******************************************************************************** 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/36/36.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 17362 1.0000 500 46383 1.0000 500 13384 1.0000 500 28433 1.0000 500 48060 1.0000 500 18194 1.0000 500 49127 1.0000 500 49381 1.0000 500 40171 1.0000 500 49978 1.0000 500 45229 1.0000 500 46032 1.0000 500 42911 1.0000 500 46991 1.0000 500 33893 1.0000 500 37743 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/36/36.seqs.fa -oc motifs/36 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.272 C 0.232 G 0.219 T 0.276 Background letter frequencies (from dataset with add-one prior applied): A 0.272 C 0.232 G 0.219 T 0.276 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 11 llr = 129 E-value = 4.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::a:4:::a5: pos.-specific C 514:9::45:1: probability G ::6:::a:5:5: matrix T 59::16:6:::a bits 2.2 * 2.0 * * * 1.8 ** * * * 1.5 * ** * * * Relative 1.3 **** * * * Entropy 1.1 ***** **** * (16.9 bits) 0.9 ********** * 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CTGACTGTGAAT consensus T C A CC G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 17362 371 1.75e-07 GTAAGTTTTG CTGACTGTGAAT ATTACCGCAC 46383 326 2.83e-07 TTGTGCACTG CTGACTGCGAGT TGTTCTTTAC 37743 241 7.10e-07 TTTATCGAAA CTGACTGCCAGT GACAGTGAGT 49978 415 8.84e-07 TCCGGAGTGA TTGACTGCGAGT CTTAATCCGC 18194 402 2.41e-06 ACACAATTGA CTCACTGCCAGT CGGTTTCTTG 40171 172 3.29e-06 AAACAAATTG CTGACTGTGACT GTGAAGTTAG 13384 25 3.29e-06 CCTCTCTGTG CTCACAGTCAAT GGGATTCGAG 28433 22 3.51e-06 TTGCTGCGAG TTCACAGTCAGT CAGTGGTTGA 42911 452 3.97e-06 GCAAAAATCG TTCACAGTCAAT CGATTCCTTT 48060 126 5.60e-06 TGATCTTTCA TCGACTGTGAAT GGAACGTAGC 46991 124 1.01e-05 CGGATGGACC TTGATAGTGAAT GCCATGGGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17362 1.8e-07 370_[+1]_118 46383 2.8e-07 325_[+1]_163 37743 7.1e-07 240_[+1]_248 49978 8.8e-07 414_[+1]_74 18194 2.4e-06 401_[+1]_87 40171 3.3e-06 171_[+1]_317 13384 3.3e-06 24_[+1]_464 28433 3.5e-06 21_[+1]_467 42911 4e-06 451_[+1]_37 48060 5.6e-06 125_[+1]_363 46991 1e-05 123_[+1]_365 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=11 17362 ( 371) CTGACTGTGAAT 1 46383 ( 326) CTGACTGCGAGT 1 37743 ( 241) CTGACTGCCAGT 1 49978 ( 415) TTGACTGCGAGT 1 18194 ( 402) CTCACTGCCAGT 1 40171 ( 172) CTGACTGTGACT 1 13384 ( 25) CTCACAGTCAAT 1 28433 ( 22) TTCACAGTCAGT 1 42911 ( 452) TTCACAGTCAAT 1 48060 ( 126) TCGACTGTGAAT 1 46991 ( 124) TTGATAGTGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 10.4997 E= 4.8e-003 -1010 123 -1010 72 -1010 -135 -1010 172 -1010 65 154 -1010 188 -1010 -1010 -1010 -1010 197 -1010 -160 42 -1010 -1010 120 -1010 -1010 219 -1010 -1010 65 -1010 120 -1010 97 131 -1010 188 -1010 -1010 -1010 74 -135 105 -1010 -1010 -1010 -1010 185 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 4.8e-003 0.000000 0.545455 0.000000 0.454545 0.000000 0.090909 0.000000 0.909091 0.000000 0.363636 0.636364 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.909091 0.000000 0.090909 0.363636 0.000000 0.000000 0.636364 0.000000 0.000000 1.000000 0.000000 0.000000 0.363636 0.000000 0.636364 0.000000 0.454545 0.545455 0.000000 1.000000 0.000000 0.000000 0.000000 0.454545 0.090909 0.454545 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT]T[GC]AC[TA]G[TC][GC]A[AG]T -------------------------------------------------------------------------------- Time 2.