******************************************************************************** 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/315/315.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42683 1.0000 500 42820 1.0000 500 42996 1.0000 500 43109 1.0000 500 46455 1.0000 500 20857 1.0000 500 46802 1.0000 500 28374 1.0000 500 47296 1.0000 500 47334 1.0000 500 47899 1.0000 500 39062 1.0000 500 43583 1.0000 500 43773 1.0000 500 49010 1.0000 500 49165 1.0000 500 30282 1.0000 500 16014 1.0000 500 49420 1.0000 500 49638 1.0000 500 40581 1.0000 500 50077 1.0000 500 16704 1.0000 500 43948 1.0000 500 3692 1.0000 500 10531 1.0000 500 50468 1.0000 500 44325 1.0000 500 33901 1.0000 500 44465 1.0000 500 2834 1.0000 500 19805 1.0000 500 3246 1.0000 500 45703 1.0000 500 45764 1.0000 500 46043 1.0000 500 43793 1.0000 500 31571 1.0000 500 48357 1.0000 500 42645 1.0000 500 44192 1.0000 500 43089 1.0000 500 44301 1.0000 500 47224 1.0000 500 48968 1.0000 500 45468 1.0000 500 44085 1.0000 500 49600 1.0000 500 49635 1.0000 500 47616 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/315/315.seqs.fa -oc motifs/315 -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= 50 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= 25000 N= 50 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.233 G 0.234 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.233 G 0.234 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 30 llr = 311 E-value = 8.8e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 6:::a:611:a4 pos.-specific C :6:4:a:::3:1 probability G 3::6:::9:5:4 matrix T 14a:::4:92:1 bits 2.1 * 1.9 * ** * 1.7 * ** * 1.5 * ** * * Relative 1.3 * ** ** * Entropy 1.1 **** ** * (15.0 bits) 0.8 ******** * 0.6 *********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACTGACAGTGAG consensus GT C T C A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 33901 72 5.90e-08 GTAAATCTGT ACTGACAGTGAG TACCGCGCAT 43583 350 5.90e-08 GGATCGAAGA ACTGACAGTGAG GACCAACCCA 47224 206 1.85e-07 TTCCAGTTTG ACTGACTGTGAG CAACGACGAT 49010 220 3.77e-07 AAATGCGTAA ATTGACAGTGAG GAGGGAATCT 43109 219 1.33e-06 TGTGAAGGAT ATTGACTGTGAA CGCTGAAACC 43793 6 1.91e-06 CTCTA GCTGACTGTGAA TCCATTCAAG 49420 249 1.91e-06 GTTGGCAGAA ACTCACAGTCAA GCAAGACACG 47899 199 1.91e-06 AAGGGATACT GTTGACAGTGAG CTGTCCTGCC 42996 464 1.91e-06 ATCACCCAAC ACTCACAGTCAA CACGGGTCTA 43773 123 2.48e-06 GGTCGAGCAG GTTGACAGTGAA GGGCTGTTTA 49638 316 4.17e-06 AATGTTAGGT ATTCACTGTCAG TCAGCCGATT 48357 68 4.54e-06 GGGGATTCTT GCTCACAGTCAA CGATGAATCC 31571 331 4.54e-06 GAGAATGATT TCTGACTGTGAG TCACTTGAAT 50468 433 5.53e-06 GGAATGTTTA TTTGACAGTGAG TGTTCGCGCA 46802 178 5.53e-06 GGAAAGGGTT TCTGACTGTGAA CATTCACAAC 48968 122 6.01e-06 ATGAATGCAT GCTCACTGTCAA TGAGCAGGGC 39062 186 6.96e-06 GGTTCATCTG ATTCACTGTTAG CCTCACTGTC 42683 339 6.96e-06 