******************************************************************************** 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/182/182.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21708 1.0000 500 21984 1.0000 500 23288 1.0000 500 23414 1.0000 500 24300 1.0000 500 25194 1.0000 500 26002 1.0000 500 263946 1.0000 500 268293 1.0000 500 270137 1.0000 500 7054 1.0000 500 9338 1.0000 500 9522 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/182/182.seqs.fa -oc motifs/182 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.239 G 0.227 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.239 G 0.227 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 13 llr = 147 E-value = 1.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :24:6:223114:11: pos.-specific C 86:a126:148:a7:9 probability G :21:2:2311:::1:1 matrix T 2:5:28155516:29: bits 2.1 * * 1.9 * * 1.7 * * * 1.5 * * * ** Relative 1.3 * * * * ** Entropy 1.1 * * * * * ** (16.3 bits) 0.9 * * * *** ** 0.6 **** * * ****** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CCTCATCTTTCTCCTC consensus GA C GAC A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 9522 446 3.99e-08 CCAAACGACG CCTCACCGACCTCCTC CAACTCCTAC 268293 460 2.88e-07 CTCAACACAA CCTCATAAACCTCCTC CTTCCCTAGC 26002 478 4.56e-07 CCAGCACCTT CCACACCTCTCACCTC TCCTTCT 23414 36 5.10e-07 GTACAAAATG CCACATGGTACTCCTC CAAAGATGCT 21984 97 6.29e-07 AAGGCAGTAT TCTCCTCTTCCTCCTC CATCCAAACA 24300 145 8.57e-07 TGGACTTTGG CGGCTTCTTTCTCCTC ACCTACGAGT 21708 471 1.28e-06 TCCAGCACTG CCTCATCTAGCTCATC ACAACATAAC 270137 58 1.41e-06 AATTTCCTAC TCACATCGTCCACTTC CACTACAGAA 9338 286 2.06e-06 ATCTCATGCA CGTCTTCTTTATCCTC TGCACGTTGA 7054 438 4.10e-06 CGTACAACTT CAACATTATTCACCTC CGCCCACCGC 23288 11 1.89e-05 TCCCCCAGTG CATCGTCTATTTCTTC TGTAAAACGT 25194 362 3.06e-05 TTGGGGTGTG CCTCATGTGTCACGTG CAACTTTTTA 263946 309 3.25e-05 AACAGCATAG CGACGCAGTCCACCAC TGGTATCGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9522 4e-08 445_[+1]_39 268293 2.9e-07 459_[+1]_25 26002 4.6e-07 477_[+1]_7 23414 5.1e-07 35_[+1]_449 21984 6.3e-07 96_[+1]_388 24300 8.6e-07 144_[+1]_340 21708 1.3e-06 470_[+1]_14 270137 1.4e-06 57_[+1]_427 9338 2.1e-06 285_[+1]_199 7054 4.1e-06 437_[+1]_47 23288 1.9e-05 10_[+1]_474 25194 3.1e-05 361_[+1]_123 263946 3.2e-05 308_[+1]_176 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=13 9522 ( 446) CCTCACCGACCTCCTC 1 268293 ( 460) CCTCATAAACCTCCTC 1 26002 ( 478) CCACACCTCTCACCTC 1 23414 ( 36) CCACATGGTACTCCTC 1 21984 ( 97) TCTCCTCTTCCTCCTC 1 24300 ( 145) CGGCTTCTTTCTCCTC 1 21708 ( 471) CCTCATCTAGCTCATC 1 270137 ( 58) TCACATCGTCCACTTC 1 9338 ( 286) CGTCTTCTTTATCCTC 1 7054 ( 438) CAACATTATTCACCTC 1 23288 ( 11) CATCGTCTATTTCTTC 1 25194 ( 362) CCTCATGTGTCACGTG 1 263946 ( 309) CGACGCAGTCCACCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 8.91886 E= 1.3e-001 -1035 183 -1035 -83 -76 137 2 -1035 56 -1035 -156 98 -1035 207 -1035 -1035 124 -163 -56 -83 -1035 -5 -1035 149 -76 137 -56 -183 -76 -1035 44 98 24 -163 -156 98 -176 69 -156 75 -176 183 -1035 -183 56 -1035 -1035 117 -1035 207 -1035 -1035 -176 154 -156 -83 -176 -1035 -1035 175 -1035 195 -156 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 13 E= 1.3e-001 0.000000 0.846154 0.000000 0.153846 0.153846 0.615385 0.230769 0.000000 0.384615 0.000000 0.076923 0.538462 0.000000 1.000000 0.000000 0.000000 0.615385 0.076923 0.153846 0.153846 0.000000 0.230769 0.000000 0.769231 