******************************************************************************** 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/353/353.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 28348 1.0000 500 13643 1.0000 500 3145 1.0000 500 9794 1.0000 500 40154 1.0000 500 981 1.0000 500 34273 1.0000 500 44907 1.0000 500 34543 1.0000 500 34675 1.0000 500 48506 1.0000 500 46663 1.0000 500 44823 1.0000 500 37425 1.0000 500 50562 1.0000 500 50268 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/353/353.seqs.fa -oc motifs/353 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.265 C 0.238 G 0.238 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.265 C 0.238 G 0.238 T 0.259 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 10 llr = 121 E-value = 8.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2555:2:::2::::: pos.-specific C :45:a47:a14::13 probability G 8::2:3:::618:17 matrix T :1:3:13a:152a8: bits 2.1 * * 1.9 * ** * 1.7 * ** * 1.5 * ** * Relative 1.2 * * *** ** * Entropy 1.0 * * * *** **** (17.5 bits) 0.8 * * * *** **** 0.6 *** * *** ***** 0.4 ***** ********* 0.2 *************** 0.0 --------------- Multilevel GAAACCCTCGTGTTG consensus ACCT GT ACT C sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 44823 274 3.56e-08 CAAATGAGGG GAAACCCTCGTGTTC TCGTTTTTGT 50562 481 5.83e-08 ATACCCCAAA GCAACACTCGCGTTG AAAGA 981 479 1.85e-07 TAGTGCACTT GCCACCCTCCTGTTG TCAAACG 44907 348 5.97e-07 GATTTCCACT GCCTCGCTCGTGTCG ATCACAGTCA 34273 265 9.90e-07 ATATATATGT GACACCTTCACGTTC GATACCTATT 50268 336 1.55e-06 GTTTGACTTT GAAGCCCTCATTTTG CGCACCTCAT 9794 288 3.90e-06 CGCCTACCAT AAAGCGTTCGCGTTC CTTTGCTAAG 3145 174 4.45e-06 AGCGCTGTCG GCCTCACTCGTTTGG TACGCCTCTT 34675 405 5.03e-06 GATAGTCACC GTATCGTTCGGGTTG TCGTCACTGA 46663 461 5.66e-06 ACAGAACGGG AACACTCTCTCGTTG GGAAAGGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44823 3.6e-08 273_[+1]_212 50562 5.8e-08 480_[+1]_5 981 1.8e-07 478_[+1]_7 44907 6e-07 347_[+1]_138 34273 9.9e-07 264_[+1]_221 50268 1.5e-06 335_[+1]_150 9794 3.9e-06 287_[+1]_198 3145 4.5e-06 173_[+1]_312 34675 5e-06 404_[+1]_81 46663 5.7e-06 460_[+1]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=10 44823 ( 274) GAAACCCTCGTGTTC 1 50562 ( 481) GCAACACTCGCGTTG 1 981 ( 479) GCCACCCTCCTGTTG 1 44907 ( 348) GCCTCGCTCGTGTCG 1 34273 ( 265) GACACCTTCACGTTC 1 50268 ( 336) GAAGCCCTCATTTTG 1 9794 ( 288) AAAGCGTTCGCGTTC 1 3145 ( 174) GCCTCACTCGTTTGG 1 34675 ( 405) GTATCGTTCGGGTTG 1 46663 ( 461) AACACTCTCTCGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 7776 bayes= 9.85286 E= 8.0e+002 -41 -997 175 -997 91 75 -997 -137 91 107 -997 -997 91 -997 -25 21 -997 207 -997 -997 -41 75 33 -137 -997 156 -997 21 -997 -997 -997 195 -997 207 -997 -997 -41 -125 133 -137 -997 75 -125 95 -997 -997 175 -37 -997 -997 -997 195 -997 -125 -125 163 -997 34 156 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 8.0e+002 0.200000 0.000000 0.800000 0.000000 0.500000 0.400000 0.000000 0.100000 0.500000 0.500000 0.000000 0.000000 0.500000 0.000000 0.200000 0.300000 0.000000 1.000000 0.000000 0.000000 0.200000 0.400000 0.300000 0.100000 0.000000 0.700000 0.000000 0.300000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.100000 0.600000 0.100000 0.000000 0.400000 0.100000 0.500000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.100000 0.100000 0.800000 0.000000 0.300000 0.700000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA][AC][AC][ATG]C[CGA][CT]TC[GA][TC][GT]TT[GC] -------------------------------------------------------------------------------- Time 2.03 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 10 llr = 118 E-value = 3.