******************************************************************************** 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/443/443.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10527 1.0000 500 12135 1.0000 500 1338 1.0000 500 21697 1.0000 500 24972 1.0000 500 261569 1.0000 500 269744 1.0000 500 32914 1.0000 500 41687 1.0000 500 42867 1.0000 500 7426 1.0000 500 7729 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/443/443.seqs.fa -oc motifs/443 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.265 C 0.239 G 0.228 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.265 C 0.240 G 0.228 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 18 sites = 7 llr = 109 E-value = 9.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :1::::19:::::::1:: pos.-specific C 1:36:4::4:::6:1337 probability G 9::4:49:36aa1:9371 matrix T :97:a1:134::3a:3:1 bits 2.1 ** 1.9 * ** * 1.7 * ** * 1.5 * * * ** ** Relative 1.3 ** * ** ** ** * Entropy 1.1 ***** ** *** ** * (22.5 bits) 0.9 ***** ** *** ** ** 0.6 ******** ****** ** 0.4 *************** ** 0.2 *************** ** 0.0 ------------------ Multilevel GTTCTCGACGGGCTGCGC consensus CG G GT T GC sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 41687 262 3.13e-11 GAGTGCCATC GTTCTCGACGGGCTGCGC CGTGGGCTGT 10527 252 5.91e-10 CCGAAGCTTT GTTGTCGATGGGCTGTGC TATGACGATC 269744 144 1.56e-08 CTCTGTGTGT GTTGTTGAGGGGCTGTCC GAGGGAGGTT 12135 265 5.07e-08 TCCTTCCTGA GTTCTGGTTGGGCTGGGT TGGCTTGTCT 32914 71 1.13e-07 GTTATGAATC GTCCTGGACTGGGTGAGG CGGAGCGTAT 7729 20 1.85e-07 AGACGAGACC GATGTGGAGTGGTTCGGC GGAGGATTCG 7426 453 4.11e-07 AAAGAAAAGT CTCCTCAACTGGTTGCCC TTTATCCCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41687 3.1e-11 261_[+1]_221 10527 5.9e-10 251_[+1]_231 269744 1.6e-08 143_[+1]_339 12135 5.1e-08 264_[+1]_218 32914 1.1e-07 70_[+1]_412 7729 1.8e-07 19_[+1]_463 7426 4.1e-07 452_[+1]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=18 seqs=7 41687 ( 262) GTTCTCGACGGGCTGCGC 1 10527 ( 252) GTTGTCGATGGGCTGTGC 1 269744 ( 144) GTTGTTGAGGGGCTGTCC 1 12135 ( 265) GTTCTGGTTGGGCTGGGT 1 32914 ( 71) GTCCTGGACTGGGTGAGG 1 7729 ( 20) GATGTGGAGTGGTTCGGC 1 7426 ( 453) CTCCTCAACTGGTTGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 5796 bayes= 9.53542 E= 9.6e-001 -945 -74 191 -945 -89 -945 -945 168 -945 25 -945 142 -945 125 91 -945 -945 -945 -945 190 -945 84 91 -90 -89 -945 191 -945 169 -945 -945 -90 -945 84 32 10 -945 -945 132 68 -945 -945 213 -945 -945 -945 213 -945 -945 125 -68 10 -945 -945 -945 190 -945 -74 191 -945 -89 25 32 10 -945 25 164 -945 -945 158 -68 -90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 7 E= 9.6e-001 0.000000 0.142857 0.857143 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.285714 0.000000 0.714286 0.000000 0.571429 0.428571 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.428571 0.142857 0.142857 0.000000 0.857143 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 0.428571 0.285714 0.285714 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.571429 0.142857 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.857143 0.000000 0.142857 0.285714 0.285714 0.285714 0.000000 0.285714 0.714286 0.000000 0.000000 0.714286 0.142857 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GT[TC][CG]T[CG]GA[CGT][GT]GG[CT]TG[CGT][GC]C -------------------------------------------------------------------------------- Time 1.35 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 8 llr = 107 E-value = 9.8e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :115::::1:::1::: pos.