******************************************************************************** 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/60/60.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 8821 1.0000 500 46365 1.0000 500 36641 1.0000 500 13537 1.0000 500 13791 1.0000 500 47426 1.0000 500 43438 1.0000 500 43551 1.0000 500 16537 1.0000 500 41150 1.0000 500 41351 1.0000 500 33427 1.0000 500 44627 1.0000 500 11373 1.0000 500 34995 1.0000 500 45515 1.0000 500 36081 1.0000 500 49159 1.0000 500 36744 1.0000 500 45274 1.0000 500 40193 1.0000 500 47922 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/60/60.seqs.fa -oc motifs/60 -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= 22 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= 11000 N= 22 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.263 C 0.241 G 0.229 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.263 C 0.241 G 0.229 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 134 E-value = 9.8e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :6497:4312:::a19 pos.-specific C 825::a:46::29:8: probability G 22::::13::::1:1: matrix T ::113:5:38a8:::1 bits 2.1 * 1.9 * * * 1.7 * * * 1.5 * * * ** * Relative 1.3 * * * ***** * Entropy 1.1 * *** ******* (19.3 bits) 0.8 * *** ******* 0.6 ******* ******** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CACAACTCCTTTCACA consensus GCA T AATA C sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 13537 74 8.74e-10 GTTCCAGTAG CACAACTGCTTTCACA ACTTCTTCGT 47426 390 3.20e-08 TCCGTTCCAA CACATCACTTTTCACA ACACTTGACT 13791 61 4.62e-08 TGGCAATTTC GAAAACAACTTTCACA TTCAAATACG 41351 54 9.58e-08 TCGTAGTGGA CAAAACAGATTTCACA CTTTCCGAAT 16537 434 2.25e-07 ATGTGCCAAC CCAAACTCCTTTGACA CAGCACGCTG 43438 109 4.83e-07 CGATACAGAG CCCATCTACTTTCAGA TCCAACGATA 36744 342 8.27e-07 AAACGCGCGT CACAACAATTTCCAAA TTCGGCTCTT 49159 379 1.09e-06 TCATCCCGAC GGAATCTGCATTCACA ATCAGACCCA 40193 422 2.14e-06 AAATCATGTA CGCTACGCCATTCACA GGTTGTCTAC 45515 140 2.14e-06 CAAATCCGTA CATAACTCTTTCCACT CTAGTAGCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13537 8.7e-10 73_[+1]_411 47426 3.2e-08 389_[+1]_95 13791 4.6e-08 60_[+1]_424 41351 9.6e-08 53_[+1]_431 16537 2.3e-07 433_[+1]_51 43438 4.8e-07 108_[+1]_376 36744 8.3e-07 341_[+1]_143 49159 1.1e-06 378_[+1]_106 40193 2.1e-06 421_[+1]_63 45515 2.1e-06 139_[+1]_345 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 13537 ( 74) CACAACTGCTTTCACA 1 47426 ( 390) CACATCACTTTTCACA 1 13791 ( 61) GAAAACAACTTTCACA 1 41351 ( 54) CAAAACAGATTTCACA 1 16537 ( 434) CCAAACTCCTTTGACA 1 43438 ( 109) CCCATCTACTTTCAGA 1 36744 ( 342) CACAACAATTTCCAAA 1 49159 ( 379) GGAATCTGCATTCACA 1 40193 ( 422) CGCTACGCCATTCACA 1 45515 ( 140) CATAACTCTTTCCACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 10670 bayes= 10.3097 E= 9.8e+000 -997 173 -20 -997 119 -27 -20 -997 60 105 -997 -141 177 -997 -997 -141 141 -997 -997 17 -997 205 -997 -997 60 -997 -120 91 19 73 39 -997 -140 132 -997 17 -40 -997 -997 159 -997 -997 -997 191 -997 -27 -997 159 -997 190 -120 -997 192 -997 -997 -997 -140 173 -120 -997 177 -997 -997 -141 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 9.8e+000 0.000000 0.800000 0.200000 0.000000 0.600000 0.200000 0.200000 0.000000 0.400000 0.500000 