06)]_186 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************