******************************************************************************** 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/439/439.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10551 1.0000 500 1204 1.0000 500 181 1.0000 500 20698 1.0000 500 20870 1.0000 500 23421 1.0000 500 24386 1.0000 500 25395 1.0000 500 261963 1.0000 500 263637 1.0000 500 37124 1.0000 500 38157 1.0000 500 38359 1.0000 500 573 1.0000 500 7004 1.0000 500 7102 1.0000 500 8472 1.0000 500 9336 1.0000 500 9393 1.0000 500 9907 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/439/439.seqs.fa -oc motifs/439 -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= 20 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= 10000 N= 20 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.263 C 0.227 G 0.252 T 0.259 Background letter frequencies (from dataset with add-one prior applied): A 0.263 C 0.227 G 0.252 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 139 E-value = 8.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :4:2::231::::3:1 pos.-specific C a5782953:a6:9186 probability G ::3::1::::2:1::3 matrix T :1::8:349:2a:62: bits 2.1 * * 1.9 * * * 1.7 * * * ** 1.5 * * ** ** Relative 1.3 * **** ** ** * Entropy 1.1 * **** ** ** * (20.1 bits) 0.9 * **** ** ** ** 0.6 ******* ******** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CCCCTCCTTCCTCTCC consensus AGAC TA G ATG sequence AC T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 263637 466 1.08e-09 GAAGTGACAC CCCCTCTCTCCTCTCC CCCCCCCACA 38157 467 2.46e-08 GTCCCTCCAA CCCATCTATCCTCTCC TCTAACACAT 24386 163 3.60e-08 TAGTGCGCCT CTCCTCCCTCCTCTCG GCGCTGCTTT 37124 443 1.25e-07 TTGATTGCAG CCGCTCACTCCTCTTC CCTTTCTCCC 8472 14 2.54e-07 CAAAGAAGTG CAGCTCCTTCCTGACC TTGTTTCATC 23421 461 2.97e-07 ACTATTCTCC CAGCCCCTTCTTCACC TTTGTCATCC 9907 371 3.46e-07 CTTCTTTTGT CCCCTGCTTCCTCCCG CTGTTAACAA 7102 457 4.05e-07 TAGCTGCACA CCCATCCATCGTCTCA TGAGGTGAAC 25395 5 5.79e-07 TCCT CACCTCAATCGTCTTG GAAAGTGTAA 9393 451 1.29e-06 AGTCTCACAC CACCCCTTACTTCACC TGTAGCTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263637 1.1e-09 465_[+1]_19 38157 2.5e-08 466_[+1]_18 24386 3.6e-08 162_[+1]_322 37124 1.3e-07 442_[+1]_42 8472 2.5e-07 13_[+1]_471 23421 3e-07 460_[+1]_24 9907 3.5e-07 370_[+1]_114 7102 4e-07 456_[+1]_28 25395 5.8e-07 4_[+1]_480 9393 1.3e-06 450_[+1]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 263637 ( 466) CCCCTCTCTCCTCTCC 1 38157 ( 467) CCCATCTATCCTCTCC 1 24386 ( 163) CTCCTCCCTCCTCTCG 1 37124 ( 443) CCGCTCACTCCTCTTC 1 8472 ( 14) CAGCTCCTTCCTGACC 1 23421 ( 461) CAGCCCCTTCTTCACC 1 9907 ( 371) CCCCTGCTTCCTCCCG 1 7102 ( 457) CCCATCCATCGTCTCA 1 25395 ( 5) CACCTCAATCGTCTTG 1 9393 ( 451) CACCCCTTACTTCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 9700 bayes= 10.8645 E= 8.5e-004 -997 214 -997 -997 61 114 -997 -137 -997 162 25 -997 -39 182 -997 -997 -997 -18 -997 163 -997 199 -133 -997 -39 114 -997 21 19 40 -997 63 -139 -997 -997 180 -997 214 -997 -997 -997 140 -33 -37 -997 -997 -997 195 -997 199 -133 -997 19 -118 -997 121 -997 182 -997 -37 -139 140 25 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 8.5e-004 0.000000 1.000000 0.000000 0.000000 0.400000 0.500000 0.000000 0.100000 0.000000 0.700000 0.300000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.900000 0.100000 0.000000 0.200000 0.500000 0.000000 0.300000 0.300000 0.300000 0.000000 0.400000 0.100000 0.000000 0.000000 0.900000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.200000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.900000 0.100000 0.000000 0.300000 0.100000 0.000000 0.600000 0.000000 0.800000 0.000000 0.200000 0.100000 0.600000 0.300000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[CA][CG][CA][TC]C[CTA][TAC]TC[CGT]TC[TA][CT][CG] -------------------------------------------------------------------------------- Time 3.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 9 llr = 137 E-value = 1.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :71::2:131::14:482: pos.-specific C 63:a96a9221a7393:19 probability G ::7::1:::29::::::71 matrix T 4:2:11::44::22122:: bits 2.1 * * * 1.9 * * * 1.7 ** ** * * * 1.5 ** ** ** * * Relative 1.3 ** ** ** * * Entropy 1.1 ** ** ** ** * * * (22.0 bits) 0.9 ***** ** *** * *** 0.6 ***** ** *** * *** 0.4 ********* ********* 0.2 ******************* 0.0 ------------------- Multilevel CAGCCCCCTTGCCACAAGC consensus TCT A AC TC CTA sequence CG T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 20698 1 1.18e-10 . TAGCCCCCTTGCCTCCAGC AGAGGTGACG 20870 453 7.05e-09 AGGGGGGATT TCGCCCCCTGGCTACTAGC TGTTCCACTA 9393 22 2.91e-08 TCTGCTCATG CCGCCGCCAGGCCACCTGC CCATTGCTCC 38157 419 3.50e-08 CTCTTCACGT CATCCACCTCGCAACAAGC AGCAACGACA 8472 67 4.91e-08 CCTCTGTTCG TATCCCCCCCGCCCTCAGC TCTCTCTATG 7102 59 1.08e-07 GATAGGAGTA CAGCCCCACTGCCACTTAC CACTTGCAGG 24386 393 1.25e-07 ATTCATACCA CAGCCACCATGCCTCAACG CTACACTACG 573 469 1.65e-07 AACGCACCCG CCACTCCCAAGCCCCAAGC CAACACAAAC 9907 473 1.88e-07 GCGTTGGTTC TAGCCTCCTTCCTCCAAAC ACCATCACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20698 1.2e-10 [+2]_481 20870 7.1e-09 452_[+2]_29 9393 2.9e-08 21_[+2]_460 38157 3.5e-08 418_[+2]_63 8472 4.9e-08 66_[+2]_415 7102 1.1e-07 58_[+2]_423 24386 1.2e-07 392_[+2]_89 573 1.6e-07 468_[+2]_13 9907 1.9e-07 472_[+2]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=9 20698 ( 1) TAGCCCCCTTGCCTCCAGC 1 20870 ( 453) TCGCCCCCTGGCTACTAGC 1 9393 ( 22) CCGCCGCCAGGCCACCTGC 1 38157 ( 419) CATCCACCTCGCAACAAGC 1 8472 ( 67) TATCCCCCCCGCCCTCAGC 1 7102 ( 59) CAGCCCCACTGCCACTTAC 1 24386 ( 393) CAGCCACCATGCCTCAACG 1 573 ( 469) CCACTCCCAAGCCCCAAGC 1 9907 ( 473) TAGCCTCCTTCCTCCAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 9640 bayes= 10.198 E= 1.4e-002 -982 129 -982 78 134 55 -982 -982 -124 -982 140 -22 -982 214 -982 -982 -982 197 -982 -122 -24 129 -118 -122 -982 214 -982 -982 -124 197 -982 -982 