-specific C :16::31363::3:4: probability G a4353498:1a::96: matrix T :4::84::36:a61:a bits 2.1 * * 1.9 * ** * 1.7 * ** * 1.5 * * ** * * Relative 1.3 * ** ** * * Entropy 1.1 * ** ** ** *** (19.3 bits) 0.9 * *** ** ** *** 0.6 * *** ********** 0.4 * ************** 0.2 **************** 0.0 ---------------- Multilevel GGCATGGGCTGTTGGT consensus TGGGT CTC C C sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 41687 294 1.63e-08 GGCTGTCCGT GGCGTGGGCTGTAGGT TGTACCAGGG 7729 150 5.96e-08 TGGTTGTTCA GTGATGGGTTGTTGGT GGATCTTTAT 1338 225 1.06e-07 GTTGCTGGTG GGCGTCGGCGGTCGGT GGTATTTTTC 261569 33 1.48e-07 TGACTTCTTG GGCGTTGCTTGTTGCT GCTGTTGTGA 21697 337 4.27e-07 AACTGCGAAG GCAGTTGGCTGTCGGT TCATCTCTCA 7426 7 5.06e-07 GCATTT GTCAGTGGACGTTGGT ATATATGTTC 269744 100 1.06e-06 GCTATCAAAT GAGATGCGCTGTTGCT GTTGACGAGG 10527 450 3.00e-06 TAATCCAGTC GTCAGCGCCCGTTTCT CACACCACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41687 1.6e-08 293_[+2]_191 7729 6e-08 149_[+2]_335 1338 1.1e-07 224_[+2]_260 261569 1.5e-07 32_[+2]_452 21697 4.3e-07 336_[+2]_148 7426 5.1e-07 6_[+2]_478 269744 1.1e-06 99_[+2]_385 10527 3e-06 449_[+2]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=8 41687 ( 294) GGCGTGGGCTGTAGGT 1 7729 ( 150) GTGATGGGTTGTTGGT 1 1338 ( 225) GGCGTCGGCGGTCGGT 1 261569 ( 33) GGCGTTGCTTGTTGCT 1 21697 ( 337) GCAGTTGGCTGTCGGT 1 7426 ( 7) GTCAGTGGACGTTGGT 1 269744 ( 100) GAGATGCGCTGTTGCT 1 10527 ( 450) GTCAGCGCCCGTTTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5820 bayes= 9.50482 E= 9.8e+000 -965 -965 213 -965 -108 -94 71 49 -108 138 13 -965 92 -965 113 -965 -965 -965 13 149 -965 6 71 49 -965 -94 194 -965 -965 6 171 -965 -108 138 -965 -10 -965 6 -87 122 -965 -965 213 -965 -965 -965 -965 190 -108 6 -965 122 -965 -965 194 -109 -965 65 145 -965 -965 -965 -965 190 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 9.8e+000 0.000000 0.000000 1.000000 0.000000 0.125000 0.125000 0.375000 0.375000 0.125000 0.625000 0.250000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.375000 0.375000 0.000000 0.125000 0.875000 0.000000 0.000000 0.250000 0.750000 0.000000 0.125000 0.625000 0.000000 0.250000 0.000000 0.250000 0.125000 0.625000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.125000 0.250000 0.000000 0.625000 0.000000 0.000000 0.875000 0.125000 0.000000 0.375000 0.625000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[GT][CG][AG][TG][GTC]G[GC][CT][TC]GT[TC]G[GC]T -------------------------------------------------------------------------------- Time 2.60 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 7 llr = 100 E-value = 4.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :93:3:6:3::71::7 pos.