******************************************************************************** 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/378/378.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9185 1.0000 500 31822 1.0000 500 42927 1.0000 500 42944 1.0000 500 46642 1.0000 500 14449 1.0000 500 48783 1.0000 500 48786 1.0000 500 48971 1.0000 500 49417 1.0000 500 40588 1.0000 500 49867 1.0000 500 40690 1.0000 500 50220 1.0000 500 33833 1.0000 500 34192 1.0000 500 34244 1.0000 500 6725 1.0000 500 45011 1.0000 500 45460 1.0000 500 38107 1.0000 500 41411 1.0000 500 47567 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/378/378.seqs.fa -oc motifs/378 -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= 23 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= 11500 N= 23 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.257 G 0.227 T 0.255 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.257 G 0.227 T 0.255 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 11 llr = 137 E-value = 6.7e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :7:::6:4:::6 pos.-specific C 718:::a::::: probability G 32::a1::a1a: matrix T ::2a:3:6:9:4 bits 2.1 * * * 1.9 ** * * * 1.7 ** * * * 1.5 ** * *** Relative 1.3 *** * *** Entropy 1.1 * *** ****** (18.0 bits) 0.9 ***** ****** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CACTGACTGTGA consensus G T A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 42944 94 5.85e-08 AATGAATTTG CACTGACTGTGA CTTCACTTCA 9185 68 2.85e-07 ACAGTTAGCA CACTGTCTGTGA AACATAACAG 48783 400 3.94e-07 TAGAGATCAT CGCTGACTGTGA AACCATTTCT 45460 368 5.00e-07 AATGATGTTT CACTGTCTGTGT CGGTCGGCAT 50220 368 5.00e-07 AATGATGTTT CACTGTCTGTGT CGGTCGGCAT 48971 35 5.00e-07 GTATACAAGA GACTGACTGTGT GAGAGGACCA 48786 266 8.73e-07 ATTCCGTATT CGCTGACAGTGA GGAGGCTGGC 34192 41 1.10e-06 TCTGTTGTAG CATTGACAGTGA AGGTGAGCTA 46642 127 2.54e-06 AGAATACGAT GATTGACAGTGA AAGTGCTTGA 49417 211 2.79e-06 CCCCAGGCAC GACTGACTGGGA CGATGAGGTT 49867 452 8.12e-06 TCTCGTTCCT CCCTGGCAGTGT GGAAAAGTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42944 5.9e-08 93_[+1]_395 9185 2.8e-07 67_[+1]_421 48783 3.9e-07 399_[+1]_89 45460 5e-07 367_[+1]_121 50220 5e-07 367_[+1]_121 48971 5e-07 34_[+1]_454 48786 8.7e-07 265_[+1]_223 34192 1.1e-06 40_[+1]_448 46642 2.5e-06 126_[+1]_362 49417 2.8e-06 210_[+1]_278 49867 8.1e-06 451_[+1]_37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=11 42944 ( 94) CACTGACTGTGA 1 9185 ( 68) CACTGTCTGTGA 1 48783 ( 400) CGCTGACTGTGA 1 45460 ( 368) CACTGTCTGTGT 1 50220 ( 368) CACTGTCTGTGT 1 48971 ( 35) GACTGACTGTGT 1 48786 ( 266) CGCTGACAGTGA 1 34192 ( 41) CATTGACAGTGA 1 46642 ( 127) GATTGACAGTGA 1 49417 ( 211) GACTGACTGGGA 1 49867 ( 452) CCCTGGCAGTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 11247 bayes= 11.0236 E= 6.7e-005 -1010 150 26 -1010 148 -149 -32 -1010 -1010 167 -1010 -49 -1010 -1010 -1010 197 -1010 -1010 214 -1010 128 -1010 -132 10 -1010 196 -1010 -1010 48 -1010 -1010 132 -1010 -1010 214 -1010 -1010 -1010 -132 183 -1010 -1010 214 -1010 128 -1010 -1010 51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 6.7e-005 0.000000 0.727273 0.272727 0.000000 0.727273 0.090909 0.181818 0.000000 0.000000 0.818182 0.000000 0.181818 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.636364 0.000000 0.090909 0.272727 0.000000 1.000000 0.000000 0.000000 0.363636 0.000000 0.000000 0.636364 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 1.000000 0.000000 0.636364 0.000000 0.000000 0.363636 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG]ACTG[AT]C[TA]GTG[AT] -------------------------------------------------------------------------------- Time 4.