******************************************************************************** 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/495/495.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 37367 1.0000 500 37652 1.0000 500 48359 1.0000 500 48680 1.0000 500 49151 1.0000 500 49795 1.0000 500 52648 1.0000 500 4550 1.0000 500 45565 1.0000 500 12420 1.0000 500 32684 1.0000 500 38175 1.0000 500 44348 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/495/495.seqs.fa -oc motifs/495 -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 0.247 C 0.241 G 0.248 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.247 C 0.241 G 0.248 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 10 llr = 109 E-value = 1.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :2:::8:2:::8 pos.-specific C 623::19::::: probability G 143:a:::a1a: matrix T 324a:118:9:2 bits 2.1 * * * 1.8 ** * * 1.6 ** * * * 1.4 ** * *** Relative 1.2 ** ****** Entropy 1.0 ********* (15.8 bits) 0.8 ********* 0.6 * ********* 0.4 * ********** 0.2 * ********** 0.0 ------------ Multilevel CGTTGACTGTGA consensus TAC A T sequence CG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 37367 448 3.14e-07 GCGGTACACT CCTTGACTGTGA AAAGCCCAGG 48359 56 4.54e-07 TTGAGTGAGG TGTTGACTGTGA ATTGCCTTAT 45565 93 8.20e-07 CAGGAGTTGG CCGTGACTGTGA CTGTCAATGT 48680 102 1.01e-06 TCTGTCTGTG CGTTGACAGTGA TCATCTGGAT 49795 267 4.36e-06 CGGTTCGGAA CGGTGACTGGGA AGACTTGGAA 32684 159 4.88e-06 AATTGCTTAC GACTGACTGTGA CGCGGTAGAT 49151 420 6.21e-06 ATTCGAGTGC TATTGACTGTGT TCGCAGACAA 37652 161 8.15e-06 CGATGATGGA CTGTGCCTGTGA GTCACGTCAA 4550 231 2.08e-05 TTTGTTGTTT CTCTGTCAGTGA ATGATTCTTG 52648 399 2.47e-05 GCAGTCTCCT TGCTGATTGTGT ATTTTATGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37367 3.1e-07 447_[+1]_41 48359 4.5e-07 55_[+1]_433 45565 8.2e-07 92_[+1]_396 48680 1e-06 101_[+1]_387 49795 4.4e-06 266_[+1]_222 32684 4.9e-06 158_[+1]_330 49151 6.2e-06 419_[+1]_69 37652 8.2e-06 160_[+1]_328 4550 2.1e-05 230_[+1]_258 52648 2.5e-05 398_[+1]_90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=10 37367 ( 448) CCTTGACTGTGA 1 48359 ( 56) TGTTGACTGTGA 1 45565 ( 93) CCGTGACTGTGA 1 48680 ( 102) CGTTGACAGTGA 1 49795 ( 267) CGGTGACTGGGA 1 32684 ( 159) GACTGACTGTGA 1 49151 ( 420) TATTGACTGTGT 1 37652 ( 161) CTGTGCCTGTGA 1 4550 ( 231) CTCTGTCAGTGA 1 52648 ( 399) TGCTGATTGTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 9.56183 E= 1.8e+001 -997 131 -131 19 -30 -27 69 -40 -997 32 27 60 -997 -997 -997 192 -997 -997 201 -997 170 -127 -997 -140 -997 190 -997 -140 -30 -997 -997 160 -997 -997 201 -997 -997 -997 -131 177 -997 -997 201 -997 170 -997 -997 -40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 1.8e+001 0.000000 0.600000 0.100000 0.300000 0.200000 0.200000 0.400000 0.200000 0.000000 0.300000 0.300000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.100000 0.000000 0.100000 0.000000 0.900000 0.000000 0.100000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.900000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][GACT][TCG]TGAC[TA]GTG[AT] -------------------------------------------------------------------------------- Time 1.