CGACATATTT ATTCACTGTTAG TACTTGTTTT 46043 402 7.58e-06 GACTGTTGTC ACTCACAGTCAC ATCGTCCAAG 19805 31 1.05e-05 CTGTCTCTTA ATTCACAGTCAC GGAGACGACG 47616 151 1.14e-05 GCTTGCGGCG GCTGACTGTGAT CTCTGGCATA 43948 311 1.14e-05 GTGAGTTCAA TCTCACTGTCAA TCGCAGGCAG 49165 276 1.60e-05 CTGTTCAAAA ATTGACAATGAA TTCGGTCCCA 42645 481 1.84e-05 ACTGCAATTC ACTGACAGATAG ACAGAAGT 44301 64 2.16e-05 GGTATGTTTT ACTGACAGATAA GAGGGTTCCC 2834 46 2.49e-05 TGTCAGATAG ACTTACAGTTAG GGATATGAAC 44465 150 4.47e-05 TATATAGAAC AGTGACAGTGAT CCATTTTCAG 45703 406 4.76e-05 CGTTTTGGAG GTTGACATTCAG GGTTTCTTCC 44325 249 5.58e-05 CTCATTTTTT GTTGACTGCCAA AATATGCTTA 49600 129 8.00e-05 TACGAGTGGT ACTCACTATTAC CCGTTCGACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 33901 5.9e-08 71_[+1]_417 43583 5.9e-08 349_[+1]_139 47224 1.8e-07 205_[+1]_283 49010 3.8e-07 219_[+1]_269 43109 1.3e-06 218_[+1]_270 43793 1.9e-06 5_[+1]_483 49420 1.9e-06 248_[+1]_240 47899 1.9e-06 198_[+1]_290 42996 1.9e-06 463_[+1]_25 43773 2.5e-06 122_[+1]_366 49638 4.2e-06 315_[+1]_173 48357 4.5e-06 67_[+1]_421 31571 4.5e-06 330_[+1]_158 50468 5.5e-06 432_[+1]_56 46802 5.5e-06 177_[+1]_311 48968 6e-06 121_[+1]_367 39062 7e-06 185_[+1]_303 42683 7e-06 338_[+1]_150 46043 7.6e-06 401_[+1]_87 19805 1e-05 30_[+1]_458 47616 1.1e-05 150_[+1]_338 43948 1.1e-05 310_[+1]_178 49165 1.6e-05 275_[+1]_213 42645 1.8e-05 480_[+1]_8 44301 2.2e-05 63_[+1]_425 2834 2.5e-05 45_[+1]_443 44465 4.5e-05 149_[+1]_339 45703 4.8e-05 405_[+1]_83 44325 5.6e-05 248_[+1]_240 49600 8e-05 128_[+1]_360 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=30 33901 ( 72) ACTGACAGTGAG 1 43583 ( 350) ACTGACAGTGAG 1 47224 ( 206) ACTGACTGTGAG 1 49010 ( 220) ATTGACAGTGAG 1 43109 ( 219) ATTGACTGTGAA 1 43793 ( 6) GCTGACTGTGAA 1 49420 ( 249) ACTCACAGTCAA 1 47899 ( 199) GTTGACAGTGAG 1 42996 ( 464) ACTCACAGTCAA 1 43773 ( 123) GTTGACAGTGAA 1 49638 ( 316) ATTCACTGTCAG 1 48357 ( 68) GCTCACAGTCAA 1 31571 ( 331) TCTGACTGTGAG 1 50468 ( 433) TTTGACAGTGAG 1 46802 ( 178) TCTGACTGTGAA 1 48968 ( 122) GCTCACTGTCAA 1 39062 ( 186) ATTCACTGTTAG 1 42683 ( 339) ATTCACTGTTAG 1 46043 ( 402) ACTCACAGTCAC 1 19805 ( 31) ATTCACAGTCAC 1 47616 ( 151) GCTGACTGTGAT 1 43948 ( 311) TCTCACTGTCAA 1 49165 ( 276) ATTGACAATGAA 1 42645 ( 481) ACTGACAGATAG 1 44301 ( 64) ACTGACAGATAA 1 2834 ( 46) ACTTACAGTTAG 1 44465 ( 150) AGTGACAGTGAT 1 45703 ( 406) GTTGACATTCAG 1 44325 ( 249) GTTGACTGCCAA 1 49600 ( 129) ACTCACTATTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 24450 bayes= 10.3438 E= 8.8e-016 116 -1155 19 -99 -1155 128 -281 60 -1155 -1155 -1155 192 -1155 65 136 -299 190 -1155 -1155 -1155 -1155 210 -1155 -1155 108 -1155 -1155 71 -201 -1155 194 -299 -201 -280 -1155 176 -1155 52 100 -40 190 -1155 -1155 -1155 58 -122 89 -199 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 30 E= 8.8e-016 0.600000 0.000000 