34 -3 -982 78 -124 -3 -18 78 -982 -103 182 -982 -982 214 -982 -982 -124 155 -982 -22 76 55 -982 -22 -982 197 -982 -122 76 55 -982 -22 156 -982 -982 -22 -24 -103 140 -982 -982 197 -118 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 9 E= 1.4e-002 0.000000 0.555556 0.000000 0.444444 0.666667 0.333333 0.000000 0.000000 0.111111 0.000000 0.666667 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.111111 0.222222 0.555556 0.111111 0.111111 0.000000 1.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.333333 0.222222 0.000000 0.444444 0.111111 0.222222 0.222222 0.444444 0.000000 0.111111 0.888889 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.666667 0.000000 0.222222 0.444444 0.333333 0.000000 0.222222 0.000000 0.888889 0.000000 0.111111 0.444444 0.333333 0.000000 0.222222 0.777778 0.000000 0.000000 0.222222 0.222222 0.111111 0.666667 0.000000 0.000000 0.888889 0.111111 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][AC][GT]CC[CA]CC[TAC][TCG]GC[CT][ACT]C[ACT][AT][GA]C -------------------------------------------------------------------------------- Time 7.00 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 18 llr = 171 E-value = 3.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 15:67175:62: pos.-specific C :1:12::3:::: probability G 9:93:9:2a22a matrix T :4111:3::26: bits 2.1 1.9 * * 1.7 * * * * 1.5 * * * * * Relative 1.3 * * * * * Entropy 1.1 * * ** * * (13.7 bits) 0.9 * * *** * * 0.6 ******* **** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GAGAAGAAGATG consensus T G TC GG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 25395 231 8.68e-08 GGGGTAGAGG GAGAAGAAGATG CCGACATTGA 20698 274 1.72e-07 CGAGCAAGCG GTGAAGAAGATG TTGATGTGTA 10551 346 1.72e-07 TGGTGGATGT GTGAAGAAGATG CTTGAGTTGC 37124 416 1.38e-06 TTCGTCGGGG GAGAAGAAGTTG CCGGCTTGAT 23421 139 4.89e-06 GAGGCTAGAA GCGAAGAAGATG CTACGACTTG 20870 277 8.59e-06 GTAGGTCGAT GAGGAGAGGAGG AAGTGAACGA 1204 79 1.29e-05 TGCTTGGCGC GTGAAGTGGAGG AGGAAGGAGG 263637 278 1.40e-05 TGCAGCACGT GTGTAGACGATG ACTTTGGGTG 261963 255 1.71e-05 TACTTTTAAA GAGGAGTCGGTG AACTTGGAGG 181 384 1.86e-05 ATGTGTAATA GTGAAGTGGAAG GGAATGAAAG 9336 221 3.31e-05 TGCATCCTTT GTGGAGACGTAG GCTGATTTTA 573 159 3.57e-05 AGTTATGTTG GTGATGTAGGTG TAGGCGTGTG 38157 336 3.82e-05 GCCGGAGAAC GAGACGACGTGG ACACAAACAT 38359 173 4.12e-05 ATTACATCAC GTGCCGACGATG AGATCGTTCT 7004 240 4.76e-05 AGCAAGAGGC AAGAAGAGGAAG CGACCACTTC 9907 395 7.03e-05 CGCTGTTAAC AAGGAGTAGAGG CTCCTCCCGA 9393 100 1.25e-04 GCGATAGGAT GAGATAAAGGTG AGAGAGGTGC 24386 83 1.38e-04 GTTGAGAGGA GATGCGAAGGTG ATCGAGTCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25395 8.7e-08 230_[+3]_258 20698 1.7e-07 273_[+3]_215 10551 1.7e-07 345_[+3]_143 37124 1.4e-06 415_[+3]_73 23421 4.9e-06 138_[+3]_350 20870 8.6e-06 276_[+3]_212 1204 1.3e-05 78_[+3]_410 263637 1.4e-05 277_[+3]_211 261963 1.7e-05 254_[+3]_234 181 1.9e-05 383_[+3]_105 9336 3.3e-05 220_[+3]_268 573 3.6e-05 