0.153846 0.615385 0.153846 0.076923 0.153846 0.000000 0.307692 0.538462 0.307692 0.076923 0.076923 0.538462 0.076923 0.384615 0.076923 0.461538 0.076923 0.846154 0.000000 0.076923 0.384615 0.000000 0.000000 0.615385 0.000000 1.000000 0.000000 0.000000 0.076923 0.692308 0.076923 0.153846 0.076923 0.000000 0.000000 0.923077 0.000000 0.923077 0.076923 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[CG][TA]CA[TC]C[TG][TA][TC]C[TA]CCTC -------------------------------------------------------------------------------- Time 1.55 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 6 llr = 88 E-value = 1.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::7:3:::7:: pos.-specific C 35:::::::::::3: probability G 7:a8:a:872:a257 matrix T :5:2a:32:8a:223 bits 2.1 * * * 1.9 * ** ** 1.7 * ** ** 1.5 **** * ** Relative 1.3 * **** * *** Entropy 1.1 ************ * (21.1 bits) 0.9 ************ * 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel GCGGTGAGGTTGAGG consensus CT T A CT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 268293 283 1.70e-09 TGAGGACGAC GCGGTGAGGTTGACG AGGTATTTGT 21984 461 5.36e-09 TGGTTGTCGT GTGGTGTGGTTGAGG CATTGTGAAT 9338 219 1.37e-07 ATATGTACAA CTGGTGAGATTGGGG TGTTCTCGAC 23414 410 3.46e-07 TGAAAGTCAC GTGGTGATGTTGATT TTGTTCGACT 7054 330 3.62e-07 CGTGATAGTG GCGGTGAGAGTGTCG TCTGTGGTTG 23288 243 3.62e-07 TCAAAGTGAG CCGTTGTGGTTGAGT ATCGGTAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 268293 1.7e-09 282_[+2]_203 21984 5.4e-09 460_[+2]_25 9338 1.4e-07 218_[+2]_267 23414 3.5e-07 409_[+2]_76 7054 3.6e-07 329_[+2]_156 23288 3.6e-07 242_[+2]_243 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=6 268293 ( 283) GCGGTGAGGTTGACG 1 21984 ( 461) GTGGTGTGGTTGAGG 1 9338 ( 219) CTGGTGAGATTGGGG 1 23414 ( 410) GTGGTGATGTTGATT 1 7054 ( 330) GCGGTGAGAGTGTCG 1 23288 ( 243) CCGTTGTGGTTGAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 6318 bayes= 9.69752 E= 1.3e+002 -923 48 155 -923 -923 107 -923 87 -923 -923 213 -923 -923 -923 187 -71 -923 -923 -923 187 -923 -923 213 -923 136 -923 -923 28 -923 -923 187 -71 36 -923 155 -923 -923 -923 -45 160 -923 -923 -923 187 -923 -923 213 -923 136 -923 -45 -71 -923 48 114 -71 -923 -923 155 28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 6 E= 1.3e+002 0.000000 0.333333 0.666667 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.833333 0.166667 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.166667 0.166667 0.000000 0.333333 0.500000 0.166667 0.000000 0.000000 0.666667 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC][CT]GGTG[AT]G[GA]TTGA[GC][GT] -------------------------------------------------------------------------------- Time 3.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 134 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 27129:421::2:a1:a913: pos.-specific C 8:63:3312313::36::91a probability G :134:7:2419:a:23:::1: matrix T :2::1:2426:4::31:1:4: bits 2.1 * * 1.9 ** * * 1.7 * ** * * 1.5 * * ** *** * Relative 1.3 * ** * ** *** * Entropy 1.1 * ** * ** *** * (21.4 bits) 0.9 * ** * ** *** * 0.6 ****** ** ** **** * 0.4 ******* ***** **** * 0.2 ********************* 0.0 --------------------- Multilevel CACGAGATGTGTGACCAACTC consensus ATGC CCACC C TG A sequence A TGT A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9522 137 5.34e-11 TCCGGTACGC CAGCAGCTGTGTGATCAACTC CTGCGTTTGT 23414 62 2.18e-08 CAAAGATGCT CACGACAAGTGTGAAGAACGC CATCCATCCT 26002 1 