******************************************************************************** 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/216/216.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 47245 1.0000 500 47328 1.0000 500 47365 1.0000 500 47422 1.0000 500 47458 1.0000 500 47489 1.0000 500 37734 1.0000 500 37964 1.0000 500 3425 1.0000 500 47967 1.0000 500 47986 1.0000 500 14767 1.0000 500 38628 1.0000 500 14981 1.0000 500 48416 1.0000 500 48911 1.0000 500 30019 1.0000 500 49149 1.0000 500 49387 1.0000 500 49534 1.0000 500 49765 1.0000 500 50157 1.0000 500 23826 1.0000 500 41259 1.0000 500 4708 1.0000 500 50336 1.0000 500 50401 1.0000 500 43859 1.0000 500 43870 1.0000 500 43897 1.0000 500 50753 1.0000 500 33266 1.0000 500 44131 1.0000 500 45712 1.0000 500 48380 1.0000 500 33499 1.0000 500 49061 1.0000 500 48967 1.0000 500 49108 1.0000 500 47246 1.0000 500 50116 1.0000 500 49166 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/216/216.seqs.fa -oc motifs/216 -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= 42 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= 21000 N= 42 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.265 C 0.237 G 0.224 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.265 C 0.237 G 0.224 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 29 llr = 275 E-value = 7.6e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 11:6:72::984 pos.-specific C 4:8:a:::7:2: probability G 1:24:1823::: matrix T 39:::2:8:1:5 bits 2.2 * 1.9 * 1.7 * 1.5 * * * Relative 1.3 ** * ** * Entropy 1.1 ** * ***** (13.7 bits) 0.9 ********** 0.6 *********** 0.4 *********** 0.2 ************ 0.0 ------------ Multilevel CTCACAGTCAAT consensus T GG T GG CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 48911 37 3.43e-07 GAGAATGGGA TTCACAGTCAAT ACCGTTGAAG 50401 432 4.23e-07 ACCGTATAAT TTCACAGTCAAA CACTTCTTCT 48416 425 6.94e-07 TCCCTGAATG CTCACAGTGAAA ACCCGAACGA 44131 355 1.02e-06 ACCGCGCTCT CTCACTGTCAAT ACTGTCATAC 50116 134 1.41e-06 GTGGTAGAAA CTCACAGGCAAA TACCAAAAGC 47328 428 2.36e-06 ACAAAAGCTG TTCACTGTCAAT TGAATCCAAC 47246 85 3.81e-06 TGGCTCTGCG TTGGCAGTCAAT ATCGATGATC 33499 291 5.10e-06 TTTTCTAACC TTCACAATCAAT AAATAGTGTG 48380 121 5.10e-06 TTCACCTAAA CTGACAGTGAAA TGAATCTGAA 37734 89 7.76e-06 ATGTCCGAGA CTCACTGTCACA TCCGTGTGTG 45712 333 1.42e-05 CCAAGCTGTG CTCGCAGTCTAA TCATGGGATT 47245 333 1.42e-05 CCAAGCTGTG CTCGCAGTCTAA TCATGGGATT 49166 308 1.56e-05 GTGAGCACCC TTCCCAGTCAAT AGTTCGGGCA 49534 196 1.56e-05 TTCCACTCGA TTCGCAGGCACA CGATTCGGTA 47458 252 1.69e-05 AGGTCGCACG GTCACGGTCAAT TACCTATATT 48967 188 2.06e-05 ATACCGCGGA CTGACAGTGACA GCTTTCCCAA 30019 324 2.72e-05 TTTTCAGATT GTCGCTGGCAAA AATACCACTA 38628 231 2.72e-05 TCGGAGTGTT TTCACTGTGACA TCACAGCTTC 47422 388 2.72e-05 ACAATCTATA TTCACGGGCAAT CGAAAGTGTT 47967 97 3.49e-05 TAGCACAGCT CTCGCTGTCAAC AGGGAGAGAA 