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 9 llr = 122 E-value = 2.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::3:761::2:::9a8 pos.-specific C 1::4::36:1::11:: probability G 3::6:::33::a9::: matrix T 6a7:346177a::::2 bits 2.2 * 2.0 * * 1.8 * *** * 1.5 * *** * Relative 1.3 * ***** Entropy 1.1 * * * ****** (19.6 bits) 0.9 ***** * ****** 0.7 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TTTGAATCTTTGGAAA consensus G ACTTCGGA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 17362 451 4.43e-09 TATTCGAAAA TTTGATCCTTTGGAAA GTATTAGACC 48060 175 6.08e-08 GCTTCAGCCG TTTGAATGTTTGGAAT TCGAACATCT 46383 16 1.02e-07 GCCTTGGCCC GTTCAATCGATGGAAA AGTAGCATAC 42911 193 1.60e-07 ATTGTCGCAT TTTCATTGGATGGAAA TGTAGCAGAG 46991 28 2.19e-07 GAACCAAACG TTACTTCCGTTGGAAA AGGGACGATT 18194 297 3.20e-07 AATGGAATAT TTTGTATCTTTGCAAA GCATGAATTA 28433 141 6.99e-07 CTTCATACGA CTAGAATGTTTGGAAT CGAGAAAGGA 33893 202 7.99e-07 GTCTTCATAT GTAGTACCTTTGGCAA AAGAGCATTT 40171 354 2.29e-06 ACATCTCCTT GTTCATATTCTGGAAA GCATACCGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17362 4.4e-09 450_[+2]_34 48060 6.1e-08 174_[+2]_310 46383 1e-07 15_[+2]_469 42911 1.6e-07 192_[+2]_292 46991 2.2e-07 27_[+2]_457 18194 3.2e-07 296_[+2]_188 28433 7e-07 140_[+2]_344 33893 8e-07 201_[+2]_283 40171 2.3e-06 353_[+2]_131 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=9 17362 ( 451) TTTGATCCTTTGGAAA 1 48060 ( 175) TTTGAATGTTTGGAAT 1 46383 ( 16) GTTCAATCGATGGAAA 1 42911 ( 193) TTTCATTGGATGGAAA 1 46991 ( 28) TTACTTCCGTTGGAAA 1 18194 ( 297) TTTGTATCTTTGCAAA 1 28433 ( 141) CTAGAATGTTTGGAAT 1 33893 ( 202) GTAGTACCTTTGGCAA 1 40171 ( 354) GTTCATATTCTGGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 7760 bayes= 9.88469 E= 2.6e+000 -982 -106 60 101 -982 -982 -982 185 29 -982 -982 127 -982 94 134 -982 129 -982 -982 27 103 -982 -982 69 -129 52 -982 101 -982 126 60 -131 -982 -982 60 127 -29 -106 -982 127 -982 -982 -982 185 -982 -982 219 -982 -982 -106 202 -982 171 -106 -982 -982 188 -982 -982 -982 151 -982 -982 -31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 9 E= 2.6e+000 0.000000 0.111111 0.333333 0.555556 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.444444 0.555556 0.000000 0.666667 0.000000 0.000000 0.333333 0.555556 0.000000 0.000000 0.444444 0.111111 0.333333 0.000000 0.555556 0.000000 0.555556 0.333333 0.111111 0.000000 0.000000 0.333333 0.666667 0.222222 0.111111 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.888889 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.000000 0.222222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG]T[TA][GC][AT][AT][TC][CG][TG][TA]TGGAA[AT] -------------------------------------------------------------------------------- Time 4.47 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 83 E-value = 1.