2.97e-08 . CAGGAGTTGCCCGATGAACTC TTTTCTCCTT 21708 257 4.83e-08 GCCGTGATTT CTCGAGACTCGAGACGAACAC AAATACAAGA 9338 349 1.55e-07 GAACACAATG CAACAGCATTGCGATTAACAC CACAACAACA 7054 461 1.55e-07 CTCCGCCCAC CGCCACCGCCGCGACCAACCC CTCTGCGTTC 23288 126 1.55e-07 CAAGTGACGA AACGAGATCGGTGAGCAAATC TTCATCATAA 270137 79 1.67e-07 ACTTCCACTA CAGAACTTGTGAGAGCATCAC GATTGGACAC 268293 61 4.49e-07 TCCTCCACTC ATCATGAGATGTGACCAACTC TGACGATTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9522 5.3e-11 136_[+3]_343 23414 2.2e-08 61_[+3]_418 26002 3e-08 [+3]_479 21708 4.8e-08 256_[+3]_223 9338 1.6e-07 348_[+3]_131 7054 1.6e-07 460_[+3]_19 23288 1.6e-07 125_[+3]_354 270137 1.7e-07 78_[+3]_401 268293 4.5e-07 60_[+3]_419 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 9522 ( 137) CAGCAGCTGTGTGATCAACTC 1 23414 ( 62) CACGACAAGTGTGAAGAACGC 1 26002 ( 1) CAGGAGTTGCCCGATGAACTC 1 21708 ( 257) CTCGAGACTCGAGACGAACAC 1 9338 ( 349) CAACAGCATTGCGATTAACAC 1 7054 ( 461) CGCCACCGCCGCGACCAACCC 1 23288 ( 126) AACGAGATCGGTGAGCAAATC 1 270137 ( 79) CAGAACTTGTGAGAGCATCAC 1 268293 ( 61) ATCATGAGATGTGACCAACTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 9.56981 E= 1.4e-001 -23 170 -982 -982 136 -982 -103 -30 -123 122 55 -982 -23 48 97 -982 177 -982 -982 -130 -982 48 155 -982 77 48 -982 -30 -23 -110 -3 70 -123 -10 97 -30 -982 48 -103 102 -982 -110 197 -982 -23 48 -982 70 -982 -982 214 -982 194 -982 -982 -982 -123 48 -3 28 -982 122 55 -130 194 -982 -982 -982 177 -982 -982 -130 -123 190 -982 -982 36 -110 -103 70 -982 207 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 1.4e-001 0.222222 0.777778 0.000000 0.000000 0.666667 0.000000 0.111111 0.222222 0.111111 0.555556 0.333333 0.000000 0.222222 0.333333 0.444444 0.000000 0.888889 0.000000 0.000000 0.111111 0.000000 0.333333 0.666667 0.000000 0.444444 0.333333 0.000000 0.222222 0.222222 0.111111 0.222222 0.444444 0.111111 0.222222 0.444444 0.222222 0.000000 0.333333 0.111111 0.555556 0.000000 0.111111 0.888889 0.000000 0.222222 0.333333 0.000000 0.444444 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.111111 0.333333 0.222222 0.333333 0.000000 0.555556 0.333333 0.111111 1.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.000000 0.111111 0.111111 0.888889 0.000000 0.000000 0.333333 0.111111 0.111111 0.444444 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CA][AT][CG][GCA]A[GC][ACT][TAG][GCT][TC]G[TCA]GA[CTG][CG]AAC[TA]C -------------------------------------------------------------------------------- Time 4.51 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21708 1.12e-06 256_[+3(4.83e-08)]_193_\ [+1(1.28e-06)]_14 21984 1.27e-07 9_[+1(4.50e-05)]_71_[+1(6.29e-07)]_\ 348_[+2(5.36e-09)]_25 23288 3.40e-08 10_[+1(1.89e-05)]_99_[+3(1.55e-07)]_\ 96_[+2(3.62e-07)]_243 23414 1.89e-10 35_[+1(5.10e-07)]_10_[+3(2.18e-08)]_\ 187_[+2(1.67e-05)]_125_[+2(3.46e-07)]_76 24300 3.15e-03 144_[+1(8.57e-07)]_340 25194 3.68e-02 361_[+1(3.06e-05)]_123 26002 4.18e-07 [+3(2.97e-08)]_456_[+1(4.56e-07)]_7 263946 4.97e-02 308_[+1(3.25e-05)]_176 268293 1.30e-11 60_[+3(4.49e-07)]_201_\ [+2(1.70e-09)]_162_[+1(2.88e-07)]_25 270137 2.17e-06 57_[+1(1.41e-06)]_5_[+3(1.67e-07)]_\ 401 7054 8.38e-09 329_[+2(3.62e-07)]_93_\ [+1(4.10e-06)]_7_[+3(1.55e-07)]_19 9338 1.81e-09 218_[+2(1.37e-07)]_52_\ [+1(2.06e-06)]_47_[+3(1.55e-07)]_131 9522 3.40e-11 136_[+3(5.34e-11)]_288_\ [+1(3.99e-08)]_39 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************