******************************************************************************** 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/132/132.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42808 1.0000 500 42832 1.0000 500 36392 1.0000 500 46687 1.0000 500 47306 1.0000 500 47449 1.0000 500 47619 1.0000 500 14457 1.0000 500 54935 1.0000 500 29812 1.0000 500 51157 1.0000 500 43398 1.0000 500 32940 1.0000 500 55192 1.0000 500 43943 1.0000 500 24223 1.0000 500 50615 1.0000 500 44790 1.0000 500 11674 1.0000 500 45630 1.0000 500 45811 1.0000 500 46323 1.0000 500 36105 1.0000 500 47569 1.0000 500 8511 1.0000 500 47572 1.0000 500 44488 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/132/132.seqs.fa -oc motifs/132 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.244 G 0.217 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.244 G 0.217 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 24 llr = 212 E-value = 1.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 5::27:2::4a4 pos.-specific C 22:41a:::3:1 probability G 2::42::a14:3 matrix T 28a1::8:9::2 bits 2.2 2.0 * * * 1.8 * * * * 1.5 * * * * Relative 1.3 * * ** * Entropy 1.1 ** * ** * (12.7 bits) 0.9 ** **** * 0.7 ** ***** * 0.4 ** ******* 0.2 ************ 0.0 ------------ Multilevel ATTCACTGTAAA consensus TC GG A G G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 45630 429 1.26e-07 GTATTCTGAT ATTGACTGTGAA GCATATCAAA 51157 182 5.96e-07 TTCGAAGACG ATTCACTGTAAG CATTGGAATG 47619 358 1.67e-06 TTGCAATGCT ATTGACTGTGAT GACTTTGAAT 50615 348 3.92e-06 GTATCGAGCG ATTGACAGTGAA AATAGATCCA 43398 224 3.92e-06 CTGTGAGCTG ACTGACTGTGAA GGAGAAGTGA 46687 19 6.39e-06 GTAAGAATGG ATTCGCTGTCAG CAAGAAACCT 42832 178 8.64e-06 TGCTGAGATT GTTAACTGTGAG TAGAATAATT 36392 295 1.01e-05 CGAATAGCAT ACTCACTGTCAA GCTTGGCGCG 54935 115 1.26e-05 TTACAGTTAC CTTAACTGTAAA TTATAGTTTT 43943 480 1.88e-05 CAGCTGCAGG TTTCACTGTCAT CATTTACCA 42808 253 1.88e-05 TTTTTGGCCC ATTGGCAGTAAA AACCCGTCGG 44790 311 2.25e-05 TACTGTCCGT ATTCGCTGTGAC CATTTAGGGC 47572 10 3.21e-05 TTTGGGTCG TTTGCCTGTCAG CCTCGGATTT 47449 97 3.92e-05 ATAAAGCTTT CTTGACAGTGAT TTCTGCAAGC 11674 175 4.71e-05 GAAATCGTTA CTTCACTGGAAG TGCTCTTGTA 36105 198 7.33e-05 TTCGCATTGT TCTTACTGTGAA ACAGGTGAGA 14457 79 7.33e-05 ACAGGACAAA ATTTCCTGTCAA CCCGGTGTAC 8511 90 9.30e-05 CACAAAAGAC TTTGACTTTGAG TCATGCAGCT 47569 48 9.30e-05 GCCGATTCTC GTTCAGTGTAAG TATCCGTTCC 45811 44 9.30e-05 TTTGTCAATA CCTCACAGTCAA TAGATCCGGT 46323 43 1.73e-04 TTTGTCTTGT ATTAACTGCAAT ATAAAAAGTG 44488 51 1.95e-04 CGCCGAACAA GTTGCCGGTAAG TTATGGTTTT 29812 10 2.21e-04 CGTACTATT TTTCGCAGGAAA CGTGTTGGCG 32940 246 2.73e-04 AAAATCTCGA GCTAGCTGTAAC AAAAATATGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45630 1.3e-07 428_[+1]_60 51157 6e-07 181_[+1]_307 47619 1.7e-06 357_[+1]_131 50615 3.9e-06 347_[+1]_141 43398 3.9e-06 223_[+1]_265 46687 6.4e-06 18_[+1]_470 42832 8.6e-06 177_[+1]_311 36392 1e-05 294_[+1]_194 54935 1.3e-05 114_[+1]_374 43943 1.9e-05 479_[+1]_9 42808 1.9e-05 252_[+1]_236 44790 2.3e-05 310_[+1]_178 47572 3.2e-05 