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 9 llr = 118 E-value = 2.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 63aa:46278:a:116 pos.-specific C :7::7123:2a:1:61 probability G 4:::3:233:::8:33 matrix T :::::4:1::::19:: bits 2.1 ** ** 1.8 ** ** 1.6 ** ** 1.4 ** ** * Relative 1.2 ** *** * Entropy 1.0 ***** ****** (18.8 bits) 0.8 ***** ****** 0.6 ******* ******** 0.4 ******* ******** 0.2 **************** 0.0 ---------------- Multilevel ACAACAACAACAGTCA consensus GA GTCGGC GG sequence GA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 49795 416 1.82e-10 AAAGGAACCT ACAACAACAACAGTCA GGGATGGAAA 4550 20 1.82e-08 TTCAGGACCG ACAACAACGACAGTCG ATGACGAGAA 12420 152 7.49e-08 GATTCCTGAG ACAAGTAGAACAGTGG TTTCGCAGGA 45565 329 2.98e-07 GACCTTTTCG GAAACAGAAACAGTGA CGTGTTTTGG 37652 58 7.80e-07 GGCGAATGTG GCAACAAGGCCAGTCC GTCTCGGTCA 44348 475 9.76e-07 ATTAGTAATT GCAACTGTAACAGTAA GTGTTACACA 52648 8 2.24e-06 ACAAACA GAAACTCCGACAGAGA AAGTTTAAAA 48680 419 2.50e-06 CGGTCGTCGA ACAAGCAGACCACTCA CTGTTAGATC 48359 119 2.77e-06 AATCTATTCT AAAAGTCAAACATTCG AAAAGCTTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49795 1.8e-10 415_[+2]_69 4550 1.8e-08 19_[+2]_465 12420 7.5e-08 151_[+2]_333 45565 3e-07 328_[+2]_156 37652 7.8e-07 57_[+2]_427 44348 9.8e-07 474_[+2]_10 52648 2.2e-06 7_[+2]_477 48680 2.5e-06 418_[+2]_66 48359 2.8e-06 118_[+2]_366 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=9 49795 ( 416) ACAACAACAACAGTCA 1 4550 ( 20) ACAACAACGACAGTCG 1 12420 ( 152) ACAAGTAGAACAGTGG 1 45565 ( 329) GAAACAGAAACAGTGA 1 37652 ( 58) GCAACAAGGCCAGTCC 1 44348 ( 475) GCAACTGTAACAGTAA 1 52648 ( 8) GAAACTCCGACAGAGA 1 48680 ( 419) ACAAGCAGACCACTCA 1 48359 ( 119) AAAAGTCAAACATTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 9.58478 E= 2.6e+001 117 -982 84 -982 43 147 -982 -982 202 -982 -982 -982 202 -982 -982 -982 -982 147 42 -982 85 -112 -982 75 117 -12 -16 -982 -15 47 42 -125 143 -982 42 -982 166 -12 -982 -982 -982 205 -982 -982 202 -982 -982 -982 -982 -112 165 -125 -115 -982 -982 175 -115 120 42 -982 117 -112 42 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 9 E= 2.6e+001 0.555556 0.000000 0.444444 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.444444 0.111111 0.000000 0.444444 0.555556 0.222222 0.222222 0.000000 0.222222 0.333333 0.333333 0.111111 0.666667 0.000000 0.333333 0.000000 0.777778 0.222222 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.777778 0.111111 0.111111 0.000000 0.000000 0.888889 0.111111 0.555556 0.333333 0.000000 0.555556 0.111111 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AG][CA]AA[CG][AT][ACG][CGA][AG][AC]CAGT[CG][AG] -------------------------------------------------------------------------------- Time 2.83 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 9 llr = 111 E-value = 5.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::1:374::2:::16a pos.