******************************************************************************** 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/357/357.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11177 1.0000 500 11907 1.0000 500 20911 1.0000 500 2200 1.0000 500 23810 1.0000 500 24680 1.0000 500 2487 1.0000 500 25703 1.0000 500 261059 1.0000 500 3405 1.0000 500 35085 1.0000 500 3779 1.0000 500 518 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/357/357.seqs.fa -oc motifs/357 -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 0.272 C 0.239 G 0.219 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.272 C 0.239 G 0.219 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 8 llr = 127 E-value = 7.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :91:98:1:4::::1:31:: pos.-specific C a:361:a1a::3:96536:9 probability G :::4:::::3:341:31:11 matrix T :16::3:8:4a56:33439: bits 2.2 2.0 * * * * 1.8 * * * * 1.5 * * * * * * Relative 1.3 ** * * * * * ** Entropy 1.1 ** **** * * ** ** (22.9 bits) 0.9 ** ****** * ** ** 0.7 ********* * **** *** 0.4 **************** *** 0.2 **************** *** 0.0 -------------------- Multilevel CATCAACTCATTTCCCTCTC consensus CG T T CG TGAT sequence G G TC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 24680 303 5.97e-10 AATGGTGTAC CATCAACTCATTTCCGCTTC TGTCTCTTGA 518 285 8.03e-10 GTTGCATTAA CATGATCTCGTTGCCCTCTC CTCCTGATAT 35085 285 8.03e-10 GTTGCATTAA CATGATCTCGTTGCCCTCTC CTCCTGATAT 2200 461 3.04e-08 GTACTACCAA CACCAACTCATCTCTCACTG GCTGTCAATA 11177 469 4.88e-08 TTGAATCGTT CATCAACACATCTCTCTCGC AATCTTATCA 261059 400 5.26e-08 TTACCCTCCC CACCCACTCTTGTCCTCTTC ACCGGCTCTC 11907 321 8.59e-08 CGTCAAAGAC CTTGAACTCTTGGCAGACTC AGCTACAGCA 25703 375 4.91e-07 CATCCTCCTC CAACAACCCTTTTGCTGATC GAGCTGTGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24680 6e-10 302_[+1]_178 518 8e-10 284_[+1]_196 35085 8e-10 284_[+1]_196 2200 3e-08 460_[+1]_20 11177 4.9e-08 468_[+1]_12 261059 5.3e-08 399_[+1]_81 11907 8.6e-08 320_[+1]_160 25703 4.9e-07 374_[+1]_106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=8 24680 ( 303) CATCAACTCATTTCCGCTTC 1 518 ( 285) CATGATCTCGTTGCCCTCTC 1 35085 ( 285) CATGATCTCGTTGCCCTCTC 1 2200 ( 461) CACCAACTCATCTCTCACTG 1 11177 ( 469) CATCAACACATCTCTCTCGC 1 261059 ( 400) CACCCACTCTTGTCCTCTTC 1 11907 ( 321) CTTGAACTCTTGGCAGACTC 1 25703 ( 375) CAACAACCCTTTTGCTGATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 6253 bayes= 9.0226 E= 7.7e-002 -965 206 -965 -965 169 -965 -965 -111 -112 7 -965 121 -965 139 77 -965 169 -93 -965 -965 146 -965 -965 -11 -965 206 -965 -965 -112 -93 -965 147 -965 206 -965 -965 46 -965 19 47 -965 -965 -965 189 -965 7 19 89 -965 -965 77 121 -965 187 -81 -965 -112 139 -965 -11 -965 106 19 -11 -12 7 -81 47 -112 139 -965 -11 -965 -965 -81 169 -965 187 -81 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 7.7e-002 0.000000 1.000000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.125000 0.250000 0.000000 0.625000 0.000000 0.625000 0.375000 0.000000 0.875000 0.125000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.125000 0.125000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.375000 0.000000 0.250000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.375000 0.625000 0.000000 0.875000 0.125000 0.000000 0.125000 0.625000 0.000000 0.250000 0.000000 0.500000 0.250000 0.250000 0.250000 0.250000 0.125000 0.375000 0.125000 0.625000 0.000000 0.250000 0.000000 0.000000 0.125000 0.875000 0.000000 0.875000 0.125000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[TC][CG]A[AT]CTC[ATG]T[TCG][TG]C[CT][CGT][TAC][CT]TC -------------------------------------------------------------------------------- Time 1.70 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 11 llr = 120 E-value = 1.