0.266667 0.133333 0.000000 0.566667 0.033333 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.366667 0.600000 0.033333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.566667 0.000000 0.000000 0.433333 0.066667 0.000000 0.900000 0.033333 0.066667 0.033333 0.000000 0.900000 0.000000 0.333333 0.466667 0.200000 1.000000 0.000000 0.000000 0.000000 0.400000 0.100000 0.433333 0.066667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AG][CT]T[GC]AC[AT]GT[GCT]A[GA] -------------------------------------------------------------------------------- Time 18.39 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 22 llr = 268 E-value = 3.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :62381381:68674356275 pos.-specific C 212:251:5:12::6334132 probability G 8357:4611a3:41:41:6:: matrix T ::1:::::3::::1::1:::2 bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * ** * * ** * * * (17.6 bits) 0.8 * ** ** * ** * * * 0.6 ** ***** * **** *** 0.4 ** ***** ******* **** 0.2 ********************* 0.0 --------------------- Multilevel GAGGACGACGAAAACGAAGAA consensus GAA GA T GCG AACCACC sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10531 231 1.98e-09 TGACGACGAA GAGGACGACGAAGACCTCGAC CTATCGATCA 49635 372 1.73e-08 CAAATTTGAT GAGGAGGGCGAAAAACCAGCC ATTCATAGAT 16704 162 7.92e-08 TGTTCAGGGA GAAGCGGGCGAAAACGAAGAC CCATTCACCA 19805 308 1.02e-07 AGCACCAAAA GAAGACGAGGGAAACGGCGAA CTGCACACGT 42683 478 1.30e-07 CTTCTCCACA GAGAAGCACGAAGAAGCAAAA CT 39062 147 1.47e-07 CATTCCCTGC CAGGACGATGTAAACCACGAA AACGGTGCGG 48357 474 1.86e-07 GTTCCTAGTC GCCAAGGACGACGACGAAGAA TCTACC 46802 238 3.26e-07 TAGGGTCAAG GAAGACCATGGAAACGTAGAC GGAAACACTT 46043 432 3.64e-07 AGTCCAAACA GAGGCGGACGACAGAACCGCA GCTCTCCTCC 16014 342 7.47e-07 ACGTAAACTT CAGGACAAAGAAGCCAAAGAA GCCAAGGCGC 47899 61 9.07e-07 ACGACTATTG GAGGAAAACGACGGCCCAACA AACAAACGGG 45468 285 1.20e-06 TACAAGCCGA GAGGACAAAGCAGAACCAGAG CTCCGGAATG 28374 41 1.32e-06 CGAAGGCTCC GATGACGACGGAATCAGCGAT TCGTCACGAC 47224 402 1.44e-06 CAGGCAACTC GCGGACAGTGAAAACGCAAAT CGCAGCTGGT 44301 475 1.58e-06 TTTCTTTTGG GGGAAGAACGGAAAAAACACT TTCCC 45764 375 1.88e-06 TTTGAATGTT GAGGAGAAGGGCGACAAATAA TTTTGAATAA 42996 300 3.63e-06 ATATGTATTG CGCGACAAAGAAAGCAAAGCC TACGAGGAGA 42645 223 5.70e-06 TACGATTGCC CGCGAAGATGGAGAACACGCT CAAAATTATA 44465 340 6.12e-06 GTGTTGCGAC GGCCAAGACGAAAAACCACCA TGGCAAAATC 47616 201 6.57e-06 GGGCTATTTT GGAACCGACGCAGTCATAGAA AAGTACTACT 44085 28 7.56e-06 CTTCTGAACA GAAAAGGTTGACAAAGAACAA TCCAGACCAA 45703 265 8.09e-06 CTGTACGTCG GGTACCGATGAAATAGACAAA AACGGCCGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10531 2e-09 230_[+2]_249 49635 1.7e-08 371_[+2]_108 16704 7.9e-08 161_[+2]_318 19805 1e-07 307_[+2]_172 42683 1.3e-07 477_[+2]_2 39062 1.5e-07 146_[+2]_333 48357 1.9e-07 473_[+2]_6 46802 3.3e-07 237_[+2]_242 46043 3.6e-07 431_[+2]_48 