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :5::::2::1:::7: pos.-specific C 9:5:2:1::3862:: probability G :42a8352:5:17:: matrix T 113::728a12313a bits 2.1 * 1.9 * * * 1.7 * * * * 1.5 * ** * * Relative 1.2 * ** ** * * Entropy 1.0 * *** ** * ** (17.1 bits) 0.8 * *** ** ***** 0.6 ****** ** ***** 0.4 ****** ******** 0.2 *************** 0.0 --------------- Multilevel CACGGTGTTGCCGAT consensus GT CGAG CTTCT sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 46663 337 6.85e-09 CATAGAATTC CACGGTGTTGCCGTT GCCACTGCTA 44907 81 3.73e-07 ATAGTCCAGA CATGGTAGTGCCGAT GAACGGAGCA 34675 91 5.40e-07 GATTTCACGT CACGGGTTTGTCGAT GGGAGGGTGT 48506 352 8.88e-07 AACCAGATCT CGGGCGGTTCCCGAT GCCCCCATCG 34543 238 1.21e-06 TCTCATACTT CACGGTTTTGCTTAT ATCACTGTTA 50268 139 1.88e-06 TAACATGCGA TGTGGTGTTCCTGAT CCATGAACGA 37425 261 2.85e-06 GGGCAACTTG CTGGGTGTTGTTGAT GATGGTTGAA 40154 459 4.16e-06 TGTTTCACTT CGCGGGGGTACCCAT TAGAGGAGGC 3145 445 6.25e-06 ACTCCGGATA CGCGCTCTTCCCCTT CTGCTCAAAA 13643 373 8.48e-06 TGTACACAGA CATGGTATTTCGGTT TCGAATTCGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46663 6.8e-09 336_[+2]_149 44907 3.7e-07 80_[+2]_405 34675 5.4e-07 90_[+2]_395 48506 8.9e-07 351_[+2]_134 34543 1.2e-06 237_[+2]_248 50268 1.9e-06 138_[+2]_347 37425 2.8e-06 260_[+2]_225 40154 4.2e-06 458_[+2]_27 3145 6.2e-06 444_[+2]_41 13643 8.5e-06 372_[+2]_113 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=10 46663 ( 337) CACGGTGTTGCCGTT 1 44907 ( 81) CATGGTAGTGCCGAT 1 34675 ( 91) CACGGGTTTGTCGAT 1 48506 ( 352) CGGGCGGTTCCCGAT 1 34543 ( 238) CACGGTTTTGCTTAT 1 50268 ( 139) TGTGGTGTTCCTGAT 1 37425 ( 261) CTGGGTGTTGTTGAT 1 40154 ( 459) CGCGGGGGTACCCAT 1 3145 ( 445) CGCGCTCTTCCCCTT 1 13643 ( 373) CATGGTATTTCGGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 7776 bayes= 10.5453 E= 3.6e+003 -997 192 -997 -137 91 -997 75 -137 -997 107 -25 21 -997 -997 207 -997 -997 -25 175 -997 -997 -997 33 143 -41 -125 107 -37 -997 -997 -25 163 -997 -997 -997 195 -140 34 107 -137 -997 175 -997 -37 -997 133 -125 21 -997 -25 156 -137 140 -997 -997 21 -997 -997 -997 195 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 3.6e+003 0.000000 0.900000 0.000000 0.100000 0.500000 0.000000 0.400000 0.100000 0.000000 0.500000 0.200000 0.300000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.300000 0.700000 0.200000 0.100000 0.500000 0.200000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.100000 0.300000 0.500000 0.100000 0.000000 0.800000 0.000000 0.200000 0.000000 0.600000 0.100000 0.300000 0.000000 0.200000 0.700000 0.100000 0.700000 0.000000 0.000000 0.300000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[AG][CTG]G[GC][TG][GAT][TG]T[GC][CT][CT][GC][AT]T -------------------------------------------------------------------------------- Time 4.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 14 llr = 132 E-value = 9.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1473:::::::1 pos.