49061 250 4.00e-05 CCATCCACCA CTGGCAATGAAT CATCCCCGCT 43897 151 4.00e-05 TGTTAGCGAG CTGGCAATGAAT TTCTGTATAC 50336 379 4.38e-05 GTGAAATCGG CTCACTGTTAAT CGTTATGCGC 49149 365 5.05e-05 TCTCTCGAGC TACACAGGGAAT TTGAGAGTTG 50157 162 5.90e-05 AGCATAACCT ATCACAGTCATT TCCGATCATA 14767 9 5.90e-05 CCTGGCGA GACGCAGGCAAA AAGGATCAAG 37964 230 6.78e-05 TTCCGCATCC ATCGCAATCACT TTTCTGTTCG 47365 97 7.27e-05 TGACAGTGAA GTGACAATGAAT ACGATCGATC 3425 135 8.80e-05 TTATGTGAGG AACGCAGTCACA TCGGGAGCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48911 3.4e-07 36_[+1]_452 50401 4.2e-07 431_[+1]_57 48416 6.9e-07 424_[+1]_64 44131 1e-06 354_[+1]_134 50116 1.4e-06 133_[+1]_355 47328 2.4e-06 427_[+1]_61 47246 3.8e-06 84_[+1]_404 33499 5.1e-06 290_[+1]_198 48380 5.1e-06 120_[+1]_368 37734 7.8e-06 88_[+1]_400 45712 1.4e-05 332_[+1]_156 47245 1.4e-05 332_[+1]_156 49166 1.6e-05 307_[+1]_181 49534 1.6e-05 195_[+1]_293 47458 1.7e-05 251_[+1]_237 48967 2.1e-05 187_[+1]_301 30019 2.7e-05 323_[+1]_165 38628 2.7e-05 230_[+1]_258 47422 2.7e-05 387_[+1]_101 47967 3.5e-05 96_[+1]_392 49061 4e-05 249_[+1]_239 43897 4e-05 150_[+1]_338 50336 4.4e-05 378_[+1]_110 49149 5e-05 364_[+1]_124 50157 5.9e-05 161_[+1]_327 14767 5.9e-05 8_[+1]_480 37964 6.8e-05 229_[+1]_259 47365 7.3e-05 96_[+1]_392 3425 8.8e-05 134_[+1]_354 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=29 48911 ( 37) TTCACAGTCAAT 1 50401 ( 432) TTCACAGTCAAA 1 48416 ( 425) CTCACAGTGAAA 1 44131 ( 355) CTCACTGTCAAT 1 50116 ( 134) CTCACAGGCAAA 1 47328 ( 428) TTCACTGTCAAT 1 47246 ( 85) TTGGCAGTCAAT 1 33499 ( 291) TTCACAATCAAT 1 48380 ( 121) CTGACAGTGAAA 1 37734 ( 89) CTCACTGTCACA 1 45712 ( 333) CTCGCAGTCTAA 1 47245 ( 333) CTCGCAGTCTAA 1 49166 ( 308) TTCCCAGTCAAT 1 49534 ( 196) TTCGCAGGCACA 1 47458 ( 252) GTCACGGTCAAT 1 48967 ( 188) CTGACAGTGACA 1 30019 ( 324) GTCGCTGGCAAA 1 38628 ( 231) TTCACTGTGACA 1 47422 ( 388) TTCACGGGCAAT 1 47967 ( 97) CTCGCTGTCAAC 1 49061 ( 250) CTGGCAATGAAT 1 43897 ( 151) CTGGCAATGAAT 1 50336 ( 379) CTCACTGTTAAT 1 49149 ( 365) TACACAGGGAAT 1 50157 ( 162) ATCACAGTCATT 1 14767 ( 9) GACGCAGGCAAA 1 37964 ( 230) ATCGCAATCACT 1 47365 ( 97) GTGACAATGAAT 1 3425 ( 135) AACGCAGTCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 20538 bayes= 10.1075 E= 7.6e-006 -136 81 -70 33 -136 -1150 -1150 171 -1150 174 -12 -1150 114 -278 76 -1150 -1150 208 -1150 -1150 138 -1150 -170 -18 -62 -1150 188 -1150 -1150 -1150 -12 154 -1150 154 30 -298 181 -1150 -1150 -199 152 -19 -1150 -298 76 -278 -1150 92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 29 E= 7.6e-006 0.103448 0.413793 0.137931 0.344828 0.103448 0.000000 0.000000 0.896552 0.000000 0.793103 0.206897 0.000000 0.586207 0.034483 0.379310 0.000000 0.000000 1.000000 0.000000 0.000000 0.689655 0.000000 0.068966 0.241379 0.172414 0.000000 0.827586 0.000000 0.000000 0.000000 0.206897 0.793103 0.000000 0.689655 0.275862 0.034483 0.931034 0.000000 0.000000 0.068966 0.758621 0.206897 0.000000 0.034483 0.448276 0.034483 0.000000 0.517241 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT]T[CG][AG]C[AT]G[TG][CG]A[AC][TA] -------------------------------------------------------------------------------- Time 14.13 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 21 llr = 245 E-value = 3.