0.000000 0.100000 0.900000 0.000000 0.000000 0.100000 0.700000 0.000000 0.000000 0.300000 0.000000 1.000000 0.000000 0.000000 0.400000 0.000000 0.100000 0.500000 0.300000 0.400000 0.300000 0.000000 0.100000 0.600000 0.000000 0.300000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.900000 0.100000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.800000 0.100000 0.000000 0.900000 0.000000 0.000000 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][ACG][CA]A[AT]C[TA][CAG][CT][TA]T[TC]CACA -------------------------------------------------------------------------------- Time 4.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 6 llr = 104 E-value = 6.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :22:::::3:7322:5aa8a pos.-specific C a3::338:23:75:a2::2: probability G :23:752a57::38:2:::: matrix T :35a:2::::3::::2:::: bits 2.1 * * * 1.9 * * * * ** * 1.7 * * * * ** * 1.5 * * ** ** ** * Relative 1.3 * ** ** * ** **** Entropy 1.1 * ** ** *** ** **** (25.1 bits) 0.8 * ** ** *** ** **** 0.6 * ************ **** 0.4 * ************* **** 0.2 * ****************** 0.0 -------------------- Multilevel CCTTGGCGGGACCGCAAAAA consensus TG CC ACTAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 45274 75 2.14e-10 TAAAACCGCC CAGTGCCGGGACGGCAAAAA TTAGAGCTAC 41150 260 1.60e-09 GGGCAAACAT CTGTCGCGCGTCCGCAAAAA CCAAGACTAC 36081 240 1.81e-09 ACCTACCCCT CTTTGCCGACACCGCTAAAA GTCACAGTCA 41351 288 5.69e-09 GACTCGCCAG CGTTCGCGGGTACGCGAAAA CATTGCTTTT 45515 250 1.03e-08 AGCCTACTTT CCATGTCGGGACGACAAAAA GGCGGCGTCC 47426 327 6.99e-08 TTTGGAATGT CCTTGGGGACAAAGCCAACA AAATCATAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45274 2.1e-10 74_[+2]_406 41150 1.6e-09 259_[+2]_221 36081 1.8e-09 239_[+2]_241 41351 5.7e-09 287_[+2]_193 45515 1e-08 249_[+2]_231 47426 7e-08 326_[+2]_154 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=6 45274 ( 75) CAGTGCCGGGACGGCAAAAA 1 41150 ( 260) CTGTCGCGCGTCCGCAAAAA 1 36081 ( 240) CTTTGCCGACACCGCTAAAA 1 41351 ( 288) CGTTCGCGGGTACGCGAAAA 1 45515 ( 250) CCATGTCGGGACGACAAAAA 1 47426 ( 327) CCTTGGGGACAAAGCCAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 10582 bayes= 11.2312 E= 6.8e+002 -923 205 -923 -923 -66 47 -46 32 -66 -923 54 91 -923 -923 -923 191 -923 47 154 -923 -923 47 112 -67 -923 179 -46 -923 -923 -923 212 -923 34 -53 112 -923 -923 47 154 -923 134 -923 -923 32 34 147 -923 -923 -66 105 54 -923 -66 -923 186 -923 -923 205 -923 -923 92 -53 -46 -67 192 -923 -923 -923 192 -923 -923 -923 166 -53 -923 -923 192 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 6.8e+002 0.000000 1.000000 0.000000 0.000000 0.166667 0.333333 0.166667 0.333333 0.166667 0.000000 0.333333 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.500000 0.166667 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.166667 0.500000 0.000000 0.000000 0.333333 0.666667 0.000000 0.666667 0.000000 0.000000 0.333333 0.333333 0.666667 0.000000 0.000000 0.166667 0.500000 0.333333 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.166667 0.166667 0.166667 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[CT][TG]T[GC][GC]CG[GA][GC][AT][CA][CG]GCAAAAA -------------------------------------------------------------------------------- Time 8.33 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 6 llr = 92 E-value = 1.