-specific C :a622:1941:3a92: probability G 7:28::1:32::::2: matrix T 3:1:433124a7:::: bits 2.1 * * * 1.8 * * * * 1.6 * * ** * 1.4 * * * ** * Relative 1.2 * * * * ** * Entropy 1.0 ** * * * **** * (17.8 bits) 0.8 ** * * * **** * 0.6 ** * * * ****** 0.4 ****** ** ****** 0.2 **************** 0.0 ---------------- Multilevel GCCGTAACCTTTCCAA consensus T GCATT GA C C sequence C TG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 44348 250 3.34e-08 GAGGGCAATT TCCGTAACGTTCCCAA AGGTCGCAAA 49795 115 4.36e-08 TCCAAAAAAA GCCGAAACCATTCCCA CTTCTTCCTT 49151 59 1.18e-07 GGGAAACATG GCGGTATCCTTTCCGA AGAAACCCGC 45565 431 5.05e-07 TTCTTTGGAT TCGGCAACGGTTCCAA TTTTTGTCTC 52648 123 9.92e-07 GCTGCTACTG GCCCTAGCCGTCCCAA CGACGGCCTT 48359 475 2.22e-06 CTCCCAAATC TCTCATACCTTTCCAA CGTTACTATC 12420 439 2.55e-06 TCACGGTCGG GCAGCATCTTTCCCGA CCCCAGTCAC 37652 18 4.95e-06 GTACATCCTG GCCGATTCTATTCACA AATCATGCGT 37367 203 5.77e-06 GTTCCAACAA GCCGTTCTGCTTCCAA AGACCCTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44348 3.3e-08 249_[+3]_235 49795 4.4e-08 114_[+3]_370 49151 1.2e-07 58_[+3]_426 45565 5.1e-07 430_[+3]_54 52648 9.9e-07 122_[+3]_362 48359 2.2e-06 474_[+3]_10 12420 2.6e-06 438_[+3]_46 37652 4.9e-06 17_[+3]_467 37367 5.8e-06 202_[+3]_282 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=9 44348 ( 250) TCCGTAACGTTCCCAA 1 49795 ( 115) GCCGAAACCATTCCCA 1 49151 ( 59) GCGGTATCCTTTCCGA 1 45565 ( 431) TCGGCAACGGTTCCAA 1 52648 ( 123) GCCCTAGCCGTCCCAA 1 48359 ( 475) TCTCATACCTTTCCAA 1 12420 ( 439) GCAGCATCTTTCCCGA 1 37652 ( 18) GCCGATTCTATTCACA 1 37367 ( 203) GCCGTTCTGCTTCCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 9.58478 E= 5.1e+002 -982 -982 142 34 -982 205 -982 -982 -115 120 -16 -125 -982 -12 165 -982 43 -12 -982 75 143 -982 -982 34 85 -112 -116 34 -982 188 -982 -125 -982 88 42 -25 -15 -112 -16 75 -982 -982 -982 192 -982 47 -982 134 -982 205 -982 -982 -115 188 -982 -982 117 -12 -16 -982 202 -982 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 9 E= 5.1e+002 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.111111 0.555556 0.222222 0.111111 0.000000 0.222222 0.777778 0.000000 0.333333 0.222222 0.000000 0.444444 0.666667 0.000000 0.000000 0.333333 0.444444 0.111111 0.111111 0.333333 0.000000 0.888889 0.000000 0.111111 0.000000 0.444444 0.333333 0.222222 0.222222 0.111111 0.222222 0.444444 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.555556 0.222222 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT]C[CG][GC][TAC][AT][AT]C[CGT][TAG]T[TC]CC[ACG]A -------------------------------------------------------------------------------- Time 4.28 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37367 3.34e-05 202_[+3(5.77e-06)]_229_\ [+1(3.14e-07)]_41 37652 7.55e-07 17_[+3(4.95e-06)]_24_[+2(7.80e-07)]_\ 87_[+1(8.15e-06)]_328 48359 8.42e-08 55_[+1(4.54e-07)]_51_[+2(2.77e-06)]_\ 189_[+1(8.20e-07)]_139_[+3(2.22e-06)]_10 48680 5.18e-05 101_[+1(1.01e-06)]_305_\ [+2(2.50e-06)]_66 49151 8.64e-06 58_[+3(1.18e-07)]_345_\ [+1(6.21e-06)]_69 49795 2.33e-12 114_[+3(4.36e-08)]_136_\ [+1(4.36e-06)]_137_[+2(1.82e-10)]_69 52648 1.25e-06 7_[+2(2.24e-06)]_99_[+3(9.92e-07)]_\ 236_[+1(4.14e-05)]_12_[+1(2.47e-05)]_90 4550 2.60e-06 19_[+2(1.82e-08)]_195_\ [+1(2.08e-05)]_258 45565 4.80e-09 92_[+1(8.20e-07)]_224_\ [+2(2.98e-07)]_86_[+3(5.05e-07)]_54 12420 6.47e-06 151_[+2(7.49e-08)]_271_\ [+3(2.55e-06)]_46 32684 4.34e-02 158_[+1(4.88e-06)]_330 38175 4.88e-01 500 44348 1.17e-06 249_[+3(3.34e-08)]_209_\ [+2(9.76e-07)]_10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************