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 117 E-value = 4.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::2:::::723a:a:575:8: pos.-specific C :::::2a2::2:a:85332:: probability G 8:7228:7:85:::2:::8:2 matrix T 2a288::23::::::::2:28 bits 2.1 1.9 * * *** 1.7 * * *** 1.5 ** ** * *** * Relative 1.3 ** **** * **** *** Entropy 1.1 ** **** ** **** * *** (28.0 bits) 0.9 ********** ****** *** 0.6 ***************** *** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTGTTGCGAGGACACAAAGAT consensus T A CCC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 45460 37 1.86e-12 CTCACAGTCA GTGTTGCGAGGACACACAGAT ACCTTTCCTT 50220 37 1.86e-12 CTCACAGTCA GTGTTGCGAGGACACACAGAT ACCTTTCCTT 40690 185 6.99e-10 ATACCGGGGT TTGTTGCGTGCACACCATGAT GCAATGGTAC 49867 46 4.32e-09 TAGTTGGAAA GTGTGGCCAAGACACAACGAG TCCATTGACC 33833 195 4.52e-09 GGGATACTAG GTATTGCTAGAACAGCAACAT GAGGATGCTT 48783 285 9.51e-09 GCTCATTTTC GTTGTCCGTGAACACCACGTT CATTTTCTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45460 1.9e-12 36_[+2]_443 50220 1.9e-12 36_[+2]_443 40690 7e-10 184_[+2]_295 49867 4.3e-09 45_[+2]_434 33833 4.5e-09 194_[+2]_285 48783 9.5e-09 284_[+2]_195 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 45460 ( 37) GTGTTGCGAGGACACACAGAT 1 50220 ( 37) GTGTTGCGAGGACACACAGAT 1 40690 ( 185) TTGTTGCGTGCACACCATGAT 1 49867 ( 46) GTGTGGCCAAGACACAACGAG 1 33833 ( 195) GTATTGCTAGAACAGCAACAT 1 48783 ( 285) GTTGTCCGTGAACACCACGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11040 bayes= 11.2924 E= 4.3e-001 -923 -923 187 -61 -923 -923 -923 197 -65 -923 155 -61 -923 -923 -45 171 -923 -923 -45 171 -923 -62 187 -923 -923 196 -923 -923 -923 -62 155 -61 135 -923 -923 39 -65 -923 187 -923 35 -62 114 -923 193 -923 -923 -923 -923 196 -923 -923 193 -923 -923 -923 -923 170 -45 -923 93 96 -923 -923 135 38 -923 -923 93 38 -923 -61 -923 -62 187 -923 167 -923 -923 -61 -923 -923 -45 171 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 4.3e-001 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.666667 0.166667 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.666667 0.166667 0.666667 0.000000 0.000000 0.333333 0.166667 0.000000 0.833333 0.000000 0.333333 0.166667 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.500000 0.500000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.500000 0.333333 0.000000 0.166667 0.000000 0.166667 0.833333 0.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.000000 0.166667 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GTGTTGCG[AT]G[GA]ACAC[AC][AC][AC]GAT -------------------------------------------------------------------------------- Time 9.24 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 10 llr = 132 E-value = 1.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 14::::2:::::::29 pos.