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 5::5:8:3:aa:a8:2 pos.-specific C :a:22:7:2::::::7 probability G 5:8:5:378::a:282 matrix T ::2332::::::::2: bits 2.1 * * 1.9 * **** 1.7 * **** 1.5 ** ***** * Relative 1.3 ** * ******* Entropy 1.1 *** ********** (22.0 bits) 0.8 *** *********** 0.6 *** ************ 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel ACGAGACGGAAGAAGC consensus G TT GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 47922 407 4.34e-09 TGAGAACAAA GCGAGACGGAAGAAGA AAAGCGTTGA 8821 430 5.14e-09 GTCCACGATA GCGCTACGGAAGAAGC CAAGGAGAAA 44627 14 1.27e-08 GTCCTTGTCG ACGTGACGGAAGAGGC TTGGTGGGCG 46365 181 1.43e-07 CCACACCGGG GCGACAGACAAGAAGC AGAGATATCG 45515 334 1.71e-07 TGCCCCATAG ACGATAGGGAAGAATG ACGCTCGGGA 36081 19 2.30e-07 GGGCGATGCC ACTTGTCAGAAGAAGC TTTAGAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47922 4.3e-09 406_[+3]_78 8821 5.1e-09 429_[+3]_55 44627 1.3e-08 13_[+3]_471 46365 1.4e-07 180_[+3]_304 45515 1.7e-07 333_[+3]_151 36081 2.3e-07 18_[+3]_466 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=6 47922 ( 407) GCGAGACGGAAGAAGA 1 8821 ( 430) GCGCTACGGAAGAAGC 1 44627 ( 14) ACGTGACGGAAGAGGC 1 46365 ( 181) GCGACAGACAAGAAGC 1 45515 ( 334) ACGATAGGGAAGAATG 1 36081 ( 19) ACTTGTCAGAAGAAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 10670 bayes= 11.2432 E= 1.9e+003 92 -923 112 -923 -923 205 -923 -923 -923 -923 186 -67 92 -53 -923 32 -923 -53 112 32 166 -923 -923 -67 -923 147 54 -923 34 -923 154 -923 -923 -53 186 -923 192 -923 -923 -923 192 -923 -923 -923 -923 -923 212 -923 192 -923 -923 -923 166 -923 -46 -923 -923 -923 186 -67 -66 147 -46 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 1.9e+003 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.500000 0.166667 0.000000 0.333333 0.000000 0.166667 0.500000 0.333333 0.833333 0.000000 0.000000 0.166667 0.000000 0.666667 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.166667 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 0.833333 0.166667 0.166667 0.666667 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG]CG[AT][GT]A[CG][GA]GAAGAAGC -------------------------------------------------------------------------------- Time 12.36 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8821 1.00e-04 429_[+3(5.14e-09)]_55 46365 1.22e-03 180_[+3(1.43e-07)]_304 36641 9.57e-01 500 13537 1.58e-06 13_[+3(8.71e-05)]_44_[+1(8.74e-10)]_\ 411 13791 3.63e-04 60_[+1(4.62e-08)]_424 47426 9.86e-08 326_[+2(6.99e-08)]_43_\ [+1(3.20e-08)]_95 43438 2.86e-03 108_[+1(4.83e-07)]_376 43551 5.66e-01 500 16537 6.69e-04 433_[+1(2.25e-07)]_51 41150 4.77e-05 259_[+2(1.60e-09)]_221 41351 1.73e-08 53_[+1(9.58e-08)]_218_\ [+2(5.69e-09)]_193 33427 2.44e-01 500 44627 5.81e-05 13_[+3(1.27e-08)]_471 11373 4.91e-01 500 34995 8.36e-01 500 45515 1.86e-10 139_[+1(2.14e-06)]_94_\ [+2(1.03e-08)]_64_[+3(1.71e-07)]_151 36081 2.22e-08 18_[+3(2.30e-07)]_32_[+3(7.30e-05)]_\ 157_[+2(1.81e-09)]_241 49159 1.19e-03 378_[+1(1.09e-06)]_106 36744 8.21e-04 341_[+1(8.27e-07)]_143 45274 4.55e-06 74_[+2(2.14e-10)]_406 40193 6.30e-03 421_[+1(2.14e-06)]_63 47922 2.86e-05 406_[+3(4.34e-09)]_78 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************