-specific C 7:1:1426:9:7 probability G 16:71:34:192 matrix T ::1:865:a:1: bits 2.1 1.9 * 1.7 ** 1.5 *** Relative 1.2 * *** Entropy 1.0 * *** ***** (13.6 bits) 0.8 ****** ***** 0.6 ****** ***** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CGAGTTTCTCGC consensus A A CGG G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 9794 156 5.16e-08 GCGAAACGGA CGAGTTTCTCGC TGACGAGGCC 44907 429 1.21e-06 AATCTGGCCG CGAGTCTCTCGG GAAGACGTTT 50562 40 1.53e-06 CGGCGCAGCA CGAATTGCTCGC GTATTACACC 34675 344 2.69e-06 TGCACCACAC CAAGTCCGTCGC CGCATCACCA 34273 210 3.06e-06 GGCCCAGTGT CGAGTCTGTCGG ACTTCATAAC 28348 472 8.88e-06 AAGCGGCGTA GAAGTCTGTCGC CACGCCCTAT 46663 111 2.19e-05 GGAATGGAGG AAAATTGCTCGC TTCATGCTTC 37425 39 3.29e-05 GTCCAACGAG CAAGGTCGTCGC GATCGGCTGC 48506 39 3.29e-05 TCATATACGG AGTGTCGCTCGC AAGCGGCCTC 40154 313 4.44e-05 AAGTGAATTT GAAGCTCCTCGC AAGCGCGCCG 981 48 4.77e-05 CCCTTCCACC CACGTCTCTCGA GAGCAGGAAG 50268 288 5.12e-05 CGGCTATTTT CGTATTTCTCTC TCTAGCTAGT 3145 121 8.59e-05 GAGGATTGGG CGAACTTCTGGC TGTCATCAAC 44823 328 1.20e-04 AGTTCCAGTC CGCGTTGGTCTG TTGCGCGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9794 5.2e-08 155_[+3]_333 44907 1.2e-06 428_[+3]_60 50562 1.5e-06 39_[+3]_449 34675 2.7e-06 343_[+3]_145 34273 3.1e-06 209_[+3]_279 28348 8.9e-06 471_[+3]_17 46663 2.2e-05 110_[+3]_378 37425 3.3e-05 38_[+3]_450 48506 3.3e-05 38_[+3]_450 40154 4.4e-05 312_[+3]_176 981 4.8e-05 47_[+3]_441 50268 5.1e-05 287_[+3]_201 3145 8.6e-05 120_[+3]_368 44823 0.00012 327_[+3]_161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=14 9794 ( 156) CGAGTTTCTCGC 1 44907 ( 429) CGAGTCTCTCGG 1 50562 ( 40) CGAATTGCTCGC 1 34675 ( 344) CAAGTCCGTCGC 1 34273 ( 210) CGAGTCTGTCGG 1 28348 ( 472) GAAGTCTGTCGC 1 46663 ( 111) AAAATTGCTCGC 1 37425 ( 39) CAAGGTCGTCGC 1 48506 ( 39) AGTGTCGCTCGC 1 40154 ( 313) GAAGCTCCTCGC 1 981 ( 48) CACGTCTCTCGA 1 50268 ( 288) CGTATTTCTCTC 1 3145 ( 121) CGAACTTCTGGC 1 44823 ( 328) CGCGTTGGTCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 9.73036 E= 9.1e+003 -89 159 -74 -1045 69 -1045 126 -1045 143 -73 -1045 -86 11 -1045 158 -1045 -1045 -73 -173 160 -1045 85 -1045 114 -1045 -15 26 95 -1045 143 59 -1045 -1045 -1045 -1045 195 -1045 196 -173 -1045 -1045 -1045 185 -86 -189 159 -15 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 14 E= 9.1e+003 0.142857 0.714286 0.142857 0.000000 0.428571 0.000000 0.571429 0.000000 0.714286 0.142857 0.000000 0.142857 0.285714 0.000000 0.714286 0.000000 0.000000 0.142857 0.071429 0.785714 0.000000 0.428571 0.000000 0.571429 0.000000 0.214286 0.285714 0.500000 0.000000 0.642857 0.357143 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.928571 0.071429 0.000000 0.000000 0.000000 0.857143 0.142857 0.071429 0.714286 0.214286 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[GA]A[GA]T[TC][TGC][CG]TCG[CG] -------------------------------------------------------------------------------- Time 5.93 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28348 2.07e-02 471_[+3(8.88e-06)]_17 13643 6.27e-02 372_[+2(8.48e-06)]_113 3145 3.52e-05 120_[+3(8.59e-05)]_41_\ [+1(4.45e-06)]_256_[+2(6.25e-06)]_41 9794 3.35e-06 155_[+3(5.16e-08)]_120_\ [+1(3.90e-06)]_198 40154 2.18e-03 312_[+3(4.44e-05)]_134_\ [+2(4.16e-06)]_27 981 5.70e-05 47_[+3(4.77e-05)]_419_\ [+1(1.85e-07)]_7 34273 2.71e-05 209_[+3(3.06e-06)]_43_\ [+1(9.90e-07)]_221 44907 9.94e-09 80_[+2(3.73e-07)]_252_\ [+1(5.97e-07)]_66_[+3(1.21e-06)]_60 34543 1.08e-02 237_[+2(1.21e-06)]_248 34675 2.02e-07 90_[+2(5.40e-07)]_190_\ [+2(7.61e-05)]_33_[+3(2.69e-06)]_49_[+1(5.03e-06)]_81 48506 5.31e-04 38_[+3(3.29e-05)]_301_\ [+2(8.88e-07)]_134 46663 2.83e-08 110_[+3(2.19e-05)]_214_\ [+2(6.85e-09)]_109_[+1(5.66e-06)]_25 44823 5.21e-05 273_[+1(3.56e-08)]_212 37425 1.12e-03 38_[+3(3.29e-05)]_210_\ [+2(2.85e-06)]_225 50562 2.83e-06 39_[+3(1.53e-06)]_22_[+3(5.48e-05)]_\ 97_[+3(9.65e-05)]_286_[+1(5.83e-08)]_5 50268 3.04e-06 138_[+2(1.88e-06)]_134_\ [+3(5.12e-05)]_36_[+1(1.55e-06)]_150 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************