******************************************************************************** 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/104/104.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 36270 1.0000 500 37726 1.0000 500 29666 1.0000 500 39088 1.0000 500 9962 1.0000 500 40644 1.0000 500 40917 1.0000 500 33773 1.0000 500 45800 1.0000 500 32487 1.0000 500 33814 1.0000 500 33857 1.0000 500 36528 1.0000 500 46913 1.0000 500 37993 1.0000 500 32893 1.0000 500 50090 1.0000 500 40861 1.0000 500 35568 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/104/104.seqs.fa -oc motifs/104 -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= 19 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= 9500 N= 19 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.274 C 0.240 G 0.205 T 0.281 Background letter frequencies (from dataset with add-one prior applied): A 0.274 C 0.240 G 0.205 T 0.281 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 9 llr = 120 E-value = 1.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :2214:::9:7:::9 pos.-specific C :623:::1:9:::11 probability G 721::::91::a29: matrix T 3:466aa::13:8:: bits 2.3 * 2.1 * 1.8 *** * * 1.6 *** * * * Relative 1.4 ***** * ** Entropy 1.1 * ***** **** (19.3 bits) 0.9 * *********** 0.7 ** *********** 0.5 ** ************ 0.2 ** ************ 0.0 --------------- Multilevel GCTTTTTGACAGTGA consensus TAACA T G sequence GC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 37993 360 8.45e-09 ATATGTTGGA GCTTTTTGACTGTGA ATTTCGCAGT 32893 185 9.43e-09 AATTAGGATC GCATATTGACAGTGA ACACATCCAG 33814 21 3.88e-08 AGCCTACTTT TCTCATTGACAGTGA TAACCCAATC 35568 123 1.67e-07 CTTTTTCGAT GCTTTTTGGCTGTGA GAGGCGGGCA 40861 336 6.11e-07 TACAAAATTG TATAATTGACAGTGA CATACTTTTT 33857 290 8.28e-07 GATATTTTAC TGGCATTGACTGTGA GTTTATTGTC 45800 59 8.97e-07 GGGGAACAAG GGCTTTTGACAGGGC ACAGGTTTTT 40644 27 1.77e-06 AGGCTATAGT GACCTTTCACAGGGA ACGTCACGTT 39088 149 1.87e-06 ATTAACATCT GCATTTTGATAGTCA TAACGACCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37993 8.5e-09 359_[+1]_126 32893 9.4e-09 184_[+1]_301 33814 3.9e-08 20_[+1]_465 35568 1.7e-07 122_[+1]_363 40861 6.1e-07 335_[+1]_150 33857 8.3e-07 289_[+1]_196 45800 9e-07 58_[+1]_427 40644 1.8e-06 26_[+1]_459 39088 1.9e-06 148_[+1]_337 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=9 37993 ( 360) GCTTTTTGACTGTGA 1 32893 ( 185) GCATATTGACAGTGA 1 33814 ( 21) TCTCATTGACAGTGA 1 35568 ( 123) GCTTTTTGGCTGTGA 1 40861 ( 336) TATAATTGACAGTGA 1 33857 ( 290) TGGCATTGACTGTGA 1 45800 ( 59) GGCTTTTGACAGGGC 1 40644 ( 27) GACCTTTCACAGGGA 1 39088 ( 149) GCATTTTGATAGTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 9234 bayes= 10.1358 E= 1.4e+000 -982 -982 170 25 -30 121 12 -982 -30 -11 -88 66 -130 47 -982 98 70 -982 -982 98 -982 -982 -982 183 -982 -982 -982 183 -982 -111 211 -982 170 -982 -88 -982 -982 189 -982 -134 128 -982 -982 25 -982 -982 228 -982 -982 -982 12 147 -982 -111 211 -982 170 -111 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 1.4e+000 0.000000 0.000000 0.666667 0.333333 0.222222 0.555556 0.222222 0.000000 0.222222 0.222222 0.111111 0.444444 0.111111 0.333333 0.000000 0.555556 0.444444 0.000000 0.000000 0.555556 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.888889 0.000000 0.888889 0.000000 0.111111 0.000000 0.000000 0.888889 0.000000 0.111111 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.222222 0.777778 0.000000 0.111111 0.888889 0.000000 0.888889 0.111111 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT][CAG][TAC][TC][TA]TTGAC[AT]G[TG]GA -------------------------------------------------------------------------------- Time 4.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 9 llr = 135 E-value = 7.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:31272262aa37612a87 pos.-specific C ::1::28448::221:8::: probability G 8::82::1::::1139:::: matrix T 1a6161:2::::3:::::23 bits 2.3 2.1 1.8 * ** * * 1.6 * ** * * Relative 1.4 * ** * * Entropy 1.1 ** * * *** **** (21.6 bits) 0.9 ** * * **** ***** 0.7 ** * ** **** ******* 0.5 ******* **** ******* 0.2 ************ ******* 0.0 -------------------- Multilevel GTTGTACCACAAAAAGCAAA consensus A ACAACA TCG A TT sequence G T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 40917 178 2.22e-09 GCAGACTCCG GTTGTTCTACAATAAGCAAA AAAATATTCA 39088 70 1.16e-08 TTTTGAGGCC GTTGGAAACCAAAAGGCAAT ACAGAGCTTG 37993 318 1.74e-08 TGAGGTAAAT GTCGTACCCCAATCGGAAAA AGCAGTGAAC 36270 369 4.10e-08 ATTCCGAAGG GTTATCCTCCAAGAAGCAAA ACCGACATGC 37726 272 8.76e-08 CAAGGGCCAC TTAGACCAACAACAAGCAAA TCTTCGTTCC 40861 219 1.20e-07 ATCTCACTAC GTTGTAACCAAACGAGAAAA AACAGACAAG 40644 360 1.30e-07 CCATTTCTCG ATAGTACGACAAAACGCAAT CTCATCCCTG 29666 152 1.40e-07 GTACTAGAAT GTTGAACCAAAAAAGACATA GCCGACAGTG 33773 446 1.73e-07 ACTCTTCCAT GTATGACCACAATCAGCATT TCTTGGCAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40917 2.2e-09 177_[+2]_303 39088 1.2e-08 69_[+2]_411 37993 1.7e-08 317_[+2]_163 36270 4.1e-08 368_[+2]_112 37726 8.8e-08 271_[+2]_209 40861 1.2e-07 218_[+2]_262 40644 1.3e-07 359_[+2]_121 29666 1.4e-07 151_[+2]_329 33773 1.7e-07 445_[+2]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=9 40917 ( 178) GTTGTTCTACAATAAGCAAA 1 39088 ( 70) GTTGGAAACCAAAAGGCAAT 1 37993 ( 318) GTCGTACCCCAATCGGAAAA 1 36270 ( 369) GTTATCCTCCAAGAAGCAAA 1 37726 ( 272) TTAGACCAACAACAAGCAAA 1 40861 ( 219) GTTGTAACCAAACGAGAAAA 1 40644 ( 360) ATAGTACGACAAAACGCAAT 1 29666 ( 152) GTTGAACCAAAAAAGACATA 1 33773 ( 446) GTATGACCACAATCAGCATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 9139 bayes= 10.1209 E= 7.3e+000 -130 -982 192 -134 -982 -982 -982 183 28 -111 -982 98 -130 -982 192 -134 -30 -982 12 98 128 -11 -982 -134 -30 170 -982 -982 -30 89 -88 -34 102 89 -982 -982 -30 170 -982 -982 187 -982 -982 -982 187 -982 -982 -982 28 -11 -88 25 128 -11 -88 -982 102 -111 70 -982 -130 -982 211 -982 -30 170 -982 -982 187 -982 -982 -982 150 -982 -982 -34 128 -982 -982 25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 7.3e+000 0.111111 0.000000 0.777778 0.111111 0.000000 0.000000 0.000000 1.000000 0.333333 0.111111 0.000000 0.555556 0.111111 0.000000 0.777778 0.111111 0.222222 0.000000 0.222222 0.555556 0.666667 0.222222 0.000000 0.111111 0.222222 0.777778 0.000000 0.000000 0.222222 0.444444 0.111111 0.222222 0.555556 0.444444 0.000000 0.000000 0.222222 0.777778 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.222222 0.111111 0.333333 0.666667 0.222222 0.111111 0.000000 0.555556 0.111111 0.333333 0.000000 0.111111 0.000000 0.888889 0.000000 0.222222 0.777778 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.222222 0.666667 0.000000 0.000000 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GT[TA]G[TAG][AC][CA][CAT][AC][CA]AA[ATC][AC][AG]G[CA]A[AT][AT] -------------------------------------------------------------------------------- Time 8.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 11 llr = 154 E-value = 7.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::34145987647:461: pos.-specific C ::15::1:53::3:::3235: probability G 17237:1:21:::46:2512a matrix T 93723759:212:::35::3: bits 2.3 * 2.1 * 1.8 * 1.6 * Relative 1.4 ** * * * * Entropy 1.1 ** * * ***** * (20.2 bits) 0.9 *** ** * ****** * 0.7 ****** * ****** ** * 0.5 ****** ** ********* * 0.2 ********************* 0.0 --------------------- Multilevel TGTCGTTTCAAAAAGATGACG consensus T GTAA AC CGATCACT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 45800 305 1.80e-09 AATTAATATA TGTGGTTTAAATAAGATAACG TCCATGCGTT 33773 203 1.20e-08 GGAATATTCT TGTCGATTCGAAAAGACAAGG AAACAGCCGT 36270 189 1.56e-08 ATGATCAGAA TGGCGTCTGAAAAAAATGACG AGCACCGGCG 40861 168 2.85e-08 CCATAACTCA TTTGGTTTCCAAAAGACACGG ATTTGTCGGT 32893 127 7.59e-08 ATTACACCCG TTTCGTGTATAAAAAATGATG CCGAGGTGCG 33857 177 3.22e-07 ACGCACTCCC TGTCTAAAAAAAAGAATGCCG ATTTGCGATC 36528 287 4.39e-07 ATCCATTTCG TGGTGTTTCTAACGAATCATG GAAGCGACGC 40917 117 4.73e-07 GTCCAAGAAG TTTGTTATCCAACGGATCCTG TGCGCACCTT 9962 111 5.09e-07 TCTGATGGCG TGCCGTATACTAAAGTCAACG TTGATTGAAA 29666 104 8.28e-07 TTCAACGTAT GGTCGTTTCAATCAGTGGAAG CAGGAGCGGC 37993 28 1.00e-06 GGCTCATCCT TGTTTAATGAAAAGGTGGGCG TATTCTTTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45800 1.8e-09 304_[+3]_175 33773 1.2e-08 202_[+3]_277 36270 1.6e-08 188_[+3]_291 40861 2.9e-08 167_[+3]_312 32893 7.6e-08 126_[+3]_353 33857 3.2e-07 176_[+3]_303 36528 4.4e-07 286_[+3]_193 40917 4.7e-07 116_[+3]_363 9962 5.1e-07 110_[+3]_369 29666 8.3e-07 103_[+3]_376 37993 1e-06 27_[+3]_452 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=11 45800 ( 305) TGTGGTTTAAATAAGATAACG 1 33773 ( 203) TGTCGATTCGAAAAGACAAGG 1 