16014 7.5e-07 341_[+2]_138 47899 9.1e-07 60_[+2]_419 45468 1.2e-06 284_[+2]_195 28374 1.3e-06 40_[+2]_439 47224 1.4e-06 401_[+2]_78 44301 1.6e-06 474_[+2]_5 45764 1.9e-06 374_[+2]_105 42996 3.6e-06 299_[+2]_180 42645 5.7e-06 222_[+2]_257 44465 6.1e-06 339_[+2]_140 47616 6.6e-06 200_[+2]_279 44085 7.6e-06 27_[+2]_452 45703 8.1e-06 264_[+2]_215 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=22 10531 ( 231) GAGGACGACGAAGACCTCGAC 1 49635 ( 372) GAGGAGGGCGAAAAACCAGCC 1 16704 ( 162) GAAGCGGGCGAAAACGAAGAC 1 19805 ( 308) GAAGACGAGGGAAACGGCGAA 1 42683 ( 478) GAGAAGCACGAAGAAGCAAAA 1 39062 ( 147) CAGGACGATGTAAACCACGAA 1 48357 ( 474) GCCAAGGACGACGACGAAGAA 1 46802 ( 238) GAAGACCATGGAAACGTAGAC 1 46043 ( 432) GAGGCGGACGACAGAACCGCA 1 16014 ( 342) CAGGACAAAGAAGCCAAAGAA 1 47899 ( 61) GAGGAAAACGACGGCCCAACA 1 45468 ( 285) GAGGACAAAGCAGAACCAGAG 1 28374 ( 41) GATGACGACGGAATCAGCGAT 1 47224 ( 402) GCGGACAGTGAAAACGCAAAT 1 44301 ( 475) GGGAAGAACGGAAAAAACACT 1 45764 ( 375) GAGGAGAAGGGCGACAAATAA 1 42996 ( 300) CGCGACAAAGAAAGCAAAGCC 1 42645 ( 223) CGCGAAGATGGAGAACACGCT 1 44465 ( 340) GGCCAAGACGAAAAACCACCA 1 47616 ( 201) GGAACCGACGCAGTCATAGAA 1 44085 ( 28) GAAAAGGTTGACAAAGAACAA 1 45703 ( 265) GGTACCGATGAAATAGACAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 24000 bayes= 10.4454 E= 3.3e-001 -1110 -36 181 -1110 125 -136 22 -1110 -24 -36 110 -154 2 -236 154 -1110 161 -36 -1110 -1110 -98 110 64 -1110 25 -136 134 -1110 161 -1110 -78 -254 -98 110 -136 4 -1110 -1110 210 -1110 114 -136 22 -254 153 -4 -1110 -1110 114 -1110 81 -1110 135 -236 -78 -96 61 134 -1110 -1110 25 45 64 -1110 76 45 -136 -96 125 64 -1110 -1110 -24 -136 144 -254 135 45 -1110 -1110 102 -4 -236 -54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 22 E= 3.3e-001 0.000000 0.181818 0.818182 0.000000 0.636364 0.090909 0.272727 0.000000 0.227273 0.181818 0.500000 0.090909 0.272727 0.045455 0.681818 0.000000 0.818182 0.181818 0.000000 0.000000 0.136364 0.500000 0.363636 0.000000 0.318182 0.090909 0.590909 0.000000 0.818182 0.000000 0.136364 0.045455 0.136364 0.500000 0.090909 0.272727 0.000000 0.000000 1.000000 0.000000 0.590909 0.090909 0.272727 0.045455 0.772727 0.227273 0.000000 0.000000 0.590909 0.000000 0.409091 0.000000 0.681818 0.045455 0.136364 0.136364 0.409091 0.590909 0.000000 0.000000 0.318182 0.318182 0.363636 0.000000 0.454545 0.318182 0.090909 0.136364 0.636364 0.363636 0.000000 0.000000 0.227273 0.090909 0.636364 0.045455 0.681818 0.318182 0.000000 0.000000 0.545455 0.227273 0.045455 0.181818 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AG][GA][GA]A[CG][GA]A[CT]G[AG][AC][AG]A[CA][GAC][AC][AC][GA][AC][AC] -------------------------------------------------------------------------------- Time 37.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 152 E-value = 4.