158_[+3]_330 38157 3.8e-05 335_[+3]_153 38359 4.1e-05 172_[+3]_316 7004 4.8e-05 239_[+3]_249 9907 7e-05 394_[+3]_94 9393 0.00013 99_[+3]_389 24386 0.00014 82_[+3]_406 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=18 25395 ( 231) GAGAAGAAGATG 1 20698 ( 274) GTGAAGAAGATG 1 10551 ( 346) GTGAAGAAGATG 1 37124 ( 416) GAGAAGAAGTTG 1 23421 ( 139) GCGAAGAAGATG 1 20870 ( 277) GAGGAGAGGAGG 1 1204 ( 79) GTGAAGTGGAGG 1 263637 ( 278) GTGTAGACGATG 1 261963 ( 255) GAGGAGTCGGTG 1 181 ( 384) GTGAAGTGGAAG 1 9336 ( 221) GTGGAGACGTAG 1 573 ( 159) GTGATGTAGGTG 1 38157 ( 336) GAGACGACGTGG 1 38359 ( 173) GTGCCGACGATG 1 7004 ( 240) AAGAAGAGGAAG 1 9907 ( 395) AAGGAGTAGAGG 1 9393 ( 100) GAGATAAAGGTG 1 24386 ( 83) GATGCGAAGGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 9780 bayes= 9.93221 E= 3.2e-002 -124 -1081 182 -1081 93 -203 -1081 78 -1081 -1081 191 -222 122 -203 14 -222 146 -44 -1081 -122 -224 -1081 191 -1081 146 -1081 -1081 10 93 29 -18 -1081 -1081 -1081 199 -1081 122 -1081 -18 -63 -66 -1081 -18 124 -1081 -1081 199 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 3.2e-002 0.111111 0.000000 0.888889 0.000000 0.500000 0.055556 0.000000 0.444444 0.000000 0.000000 0.944444 0.055556 0.611111 0.055556 0.277778 0.055556 0.722222 0.166667 0.000000 0.111111 0.055556 0.000000 0.944444 0.000000 0.722222 0.000000 0.000000 0.277778 0.500000 0.277778 0.222222 0.000000 0.000000 0.000000 1.000000 0.000000 0.611111 0.000000 0.222222 0.166667 0.166667 0.000000 0.222222 0.611111 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AT]G[AG]AG[AT][ACG]G[AG][TG]G -------------------------------------------------------------------------------- Time 10.59 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10551 2.97e-04 9_[+3(3.57e-05)]_324_[+3(1.72e-07)]_\ 124_[+2(9.79e-05)] 1204 1.05e-02 78_[+3(1.29e-05)]_410 181 1.20e-01 383_[+3(1.86e-05)]_105 20698 8.20e-10 [+2(1.18e-10)]_193_[+2(3.41e-06)]_\ 42_[+3(1.72e-07)]_215 20870 6.92e-07 276_[+3(8.59e-06)]_164_\ [+2(7.05e-09)]_29 23421 9.40e-06 138_[+3(4.89e-06)]_310_\ [+1(2.97e-07)]_24 24386 2.04e-08 162_[+1(3.60e-08)]_134_\ [+1(3.07e-06)]_64_[+2(1.25e-07)]_89 25395 1.62e-06 4_[+1(5.79e-07)]_210_[+3(8.68e-08)]_\ 258 261963 1.85e-02 254_[+3(1.71e-05)]_234 263637 1.02e-07 277_[+3(1.40e-05)]_176_\ [+1(1.08e-09)]_19 37124 2.76e-06 415_[+3(1.38e-06)]_15_\ [+1(1.25e-07)]_42 38157 1.39e-09 335_[+3(3.82e-05)]_54_\ [+1(3.06e-05)]_1_[+2(3.50e-08)]_29_[+1(2.46e-08)]_18 38359 3.70e-02 172_[+3(4.12e-05)]_316 573 8.15e-05 158_[+3(3.57e-05)]_298_\ [+2(1.65e-07)]_13 7004 1.44e-02 239_[+3(4.76e-05)]_249 7102 4.82e-07 58_[+2(1.08e-07)]_308_\ [+1(4.82e-05)]_55_[+1(4.05e-07)]_28 8472 5.82e-07 13_[+1(2.54e-07)]_37_[+2(4.91e-08)]_\ 415 9336 4.05e-02 220_[+3(3.31e-05)]_268 9393 1.31e-07 21_[+2(2.91e-08)]_410_\ [+1(1.29e-06)]_34 9907 1.29e-07 370_[+1(3.46e-07)]_8_[+3(7.03e-05)]_\ 66_[+2(1.88e-07)]_9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************