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :557:2235934394a5:49 pos.-specific C ::2165:33::2:14:162: probability G 7:3:228211737:2:1441 matrix T 35:22::2::::::::3::: bits 2.2 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * * ** ** * * * (16.9 bits) 0.9 * * ** ** * * * 0.6 ***** * *** ** * * * 0.4 ******* *** **** *** 0.2 ******* ************ 0.0 -------------------- Multilevel GAAACCGAAAGAGACAACAA consensus TTG A CC AGA A TGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 45712 2 7.75e-09 T GTAACAGTAAGCGACAACAA CGCAACCAAC 47245 15 7.75e-09 AACAATCAAT GTAACAGTAAGCGACAACAA CGCAACCAAC 14767 83 6.46e-08 CACCAGTTTC TAAACAGTCAGAGAAAAGAA AACGGTCTGT 49108 135 8.56e-08 TCCATTAGAC GAAACCGAAAAAGAGACGGA CAAGCTCTGT 49534 333 3.05e-07 GACACCCTCA GAACCCAAAAGGAAAAAGGA CGGACCGTCA 43897 59 3.43e-07 ATAATTCTAT GTAACAGCAAGTGAAATGGA TTTGACGGGG 49765 205 8.16e-07 TGCAGTCTCC TTGTGCGGCAGAGACATCGA AACGACGACC 48416 383 9.98e-07 TTGACTGCGT GAGATCGACAGCGCCATCAA ACCACTCATC 23826 5 1.33e-06 CGAT TACACCTTCAGGGACAACGA GCTGTCCAAT 14981 268 1.33e-06 TGTGTGCAGA GTACCGGAAAGCGACATCGG CATCGGTTTG 50753 217 1.93e-06 TCTCTAGCGG GTGTTGGGAAGAAACAACCA CGAGACGGAG 37734 320 2.74e-06 GCGTGGATCG TTGACAGACAAAAAAAGGAA CCAGTATCGC 47458 433 2.74e-06 CGAAATAGAT GAATGCAGGAGGAACAACGA ATTACCAGTA 50157 101 3.51e-06 ACGACCGAGT GTCACGGAGGGGGAGAACCA GAAAGTAACC 41259 87 3.81e-06 TTTTGACGTT GCAATCGCCAGAGACAACAT GCAAATATAT 4708 227 4.12e-06 AGTCATTCGT TACATCACAAAAGAAAAGCA AAGTGGATTT 30019 428 7.52e-06 CTCTGTTTTC TACAGCGCAGAAGAAAGCAA GCAAGGCTCA 48911 236 7.52e-06 GCCTTTCTTC GTGAGCGGCAGGAAAACGAG CGGACGTTCA 44131 53 8.07e-06 ACTTCGTCCG TTGCCTGAAAAGAAAAAGAA TTGTGAGGTC 38628 317 8.07e-06 CCTACCAAAC GAATCCGCGAAGACGATCGA AACCATCACA 49149 256 1.13e-05 GCTCACGATG GAAACGACAAAAGGGATCCA AGTCGAATGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45712 7.7e-09 1_[+2]_479 47245 7.7e-09 14_[+2]_466 14767 6.5e-08 82_[+2]_398 49108 8.6e-08 134_[+2]_346 49534 3.1e-07 332_[+2]_148 43897 3.4e-07 58_[+2]_422 49765 8.2e-07 204_[+2]_276 48416 1e-06 382_[+2]_98 23826 1.3e-06 4_[+2]_476 14981 1.3e-06 267_[+2]_213 50753 1.9e-06 216_[+2]_264 37734 2.7e-06 319_[+2]_161 47458 2.7e-06 432_[+2]_48 50157 3.5e-06 100_[+2]_380 41259 3.8e-06 86_[+2]_394 4708 4.1e-06 226_[+2]_254 30019 7.5e-06 427_[+2]_53 48911 7.5e-06 235_[+2]_245 44131 8.1e-06 52_[+2]_428 38628 8.1e-06 316_[+2]_164 49149 1.1e-05 255_[+2]_225 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=21 