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3221::21:243:31::2:4 pos.-specific C :::23:::::::1:::::::: probability G a4816:73728:3:73a:8:6 matrix T :2:4:a3428:62a:6:a:a: bits 2.1 * * 1.9 * * * ** * 1.7 * * * ** * 1.5 * * * ** * Relative 1.3 * * * ** * **** Entropy 1.1 * * ** ** ** ***** (24.4 bits) 0.8 * * ** **** ** ***** 0.6 * * *** **** ******** 0.4 *** ******** ******** 0.2 ************ ******** 0.0 --------------------- Multilevel GGGTGTGTGTGTATGTGTGTG consensus AAAC TGTGAAG AG A A sequence T C A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 44301 274 1.74e-13 GGTAGTAGTA GGGTGTGTGTGTGTGTGTGTG CAAAGGTGTC 50077 214 1.05e-11 TCATCCCACC GTGTGTGTGTGTGTGTGTGTG TGTGTGTGTG 42996 128 3.81e-10 TGTTATGAAT GTGCGTGTGTGTATGGGTGTA AAAAGGTATA 49600 386 2.08e-09 TGATCGGGGC GAGTGTTGGGGATTGTGTGTG TAGCAAAGAC 45703 202 1.13e-08 AATACCGCTG GGGCGTGGGTAAATGGGTATA TGTTAACGCA 44465 305 2.55e-08 GAAACATGCA GGAACTGGGTATGTATGTGTA ACTCGTGTTG 43948 357 7.18e-08 AGTCTCAACA GAGACTGATTGATTAAGTGTG AATAACTGCC 47296 146 1.16e-07 AGCGGTTTAT GGGGATTTTGGTCTGGGTGTG ACAAAAGTGA 42645 21 1.69e-07 CTGCTGAATT GAATCTTAATGAATATGTATA GTATATGGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44301 1.7e-13 273_[+3]_206 50077 1.1e-11 213_[+3]_266 42996 3.8e-10 127_[+3]_352 49600 2.1e-09 385_[+3]_94 45703 1.1e-08 201_[+3]_278 44465 2.5e-08 304_[+3]_175 43948 7.2e-08 356_[+3]_123 47296 1.2e-07 145_[+3]_334 42645 1.7e-07 20_[+3]_459 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 44301 ( 274) GGGTGTGTGTGTGTGTGTGTG 1 50077 ( 214) GTGTGTGTGTGTGTGTGTGTG 1 42996 ( 128) GTGCGTGTGTGTATGGGTGTA 1 49600 ( 386) GAGTGTTGGGGATTGTGTGTG 1 45703 ( 202) GGGCGTGGGTAAATGGGTATA 1 44465 ( 305) GGAACTGGGTATGTATGTGTA 1 43948 ( 357) GAGACTGATTGATTAAGTGTG 1 47296 ( 146) GGGGATTTTGGTCTGGGTGTG 1 42645 ( 21) GAATCTTAATGAATATGTATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 24000 bayes= 12.785 E= 4.4e+000 -982 -982 209 -982 31 -982 93 -25 -27 -982 173 -982 -27 -7 -107 75 -127 52 125 -982 -982 -982 -982 192 -982 -982 151 33 -27 -982 51 75 -127 -982 151 -25 -982 -982 -7 155 -27 -982 173 -982 73 -982 -982 107 31 -107 51 -25 -982 -982 -982 192 31 -982 151 -982 -127 -982 51 107 -982 -982 209 -982 -982 -982 -982 192 -27 -982 173 -982 -982 -982 -982 192 73 -982 125 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 4.4e+000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.444444 0.222222 0.222222 0.000000 0.777778 0.000000 0.222222 0.222222 0.111111 0.444444 0.111111 0.333333 0.555556 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.222222 0.000000 0.333333 0.444444 0.111111 0.000000 0.666667 0.222222 0.000000 0.000000 0.222222 0.777778 0.222222 0.000000 0.777778 0.000000 0.444444 0.000000 0.000000 0.555556 0.333333 0.111111 0.333333 0.222222 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.666667 0.000000 0.111111 