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 8::5a::a::8::3::8:a:: pos.-specific C :::::8::3538:35:::::: probability G 38:5:3a:35::a5:a:8:3a matrix T :3a:::::5::3::5:33:8: bits 2.2 * * * * 2.0 * ** * * * * 1.8 * * ** * * * * 1.5 * * ** * * * * Relative 1.3 ** **** ** * ** * Entropy 1.1 ******** **** ****** (30.1 bits) 0.9 ******** **** ******* 0.7 ******** ************ 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AGTAACGATCACGGCGAGATG consensus GT G G CGCT AT TT G sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 17362 107 1.55e-10 CTTTTGCTGT AGTGAGGATGACGCCGTGATG AAAGGTAGCG 49127 215 1.71e-10 GCACCGCCCC AGTAACGACCATGGCGAGAGG CAACGTCCCG 48060 1 1.71e-10 . ATTGACGAGCCCGGTGAGATG TGGATAATCT 13384 249 3.14e-10 TGAAGATGAT GGTAACGATGACGATGATATG CCTCTTACGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17362 1.6e-10 106_[+3]_373 49127 1.7e-10 214_[+3]_265 48060 1.7e-10 [+3]_479 13384 3.1e-10 248_[+3]_231 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 17362 ( 107) AGTGAGGATGACGCCGTGATG 1 49127 ( 215) AGTAACGACCATGGCGAGAGG 1 48060 ( 1) ATTGACGAGCCCGGTGAGATG 1 13384 ( 249) GGTAACGATGACGATGATATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 10.9061 E= 1.2e+003 146 -865 19 -865 -865 -865 177 -14 -865 -865 -865 185 87 -865 119 -865 187 -865 -865 -865 -865 169 19 -865 -865 -865 219 -865 187 -865 -865 -865 -865 11 19 85 -865 110 119 -865 146 11 -865 -865 -865 169 -865 -14 -865 -865 219 -865 -12 11 119 -865 -865 110 -865 85 -865 -865 219 -865 146 -865 -865 -14 -865 -865 177 -14 187 -865 -865 -865 -865 -865 19 144 -865 -865 219 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.2e+003 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.500000 0.500000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG][GT]T[AG]A[CG]GA[TCG][CG][AC][CT]G[GAC][CT]G[AT][GT]A[TG]G -------------------------------------------------------------------------------- Time 6.50 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17362 1.09e-14 106_[+3(1.55e-10)]_243_\ [+1(1.75e-07)]_68_[+2(4.43e-09)]_34 46383 1.16e-06 15_[+2(1.02e-07)]_294_\ [+1(2.83e-07)]_163 13384 6.05e-08 24_[+1(3.29e-06)]_212_\ [+3(3.14e-10)]_231 28433 4.04e-06 21_[+1(3.51e-06)]_15_[+3(8.54e-05)]_\ 71_[+2(6.99e-07)]_114_[+1(8.49e-05)]_218 48060 3.75e-12 [+3(1.71e-10)]_104_[+1(5.60e-06)]_\ 37_[+2(6.08e-08)]_310 18194 2.36e-05 296_[+2(3.20e-07)]_89_\ [+1(2.41e-06)]_87 49127 9.13e-07 214_[+3(1.71e-10)]_265 49381 9.26e-01 500 40171 1.20e-04 171_[+1(3.29e-06)]_170_\ [+2(2.29e-06)]_131 49978 1.41e-02 414_[+1(8.84e-07)]_74 45229 2.52e-01 500 46032 9.53e-01 500 42911 2.03e-05 155_[+1(9.29e-05)]_25_\ [+2(1.60e-07)]_243_[+1(3.97e-06)]_37 46991 1.65e-05 27_[+2(2.19e-07)]_80_[+1(1.01e-05)]_\ 365 33893 5.80e-03 201_[+2(7.99e-07)]_283 37743 4.00e-03 240_[+1(7.10e-07)]_248 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************