9_[+1]_479 47449 3.9e-05 96_[+1]_392 11674 4.7e-05 174_[+1]_314 36105 7.3e-05 197_[+1]_291 14457 7.3e-05 78_[+1]_410 8511 9.3e-05 89_[+1]_399 47569 9.3e-05 47_[+1]_441 45811 9.3e-05 43_[+1]_445 46323 0.00017 42_[+1]_446 44488 0.00019 50_[+1]_438 29812 0.00022 9_[+1]_479 32940 0.00027 245_[+1]_243 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=24 45630 ( 429) ATTGACTGTGAA 1 51157 ( 182) ATTCACTGTAAG 1 47619 ( 358) ATTGACTGTGAT 1 50615 ( 348) ATTGACAGTGAA 1 43398 ( 224) ACTGACTGTGAA 1 46687 ( 19) ATTCGCTGTCAG 1 42832 ( 178) GTTAACTGTGAG 1 36392 ( 295) ACTCACTGTCAA 1 54935 ( 115) CTTAACTGTAAA 1 43943 ( 480) TTTCACTGTCAT 1 42808 ( 253) ATTGGCAGTAAA 1 44790 ( 311) ATTCGCTGTGAC 1 47572 ( 10) TTTGCCTGTCAG 1 47449 ( 97) CTTGACAGTGAT 1 11674 ( 175) CTTCACTGGAAG 1 36105 ( 198) TCTTACTGTGAA 1 14457 ( 79) ATTTCCTGTCAA 1 8511 ( 90) TTTGACTTTGAG 1 47569 ( 48) GTTCAGTGTAAG 1 45811 ( 44) CCTCACAGTCAA 1 46323 ( 43) ATTAACTGCAAT 1 44488 ( 51) GTTGCCGGTAAG 1 29812 ( 10) TTTCGCAGGAAA 1 32940 ( 246) GCTAGCTGTAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13203 bayes= 9.54915 E= 1.5e-001 77 -55 -38 -38 -1123 -23 -1123 155 -1123 -1123 -1123 188 -69 62 79 -170 131 -96 -6 -1123 -1123 197 -238 -1123 -36 -1123 -238 147 -1123 -1123 214 -270 -1123 -255 -138 169 48 4 79 -1123 190 -1123 -1123 -1123 64 -155 62 -70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 24 E= 1.5e-001 0.458333 0.166667 0.166667 0.208333 0.000000 0.208333 0.000000 0.791667 0.000000 0.000000 0.000000 1.000000 0.166667 0.375000 0.375000 0.083333 0.666667 0.125000 0.208333 0.000000 0.000000 0.958333 0.041667 0.000000 0.208333 0.000000 0.041667 0.750000 0.000000 0.000000 0.958333 0.041667 0.000000 0.041667 0.083333 0.875000 0.375000 0.250000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 0.416667 0.083333 0.333333 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT][TC]T[CG][AG]C[TA]GT[AGC]A[AG] -------------------------------------------------------------------------------- Time 7.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 126 E-value = 1.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 91:46413:9a111::44:9: pos.-specific C ::a4:191a::9:4:7::7:a probability G 1::131:6:1::9::::431: matrix T :9::13:::::::4a361::: bits 2.2 2.0 * * * * * 1.8 * * * * * 1.5 * * * * * * Relative 1.3 *** * ***** * *** Entropy 1.1 *** * ***** ** *** (26.0 bits) 0.9 *** * ***** *** *** 0.7 ***** ******* ******* 0.4 ***** *************** 0.2 ********************* 0.0 --------------------- Multilevel ATCAAACGCAACGCTCTACAC consensus CGT A T TAGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 47569 82 1.68e-11 AGTTGTTACC ATCCGACGCAACGCTCAACAC GTTTCTTAGG 51157 367 1.02e-10 TCCAAGCAGG ATCCAACGCAACGTTTTGGAC AGCACCAGCA 29812 367 1.02e-10 TCCAAGCAGG ATCCAACGCAACGTTTTGGAC AGCACCAGCA 55192 231 1.73e-09 AAACAACGAC AACAACCACAACGTTCTGCAC TTACCCTCGG 36392 436 1.56e-08 CACAAAAGGA ATCAAGAACAAAGCTCAACAC GCCGTACAGC 14457 479 2.30e-08 TGGATACGGG GTCGGTCGCGACGCTCTACGC C 43398 378 5.45e-08 AAAGATCAGC ATCATTCCCAACAATCATCAC TCAGATTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47569 1.7e-11 81_[+2]_398 51157 1e-10 366_[+2]_113 29812 1e-10 366_[+2]_113 55192 1.7e-09 230_[+2]_249 36392 1.6e-08 435_[+2]_44 14457 2.3e-08 478_[+2]_1 43398 5.5e-08 377_[+2]_102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 47569 ( 82) ATCCGACGCAACGCTCAACAC 1 51157 ( 367) ATCCAACGCAACGTTTTGGAC 1 29812 ( 367) ATCCAACGCAACGTTTTGGAC 1 55192 ( 231) AACAACCACAACGTTCTGCAC 1 36392 ( 436) ATCAAGAACAAAGCTCAACAC 1 14457 ( 479) GTCGGTCGCGACGCTCTACGC 1 43398 ( 378) ATCATTCCCAACAATCATCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 10.6974 E= 1.1e+000 168 -945 -60 -945 -91 -945 -945 166 -945 203 -945 -945 68 81 -60 -945 109 -945 40 -92 68 -77 -60 8 -91 181 -945 -945 9 -77 140 -945 -945 203 -945 -945 168 -945 -60 -945 190 -945 -945 -945 -91 181 -945 -945 -91 -945 198 -945 -91 81 -945 66 -945 -945 -945 188 -945 155 -945 8 68 -945 -945 108 68 -945 98 -92 -945 155 40 -945 168 -945 -60 -945 -945 203 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.1e+000 0.857143 0.000000 0.142857 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 0.428571 0.428571 0.142857 0.000000 0.571429 0.000000 0.285714 0.142857 0.428571 0.142857 0.142857 0.285714 0.142857 0.857143 0.000000 0.000000 0.285714 0.142857 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.142857 0.428571 0.000000 0.428571 0.000000 0.000000 0.000000 1.000000 0.000000 0.714286 0.000000 0.285714 0.428571 0.000000 0.000000 0.571429 0.428571 0.000000 0.428571 0.142857 0.000000 0.714286 0.285714 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- ATC[AC][AG][AT]C[GA]CAACG[CT]T[CT][TA][AG][CG]AC -------------------------------------------------------------------------------- Time 14.28 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 8 llr = 140 E-value = 1.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::351::1::69:9::::36: pos.-specific C a:11:1a:3941a18816131 probability G :8:4::::1::::::1::41: matrix T :36:99:961::::31943:9 bits 2.2 2.0 * * * 1.8 * * * 1.5 * * * * Relative 1.3 ** **** * *** * * Entropy 1.1 ** **** ****** ** * (25.3 bits) 0.9 ** **** ********* * 0.7 ****************** ** 0.4 ****************** ** 0.2 ********************* 0.0 --------------------- Multilevel CGTATTCTTCAACACCTCGAT consensus TAG C C T TAC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 51157 472 1.65e-11 CTTACACCGC CGTATTCTTCAACACCTCTCT ATCCCATC 29812 472 1.65e-11 CTTACACCGC CGTATTCTTCAACACCTCTCT ATCCCATC 47572 441 3.38e-11 CTCCTCTTCA CGAGTTCTCCAACACCTCGAT ACCCAAGTCT 47569 327 1.59e-09 CTGATCTTCC CGAGATCTCCAACACCTCAAT CAATACCCAA 42808 42 3.25e-08 CGAAGAGCCT CTTCTTCATCAACATCTTCAT CGTCTTGCTC 14457 237 4.38e-08 CCTTTTGATT CGTATTCTTCCCCCCCCCGAC ACGGGTGAGA 46323 295 4.63e-08 CTTGCGCGCG CTCGTCCTTCCACACGTTAAT GAGCCGGAAA 47619 53 7.85e-08 CAGTTAGTGA CGTATTCTGTCACATTTTGGT GCTGGTCGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 51157 1.7e-11 471_[+3]_8 29812 1.7e-11 471_[+3]_8 47572 3.4e-11 440_[+3]_39 47569 1.6e-09 326_[+3]_153 42808 3.2e-08 41_[+3]_438 14457 