45712 ( 2) GTAACAGTAAGCGACAACAA 1 47245 ( 15) GTAACAGTAAGCGACAACAA 1 14767 ( 83) TAAACAGTCAGAGAAAAGAA 1 49108 ( 135) GAAACCGAAAAAGAGACGGA 1 49534 ( 333) GAACCCAAAAGGAAAAAGGA 1 43897 ( 59) GTAACAGCAAGTGAAATGGA 1 49765 ( 205) TTGTGCGGCAGAGACATCGA 1 48416 ( 383) GAGATCGACAGCGCCATCAA 1 23826 ( 5) TACACCTTCAGGGACAACGA 1 14981 ( 268) GTACCGGAAAGCGACATCGG 1 50753 ( 217) GTGTTGGGAAGAAACAACCA 1 37734 ( 320) TTGACAGACAAAAAAAGGAA 1 47458 ( 433) GAATGCAGGAGGAACAACGA 1 50157 ( 101) GTCACGGAGGGGGAGAACCA 1 41259 ( 87) GCAATCGCCAGAGACAACAT 1 4708 ( 227) TACATCACAAAAGAAAAGCA 1 30019 ( 428) TACAGCGCAGAAGAAAGCAA 1 48911 ( 236) GTGAGCGGCAGGAAAACGAG 1 44131 ( 53) TTGCCTGAAAAGAAAAAGAA 1 38628 ( 317) GAATCCGCGAAGACGATCGA 1 49149 ( 256) GAAACGACAAAAGGGATCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 20202 bayes= 10.2135 E= 3.4e+000 -1104 -1104 157 28 84 -231 -1104 80 98 -31 35 -1104 133 -73 -1104 -52 -1104 139 -24 -52 -16 115 -24 -252 -48 -1104 176 -252 33 27 -24 -52 98 49 -65 -1104 177 -1104 -124 -1104 33 -1104 157 -1104 69 -31 57 -252 33 -1104 157 -1104 169 -131 -223 -1104 52 86 -24 -1104 191 -1104 -1104 -1104 98 -131 -124 6 -1104 139 76 -1104 69 -31 76 -1104 169 -1104 -124 -252 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 21 E= 3.4e+000 0.000000 0.000000 0.666667 0.333333 0.476190 0.047619 0.000000 0.476190 0.523810 0.190476 0.285714 0.000000 0.666667 0.142857 0.000000 0.190476 0.000000 0.619048 0.190476 0.190476 0.238095 0.523810 0.190476 0.047619 0.190476 0.000000 0.761905 0.047619 0.333333 0.285714 0.190476 0.190476 0.523810 0.333333 0.142857 0.000000 0.904762 0.000000 0.095238 0.000000 0.333333 0.000000 0.666667 0.000000 0.428571 0.190476 0.333333 0.047619 0.333333 0.000000 0.666667 0.000000 0.857143 0.095238 0.047619 0.000000 0.380952 0.428571 0.190476 0.000000 1.000000 0.000000 0.000000 0.000000 0.523810 0.095238 0.095238 0.285714 0.000000 0.619048 0.380952 0.000000 0.428571 0.190476 0.380952 0.000000 0.857143 0.000000 0.095238 0.047619 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][AT][AG]AC[CA]G[AC][AC]A[GA][AG][GA]A[CA]A[AT][CG][AG]A -------------------------------------------------------------------------------- Time 29.03 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 15 llr = 207 E-value = 1.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::::5:3:32531251:: pos.-specific C 55:13:6:7::181::53::6 probability G :2536:4:::3::15:118:2 matrix T 53571a:53775:2292:1a2 bits 2.2 1.9 * * 1.7 * * 1.5 * * Relative 1.3 * * * * ** Entropy 1.1 * * ** *** * * ** (19.9 bits) 0.9 * ********* * * ** 0.6 * ********* * ** **** 0.4 ************* ** **** 0.2 ********************* 0.0 --------------------- Multilevel CCGTGTCTCTTTCAGTCAGTC consensus TTTGC GATAGAATA AC G sequence G T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 45712 218 2.91e-11 TTTTTTGGCT CCGTGTCACATTCAGTCAGTC