36270 ( 189) TGGCGTCTGAAAAAAATGACG 1 40861 ( 168) TTTGGTTTCCAAAAGACACGG 1 32893 ( 127) TTTCGTGTATAAAAAATGATG 1 33857 ( 177) TGTCTAAAAAAAAGAATGCCG 1 36528 ( 287) TGGTGTTTCTAACGAATCATG 1 40917 ( 117) TTTGTTATCCAACGGATCCTG 1 9962 ( 111) TGCCGTATACTAAAGTCAACG 1 29666 ( 104) GGTCGTTTCAATCAGTGGAAG 1 37993 ( 28) TGTTTAATGAAAAGGTGGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 9120 bayes= 10.0491 E= 7.4e+001 -1010 -1010 -117 169 -1010 -1010 182 -4 -1010 -140 -17 137 -1010 118 41 -63 -1010 -1010 182 -4 -1 -1010 -1010 137 41 -140 -117 69 -159 -1010 -1010 169 41 92 -17 -1010 73 19 -117 -63 173 -1010 -1010 -163 158 -1010 -1010 -63 141 19 -1010 -1010 121 -1010 83 -1010 41 -1010 163 -1010 141 -1010 -1010 -4 -1010 19 -17 96 41 -40 115 -1010 121 19 -117 -1010 -159 92 -17 -4 -1010 -1010 228 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 7.4e+001 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 0.727273 0.272727 0.000000 0.090909 0.181818 0.727273 0.000000 0.545455 0.272727 0.181818 0.000000 0.000000 0.727273 0.272727 0.272727 0.000000 0.000000 0.727273 0.363636 0.090909 0.090909 0.454545 0.090909 0.000000 0.000000 0.909091 0.363636 0.454545 0.181818 0.000000 0.454545 0.272727 0.090909 0.181818 0.909091 0.000000 0.000000 0.090909 0.818182 0.000000 0.000000 0.181818 0.727273 0.272727 0.000000 0.000000 0.636364 0.000000 0.363636 0.000000 0.363636 0.000000 0.636364 0.000000 0.727273 0.000000 0.000000 0.272727 0.000000 0.272727 0.181818 0.545455 0.363636 0.181818 0.454545 0.000000 0.636364 0.272727 0.090909 0.000000 0.090909 0.454545 0.181818 0.272727 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[GT]T[CG][GT][TA][TA]T[CA][AC]AA[AC][AG][GA][AT][TC][GA][AC][CT]G -------------------------------------------------------------------------------- Time 11.88 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36270 1.14e-08 107_[+2(4.38e-05)]_61_\ [+3(1.56e-08)]_159_[+2(4.10e-08)]_112 37726 2.17e-03 271_[+2(8.76e-08)]_209 29666 5.29e-07 103_[+3(8.28e-07)]_27_\ [+2(1.40e-07)]_329 39088 3.79e-07 69_[+2(1.16e-08)]_59_[+1(1.87e-06)]_\ 337 9962 3.28e-03 110_[+3(5.09e-07)]_369 40644 5.07e-06 26_[+1(1.77e-06)]_318_\ [+2(1.30e-07)]_121 40917 1.04e-08 116_[+3(4.73e-07)]_40_\ [+2(2.22e-09)]_303 33773 9.40e-08 202_[+3(1.20e-08)]_222_\ [+2(1.73e-07)]_35 45800 5.83e-08 58_[+1(8.97e-07)]_231_\ [+3(1.80e-09)]_175 32487 7.77e-01 500 33814 1.88e-04 20_[+1(3.88e-08)]_465 33857 2.45e-06 176_[+3(3.22e-07)]_92_\ [+1(8.28e-07)]_196 36528 5.96e-03 286_[+3(4.39e-07)]_193 46913 6.19e-01 500 37993 8.87e-12 27_[+3(1.00e-06)]_269_\ [+2(1.74e-08)]_22_[+1(8.45e-09)]_126 32893 1.08e-08 126_[+3(7.59e-08)]_37_\ [+1(9.43e-09)]_301 50090 6.55e-01 500 40861 1.06e-10 167_[+3(2.85e-08)]_30_\ [+2(1.20e-07)]_97_[+1(6.11e-07)]_150 35568 2.17e-03 122_[+1(1.67e-07)]_363 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************