4.4e-08 236_[+3]_243 46323 4.6e-08 294_[+3]_185 47619 7.8e-08 52_[+3]_427 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=8 51157 ( 472) CGTATTCTTCAACACCTCTCT 1 29812 ( 472) CGTATTCTTCAACACCTCTCT 1 47572 ( 441) CGAGTTCTCCAACACCTCGAT 1 47569 ( 327) CGAGATCTCCAACACCTCAAT 1 42808 ( 42) CTTCTTCATCAACATCTTCAT 1 14457 ( 237) CGTATTCTTCCCCCCCCCGAC 1 46323 ( 295) CTCGTCCTTCCACACGTTAAT 1 47619 ( 53) CGTATTCTGTCACATTTTGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 10.6609 E= 1.5e-001 -965 203 -965 -965 -965 -965 179 -12 -10 -96 -965 120 90 -96 79 -965 -110 -965 -965 169 -965 -96 -965 169 -965 203 -965 -965 -110 -965 -965 169 -965 3 -79 120 -965 184 -965 -111 122 62 -965 -965 171 -96 -965 -965 -965 203 -965 -965 171 -96 -965 -965 -965 162 -965 -12 -965 162 -79 -111 -965 -96 -965 169 -965 136 -965 47 -10 -96 79 -12 122 3 -79 -965 -965 -96 -965 169 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 1.5e-001 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.250000 0.125000 0.000000 0.625000 0.500000 0.125000 0.375000 0.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.875000 0.000000 1.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.250000 0.125000 0.625000 0.000000 0.875000 0.000000 0.125000 0.625000 0.375000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.125000 0.125000 0.000000 0.125000 0.000000 0.875000 0.000000 0.625000 0.000000 0.375000 0.250000 0.125000 0.375000 0.250000 0.625000 0.250000 0.125000 0.000000 0.000000 0.125000 0.000000 0.875000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[GT][TA][AG]TTCT[TC]C[AC]ACA[CT]CT[CT][GAT][AC]T -------------------------------------------------------------------------------- Time 21.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42808 1.82e-05 41_[+3(3.25e-08)]_190_\ [+1(1.88e-05)]_236 42832 5.47e-02 177_[+1(8.64e-06)]_311 36392 5.97e-06 294_[+1(1.01e-05)]_129_\ [+2(1.56e-08)]_44 46687 1.98e-02 18_[+1(6.39e-06)]_470 47306 6.00e-01 500 47449 8.01e-02 96_[+1(3.92e-05)]_392 47619 2.57e-06 52_[+3(7.85e-08)]_284_\ [+1(1.67e-06)]_131 14457 2.88e-09 78_[+1(7.33e-05)]_146_\ [+3(4.38e-08)]_221_[+2(2.30e-08)]_1 54935 1.23e-02 114_[+1(1.26e-05)]_374 29812 2.97e-14 366_[+2(1.02e-10)]_84_\ [+3(1.65e-11)]_8 51157 1.12e-16 181_[+1(5.96e-07)]_173_\ [+2(1.02e-10)]_84_[+3(1.65e-11)]_8 43398 1.04e-06 3_[+2(3.27e-05)]_199_[+1(3.92e-06)]_\ 15_[+1(4.71e-05)]_115_[+2(5.45e-08)]_102 32940 4.00e-01 500 55192 5.52e-05 230_[+2(1.73e-09)]_249 43943 1.15e-01 479_[+1(1.88e-05)]_9 24223 1.93e-01 473_[+3(4.85e-05)]_6 50615 3.96e-02 347_[+1(3.92e-06)]_141 44790 9.41e-02 310_[+1(2.25e-05)]_178 11674 1.81e-01 174_[+1(4.71e-05)]_314 45630 2.57e-03 428_[+1(1.26e-07)]_60 45811 1.14e-01 43_[+1(9.30e-05)]_445 46323 1.06e-04 294_[+3(4.63e-08)]_185 36105 2.60e-01 197_[+1(7.33e-05)]_291 47569 1.86e-13 47_[+1(9.30e-05)]_22_[+2(1.68e-11)]_\ 224_[+3(1.59e-09)]_153 8511 6.72e-02 89_[+1(9.30e-05)]_399 47572 2.40e-08 9_[+1(3.21e-05)]_419_[+3(3.38e-11)]_\ 39 44488 3.74e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************