-specific C ::63:::::1::::33 probability G a1:76a47:9a:777: matrix T ::1:1::37::313:: bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 * * ** Relative 1.3 ** * * * ** ** Entropy 1.1 ** * ******* *** (20.6 bits) 0.9 ** * *********** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GACGGGAGTGGAGGGA consensus ACA GTA T TCC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 7729 469 2.13e-09 CAAACGATAC GACGGGGGTGGAGGCA TCGCAACGAG 261569 72 2.37e-09 GTCTATCGAG GACGGGGGTGGAGTGA GAGGTGTTGT 269744 119 1.16e-07 TGTTGCTGTT GACGAGGTAGGAGGGC TCTGTGTGTG 24972 220 3.42e-07 TGTGGTATTA GAAGTGAGAGGAAGGA TAAAATACAA 41687 242 4.39e-07 GTTCAACTCA GGACGGAGTGGAGTGC CATCGTTCTC 12135 191 4.74e-07 AGTCACTTTG GATGAGATTGGTGGCA CATGATGTGA 7426 53 5.94e-07 AGATTATACC GACCGGAGTCGTTGGA ATCAGAACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7729 2.1e-09 468_[+3]_16 261569 2.4e-09 71_[+3]_413 269744 1.2e-07 118_[+3]_366 24972 3.4e-07 219_[+3]_265 41687 4.4e-07 241_[+3]_243 12135 4.7e-07 190_[+3]_294 7426 5.9e-07 52_[+3]_432 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=7 7729 ( 469) GACGGGGGTGGAGGCA 1 261569 ( 72) GACGGGGGTGGAGTGA 1 269744 ( 119) GACGAGGTAGGAGGGC 1 24972 ( 220) GAAGTGAGAGGAAGGA 1 41687 ( 242) GGACGGAGTGGAGTGC 1 12135 ( 191) GATGAGATTGGTGGCA 1 7426 ( 53) GACCGGAGTCGTTGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5820 bayes= 10.304 E= 4.2e+001 -945 -945 213 -945 169 -945 -68 -945 11 125 -945 -90 -945 25 164 -945 11 -945 132 -90 -945 -945 213 -945 111 -945 91 -945 -945 -945 164 10 11 -945 -945 142 -945 -74 191 -945 -945 -945 213 -945 143 -945 -945 10 -89 -945 164 -90 -945 -945 164 10 -945 25 164 -945 143 25 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 7 E= 4.2e+001 0.000000 0.000000 1.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.285714 0.571429 0.000000 0.142857 0.000000 0.285714 0.714286 0.000000 0.285714 0.000000 0.571429 0.142857 0.000000 0.000000 1.000000 0.000000 0.571429 0.000000 0.428571 0.000000 0.000000 0.000000 0.714286 0.285714 0.285714 0.000000 0.000000 0.714286 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 1.000000 0.000000 0.714286 0.000000 0.000000 0.285714 0.142857 0.000000 0.714286 0.142857 0.000000 0.000000 0.714286 0.285714 0.000000 0.285714 0.714286 0.000000 0.714286 0.285714 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GA[CA][GC][GA]G[AG][GT][TA]GG[AT]G[GT][GC][AC] -------------------------------------------------------------------------------- Time 3.75 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10527 3.56e-08 251_[+1(5.91e-10)]_180_\ [+2(3.00e-06)]_35 12135 4.41e-07 190_[+3(4.74e-07)]_58_\ [+1(5.07e-08)]_218 1338 2.73e-04 207_[+2(4.58e-05)]_1_[+2(1.06e-07)]_\ 260 21697 5.15e-03 336_[+2(4.27e-07)]_148 24972 1.32e-03 219_[+3(3.42e-07)]_265 261569 7.29e-10 32_[+2(1.48e-07)]_23_[+3(2.37e-09)]_\ 243_[+2(7.99e-05)]_154 269744 9.89e-11 99_[+2(1.06e-06)]_3_[+3(1.16e-07)]_\ 9_[+1(1.56e-08)]_339 32914 2.34e-03 70_[+1(1.13e-07)]_412 41687 1.96e-14 241_[+3(4.39e-07)]_4_[+1(3.13e-11)]_\ 14_[+2(1.63e-08)]_191 42867 2.91e-01 500 7426 4.75e-09 6_[+2(5.06e-07)]_30_[+3(5.94e-07)]_\ 384_[+1(4.11e-07)]_30 7729 1.59e-12 19_[+1(1.85e-07)]_112_\ [+2(5.96e-08)]_303_[+3(2.13e-09)]_16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************