-specific C 312:93219::37:2: probability G 64:2::2:::a:2a4: matrix T :18817491a:71:21 bits 2.1 * * 1.9 ** * 1.7 ** * 1.5 * **** * * Relative 1.3 *** **** * * Entropy 1.1 **** ***** * * (19.0 bits) 0.9 * **** ******* * 0.6 * **** ******* * 0.4 * **** ******* * 0.2 ****** ********* 0.0 ---------------- Multilevel GATTCTTTCTGTCGGA consensus CGCG CA CG A sequence C C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 9185 431 6.63e-09 GCACGACTTT GCTTCTTTCTGTCGGA CTTGGTTCTC 46642 376 2.14e-08 ATCGGAAAAC GGTTCTTTCTGTGGAA ACATTGCGTA 45460 262 1.19e-07 ATGGAGACGG CGTTCCGTCTGTCGCA GATATGTCGT 50220 262 1.19e-07 ATGGAGACGG CGTTCCGTCTGTCGCA GATATGTCGT 48786 233 2.63e-07 CAAACACCAG GGTTCCATCTGTCGGT TGCTTCGATT 48971 285 6.61e-07 CGTTGGCTGA CATGCTCTCTGCCGAA TTCCTACACG 31822 231 9.11e-07 TATGCGACAT GTCGCTTTCTGCCGGA CGTGTCACAC 49417 137 1.30e-06 CGCTCACCGG AACTCTTTCTGCGGGA GCGAGGGAAG 34192 24 1.79e-06 GCTTAAAAGT GATTTTCTCTGTTGTA GCATTGACAG 49867 300 2.18e-06 GAACTGGATC GATTCTACTTGTCGTA AGTCACGCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9185 6.6e-09 430_[+3]_54 46642 2.1e-08 375_[+3]_109 45460 1.2e-07 261_[+3]_223 50220 1.2e-07 261_[+3]_223 48786 2.6e-07 232_[+3]_252 48971 6.6e-07 284_[+3]_200 31822 9.1e-07 230_[+3]_254 49417 1.3e-06 136_[+3]_348 34192 1.8e-06 23_[+3]_461 49867 2.2e-06 299_[+3]_185 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=10 9185 ( 431) GCTTCTTTCTGTCGGA 1 46642 ( 376) GGTTCTTTCTGTGGAA 1 45460 ( 262) CGTTCCGTCTGTCGCA 1 50220 ( 262) CGTTCCGTCTGTCGCA 1 48786 ( 233) GGTTCCATCTGTCGGT 1 48971 ( 285) CATGCTCTCTGCCGAA 1 31822 ( 231) GTCGCTTTCTGCCGGA 1 49417 ( 137) AACTCTTTCTGCGGGA 1 34192 ( 24) GATTTTCTCTGTTGTA 1 49867 ( 300) GATTCTACTTGTCGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 11155 bayes= 9.55596 E= 1.2e+000 -138 23 140 -997 61 -136 81 -135 -997 -36 -997 165 -997 -997 -19 165 -997 181 -997 -135 -997 23 -997 146 -39 -36 -19 65 -997 -136 -997 182 -997 181 -997 -135 -997 -997 -997 197 -997 -997 214 -997 -997 23 -997 146 -997 145 -19 -135 -997 -997 214 -997 -39 -36 81 -35 178 -997 -997 -135 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 1.2e+000 0.100000 0.300000 0.600000 0.000000 0.400000 0.100000 0.400000 0.100000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.900000 0.000000 0.100000 0.000000 0.300000 0.000000 0.700000 0.200000 0.200000 0.200000 0.400000 0.000000 0.100000 0.000000 0.900000 0.000000 0.900000 0.000000 0.100000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.300000 0.000000 0.700000 0.000000 0.700000 0.200000 0.100000 0.000000 0.000000 1.000000 0.000000 0.200000 0.200000 0.400000 0.200000 0.900000 0.000000 0.000000 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC][AG][TC][TG]C[TC][TACG]TCTG[TC][CG]G[GACT]A -------------------------------------------------------------------------------- Time 13.72 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9185 2.70e-08 67_[+1(2.85e-07)]_351_\ [+3(6.63e-09)]_54 31822 2.11e-03 230_[+3(9.11e-07)]_254 42927 7.82e-01 500 42944 3.41e-04 93_[+1(5.85e-08)]_141_\ [+1(4.47e-06)]_242 46642 3.21e-07 74_[+1(3.24e-05)]_40_[+1(2.54e-06)]_\ 237_[+3(2.14e-08)]_109 14449 5.60e-01 500 48783 1.22e-07 168_[+1(1.97e-06)]_104_\ [+2(9.51e-09)]_94_[+1(3.94e-07)]_89 48786 2.26e-06 232_[+3(2.63e-07)]_17_\ [+1(8.73e-07)]_223 48971 8.57e-06 34_[+1(5.00e-07)]_238_\ [+3(6.61e-07)]_200 49417 8.40e-05 136_[+3(1.30e-06)]_58_\ [+1(2.79e-06)]_278 40588 1.73e-01 500 49867 3.04e-09 45_[+2(4.32e-09)]_233_\ [+3(2.18e-06)]_136_[+1(8.12e-06)]_37 40690 1.42e-05 184_[+2(6.99e-10)]_295 50220 1.01e-14 36_[+2(1.86e-12)]_204_\ [+3(1.19e-07)]_90_[+1(5.00e-07)]_121 33833 7.71e-05 194_[+2(4.52e-09)]_285 34192 2.82e-05 23_[+3(1.79e-06)]_1_[+1(1.10e-06)]_\ 448 34244 2.06e-01 500 6725 3.40e-01 500 45011 1.46e-01 159_[+2(6.81e-05)]_320 45460 1.01e-14 36_[+2(1.86e-12)]_204_\ [+3(1.19e-07)]_90_[+1(5.00e-07)]_121 38107 4.58e-01 500 41411 7.56e-01 500 47567 8.79e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************