GGTCAGTCAG 47245 226 2.91e-11 TTTTTTGGCT CCGTGTCACATTCAGTCAGTC AGTCATATGG 48911 123 3.17e-09 ATCCGCGTCG TTTGGTCTCTTTCAATCCGTC AATAGACAAG 47458 322 8.10e-09 GGCCAATCAA TGGTGTCTCTTACTGTTAGTC ACTCCAAATA 37734 195 3.54e-08 TGCGTGTCTC CCGTCTGTCTTCCTGTCGGTC CGTCTGAACT 43897 432 2.34e-07 AGGCCGTATA CCTTCTCACTTTCCAAAAGTC CAGTGATTAG 3425 30 2.56e-07 TGTGGATCAT CCGTGTGTCTTTCGGTACATT ACTCTACACT 49166 181 4.99e-07 GCTTTGTTAT TTTGCTGACTTACATTTGGTC ACGTTTTTGC 49765 43 6.75e-07 TTATCGCCAT TTTTGTCTCAGTAATTAAGTG TATCAGATCT 47986 28 6.75e-07 CCATGGTGAA TTTTGTGTTTTACGATTAGTG AATTTCCTCT 50157 335 7.80e-07 TTCTAGCGGG TTGGCTCATTGAAAGTCCGTT CGAGAGTGAA 49387 189 1.33e-06 TCCCATCACG TCTCGTCTTTTACCTTGAGTC TTCGTCGTTT 43859 326 1.50e-06 AGATACTAGT CGGGGTCACAGCCAGTGATTC TGGGCGACGG 50401 124 1.79e-06 GAGGGGGAAT CGTTTTGACTGTCAAACCGTG ATTTTGCTGA 48380 143 2.00e-06 TGAATCTGAA CCGTCTGTTTGTATGTCCATT CTGGTCTGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45712 2.9e-11 217_[+3]_262 47245 2.9e-11 225_[+3]_254 48911 3.2e-09 122_[+3]_357 47458 8.1e-09 321_[+3]_158 37734 3.5e-08 194_[+3]_285 43897 2.3e-07 431_[+3]_48 3425 2.6e-07 29_[+3]_450 49166 5e-07 180_[+3]_299 49765 6.7e-07 42_[+3]_437 47986 6.7e-07 27_[+3]_452 50157 7.8e-07 334_[+3]_145 49387 1.3e-06 188_[+3]_291 43859 1.5e-06 325_[+3]_154 50401 1.8e-06 123_[+3]_356 48380 2e-06 142_[+3]_337 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=15 45712 ( 218) CCGTGTCACATTCAGTCAGTC 1 47245 ( 226) CCGTGTCACATTCAGTCAGTC 1 48911 ( 123) TTTGGTCTCTTTCAATCCGTC 1 47458 ( 322) TGGTGTCTCTTACTGTTAGTC 1 37734 ( 195) CCGTCTGTCTTCCTGTCGGTC 1 43897 ( 432) CCTTCTCACTTTCCAAAAGTC 1 3425 ( 30) CCGTGTGTCTTTCGGTACATT 1 49166 ( 181) TTTGCTGACTTACATTTGGTC 1 49765 ( 43) TTTTGTCTCAGTAATTAAGTG 1 47986 ( 28) TTTTGTGTTTTACGATTAGTG 1 50157 ( 335) TTGGCTCATTGAAAGTCCGTT 1 49387 ( 189) TCTCGTCTTTTACCTTGAGTC 1 43859 ( 326) CGGGGTCACAGCCAGTGATTC 1 50401 ( 124) CGTTTTGACTGTCAAACCGTG 1 48380 ( 143) CCGTCTGTTTGTATGTCCATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20160 bayes= 11.0659 E= 1.6e+000 -1055 117 -1055 77 -1055 98 -17 28 -1055 -1055 125 77 -1055 -183 25 128 -1055 49 142 -203 -1055 -1055 -1055 187 -1055 134 83 -1055 81 -1055 -1055 96 -1055 163 -1055 -4 1 -1055 -1055 142 -1055 -1055 57 128 33 -83 -1055 96 -41 176 -1055 -1055 101 -83 -75 -45 1 -1055 125 -45 -99 -1055 -1055 166 -41 98 -75 -45 101 49 -75 -1055 -99 -1055 183 -203 -1055 -1055 -1055 187 -1055 134 -17 -45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 15 E= 1.6e+000 0.000000 0.533333 0.000000 0.466667 0.000000 0.466667 0.200000 0.333333 0.000000 0.000000 0.533333 0.466667 0.000000 0.066667 0.266667 0.666667 0.000000 0.333333 0.600000 0.066667 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.400000 0.000000 0.466667 0.000000 0.000000 0.533333 0.000000 0.733333 0.000000 0.266667 0.266667 0.000000 0.000000 