0.000000 0.333333 0.555556 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.222222 0.000000 0.777778 0.000000 0.000000 0.000000 0.000000 1.000000 0.444444 0.000000 0.555556 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[GAT][GA][TAC][GC]T[GT][TGA][GT][TG][GA][TA][AGT]T[GA][TG]GT[GA]T[GA] -------------------------------------------------------------------------------- Time 56.10 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42683 2.06e-06 338_[+1(6.96e-06)]_127_\ [+2(1.30e-07)]_2 42820 7.05e-01 500 42996 1.33e-10 127_[+3(3.81e-10)]_151_\ [+2(3.63e-06)]_76_[+1(7.58e-06)]_55_[+1(1.91e-06)]_25 43109 6.54e-03 218_[+1(1.33e-06)]_23_\ [+1(2.22e-06)]_17_[+1(1.48e-05)]_38_[+1(1.14e-05)]_156 46455 2.39e-01 500 20857 7.15e-01 500 46802 7.45e-06 177_[+1(5.53e-06)]_48_\ [+2(3.26e-07)]_242 28374 9.43e-03 40_[+2(1.32e-06)]_439 47296 1.61e-03 145_[+3(1.16e-07)]_334 47334 9.42e-01 500 47899 1.80e-05 60_[+2(9.07e-07)]_117_\ [+1(1.91e-06)]_290 39062 8.15e-06 146_[+2(1.47e-07)]_18_\ [+1(6.96e-06)]_303 43583 2.58e-04 349_[+1(5.90e-08)]_139 43773 4.51e-03 122_[+1(2.48e-06)]_99_\ [+1(2.49e-05)]_255 49010 1.56e-03 149_[+1(8.00e-05)]_58_\ [+1(3.77e-07)]_269 49165 6.27e-02 275_[+1(1.60e-05)]_213 30282 7.54e-01 500 16014 1.00e-03 341_[+2(7.47e-07)]_138 49420 3.12e-03 248_[+1(1.91e-06)]_240 49638 4.56e-03 315_[+1(4.17e-06)]_173 40581 5.28e-01 500 50077 7.43e-07 213_[+3(1.05e-11)]_1_[+3(6.93e-06)]_\ 244 16704 2.08e-03 161_[+2(7.92e-08)]_235_\ [+2(9.90e-05)]_62 43948 4.48e-06 310_[+1(1.14e-05)]_34_\ [+3(7.18e-08)]_123 3692 8.81e-01 500 10531 7.83e-05 230_[+2(1.98e-09)]_249 50468 1.29e-02 432_[+1(5.53e-06)]_56 44325 2.13e-01 248_[+1(5.58e-05)]_240 33901 3.30e-04 71_[+1(5.90e-08)]_417 44465 1.88e-07 149_[+1(4.47e-05)]_143_\ [+3(2.55e-08)]_14_[+2(6.12e-06)]_140 2834 1.41e-01 45_[+1(2.49e-05)]_443 19805 3.29e-05 30_[+1(1.05e-05)]_265_\ [+2(1.02e-07)]_172 3246 8.30e-01 500 45703 1.22e-07 201_[+3(1.13e-08)]_42_\ [+2(8.09e-06)]_120_[+1(4.76e-05)]_83 45764 8.25e-03 374_[+2(1.88e-06)]_105 46043 2.12e-05 162_[+1(5.86e-05)]_227_\ [+1(7.58e-06)]_18_[+2(3.64e-07)]_48 43793 1.18e-02 5_[+1(1.91e-06)]_483 31571 2.07e-02 330_[+1(4.54e-06)]_158 48357 2.70e-06 67_[+1(4.54e-06)]_394_\ [+2(1.86e-07)]_6 42645 4.41e-07 20_[+3(1.69e-07)]_181_\ [+2(5.70e-06)]_237_[+1(1.84e-05)]_8 44192 7.04e-01 500 43089 8.04e-01 500 44301 4.28e-13 63_[+1(2.16e-05)]_198_\ [+3(1.74e-13)]_180_[+2(1.58e-06)]_5 47224 5.06e-06 205_[+1(1.85e-07)]_148_\ [+1(1.85e-07)]_24_[+2(1.44e-06)]_78 48968 1.67e-03 121_[+1(6.01e-06)]_367 45468 3.62e-03 284_[+2(1.20e-06)]_195 44085 8.50e-03 27_[+2(7.56e-06)]_452 49600 2.42e-06 128_[+1(8.00e-05)]_245_\ [+3(2.08e-09)]_94 49635 1.17e-04 371_[+2(1.73e-08)]_108 47616 1.26e-03 150_[+1(1.14e-05)]_38_\ [+2(6.57e-06)]_279 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************