0.733333 0.000000 0.000000 0.333333 0.666667 0.333333 0.133333 0.000000 0.533333 0.200000 0.800000 0.000000 0.000000 0.533333 0.133333 0.133333 0.200000 0.266667 0.000000 0.533333 0.200000 0.133333 0.000000 0.000000 0.866667 0.200000 0.466667 0.133333 0.200000 0.533333 0.333333 0.133333 0.000000 0.133333 0.000000 0.800000 0.066667 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.200000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][CTG][GT][TG][GC]T[CG][TA][CT][TA][TG][TA][CA][AT][GAT]T[CAT][AC]GT[CGT] -------------------------------------------------------------------------------- Time 42.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47245 2.41e-13 14_[+2(7.75e-09)]_191_\ [+3(2.91e-11)]_86_[+1(1.42e-05)]_156 47328 6.86e-03 427_[+1(2.36e-06)]_61 47365 1.44e-02 96_[+1(7.27e-05)]_392 47422 7.17e-02 387_[+1(2.72e-05)]_101 47458 1.30e-08 251_[+1(1.69e-05)]_58_\ [+3(8.10e-09)]_90_[+2(2.74e-06)]_48 47489 1.41e-01 500 37734 2.48e-08 88_[+1(7.76e-06)]_94_[+3(3.54e-08)]_\ 104_[+2(2.74e-06)]_161 37964 6.44e-02 229_[+1(6.78e-05)]_259 3425 3.04e-04 29_[+3(2.56e-07)]_84_[+1(8.80e-05)]_\ 354 47967 1.56e-01 96_[+1(3.49e-05)]_392 47986 6.23e-03 27_[+3(6.75e-07)]_452 14767 9.88e-05 8_[+1(5.90e-05)]_62_[+2(6.46e-08)]_\ 398 38628 2.87e-03 230_[+1(2.72e-05)]_74_\ [+2(8.07e-06)]_164 14981 1.56e-02 267_[+2(1.33e-06)]_149_\ [+2(9.10e-05)]_44 48416 3.80e-06 382_[+2(9.98e-07)]_22_\ [+1(6.94e-07)]_64 48911 3.81e-10 36_[+1(3.43e-07)]_74_[+3(3.17e-09)]_\ 92_[+2(7.52e-06)]_245 30019 1.51e-03 323_[+1(2.72e-05)]_92_\ [+2(7.52e-06)]_53 49149 3.63e-03 255_[+2(1.13e-05)]_89_\ [+1(5.05e-05)]_124 49387 2.07e-03 188_[+3(1.33e-06)]_291 49534 3.82e-05 195_[+1(1.56e-05)]_125_\ [+2(3.05e-07)]_148 49765 1.15e-05 42_[+3(6.75e-07)]_112_\ [+2(6.69e-05)]_9_[+2(8.16e-07)]_276 50157 3.20e-06 100_[+2(3.51e-06)]_41_\ [+1(5.90e-05)]_161_[+3(7.80e-07)]_145 23826 3.60e-03 4_[+2(1.33e-06)]_476 41259 2.93e-02 86_[+2(3.81e-06)]_394 4708 5.36e-03 226_[+2(4.12e-06)]_254 50336 2.97e-02 378_[+1(4.38e-05)]_110 50401 3.22e-06 123_[+3(1.79e-06)]_287_\ [+1(4.23e-07)]_57 43859 2.70e-03 325_[+3(1.50e-06)]_154 43870 9.72e-01 500 43897 9.31e-08 58_[+2(3.43e-07)]_72_[+1(4.00e-05)]_\ 232_[+2(1.56e-05)]_17_[+3(2.34e-07)]_48 50753 1.93e-02 216_[+2(1.93e-06)]_264 33266 4.05e-01 500 44131 5.42e-05 52_[+2(8.07e-06)]_282_\ [+1(1.02e-06)]_134 45712 2.41e-13 1_[+2(7.75e-09)]_196_[+3(2.91e-11)]_\ 94_[+1(1.42e-05)]_156 48380 1.28e-06 120_[+1(5.10e-06)]_10_\ [+3(2.00e-06)]_337 33499 9.46e-05 290_[+1(5.10e-06)]_198 49061 1.67e-01 249_[+1(4.00e-05)]_239 48967 2.52e-02 187_[+1(2.06e-05)]_301 49108 3.94e-04 134_[+2(8.56e-08)]_346 47246 1.52e-02 84_[+1(3.81e-06)]_404 50116 4.33e-03 133_[+1(1.41e-06)]_249_\ [+1(1.56e-05)]_94 49166 7.11e-05 180_[+3(4.99e-07)]_106_\ [+1(1.56e-05)]_181 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************