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 5a:9:93:9525 pos.-specific C ::1::::a1242 probability G 5:9:a17::15: matrix T :::1:::::3:4 bits 2.2 * 2.0 * * * 1.8 ** * * 1.5 ***** ** Relative 1.3 ******** Entropy 1.1 ********* (15.7 bits) 0.9 ********* 0.7 ********* * 0.4 ********* ** 0.2 ************ 0.0 ------------ Multilevel AAGAGAGCAAGA consensus G A TCT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 3405 130 1.58e-07 GCTGGAATAT GAGAGAGCAAGT TACGGCATGA 23810 344 5.64e-07 CGTCAATGGC AAGAGAGCAACT GAATATCTTT 25703 18 6.12e-07 GCGAAACACC GAGAGAGCATGT TGCATCAGGA 518 105 1.53e-06 TGCAATGACG AAGAGAGCAACC GTAGTGGCAG 35085 105 1.53e-06 TGCAATGACG AAGAGAGCAACC GTAGTGGCAG 11177 438 4.21e-06 ACAACAATCA AAGAGAACACGA ACATAACAGT 11907 468 7.32e-06 CGATAACGAA GAGAGAGCCTGA TGAAATATCG 2487 167 8.41e-06 TACCACAGAA GAGTGAGCATGA TAGATCTATG 3779 277 1.27e-05 TGTTCATTTG GAGAGAACACAT CAAACATCTC 24680 26 1.81e-05 ACGAAGAATG AAGAGGGCAGCA AGAGCGTTAT 2200 395 3.26e-05 ATTGGACACA AACAGAACAAAA TAGACAAATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3405 1.6e-07 129_[+2]_359 23810 5.6e-07 343_[+2]_145 25703 6.1e-07 17_[+2]_471 518 1.5e-06 104_[+2]_384 35085 1.5e-06 104_[+2]_384 11177 4.2e-06 437_[+2]_51 11907 7.3e-06 467_[+2]_21 2487 8.4e-06 166_[+2]_322 3779 1.3e-05 276_[+2]_212 24680 1.8e-05 25_[+2]_463 2200 3.3e-05 394_[+2]_94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=11 3405 ( 130) GAGAGAGCAAGT 1 23810 ( 344) AAGAGAGCAACT 1 25703 ( 18) GAGAGAGCATGT 1 518 ( 105) AAGAGAGCAACC 1 35085 ( 105) AAGAGAGCAACC 1 11177 ( 438) AAGAGAACACGA 1 11907 ( 468) GAGAGAGCCTGA 1 2487 ( 167) GAGTGAGCATGA 1 3779 ( 277) GAGAGAACACAT 1 24680 ( 26) AAGAGGGCAGCA 1 2200 ( 395) AACAGAACAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 9.52784 E= 1.0e-001 100 -1010 105 -1010 188 -1010 -1010 -1010 -1010 -139 205 -1010 174 -1010 -1010 -157 -1010 -1010 219 -1010 174 -1010 -127 -1010 1 -1010 173 -1010 -1010 206 -1010 -1010 174 -139 -1010 -1010 74 -39 -127 1 -58 61 105 -1010 74 -39 -1010 43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 1.0e-001 0.545455 0.000000 0.454545 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.909091 0.000000 0.909091 0.000000 0.000000 0.090909 0.000000 0.000000 1.000000 0.000000 0.909091 0.000000 0.090909 0.000000 0.272727 0.000000 0.727273 0.000000 0.000000 1.000000 0.000000 0.000000 0.909091 0.090909 0.000000 0.000000 0.454545 0.181818 0.090909 0.272727 0.181818 0.363636 0.454545 0.000000 0.454545 0.181818 0.000000 0.363636 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AG]AGAGA[GA]CA[AT][GC][AT] -------------------------------------------------------------------------------- Time 3.07 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 13 llr = 160 E-value = 8.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::7232:62:15:2:1:142 pos.-specific C 2211::22:3:12:254::18 probability G :27:164:13:83:5252121 matrix T 8722813832a:1a241883: bits 2.2 2.0 * * 1.8 * * 1.5 * * Relative 1.3 * ** * Entropy 1.1 * * ** * ** * (17.8 bits) 0.9 * * ** * ** * ** * 0.7 ****** ** ** * * ** * 0.4 ****** ** ** * **** * 0.2 ********* *********** 0.0 --------------------- Multilevel TTGATGGTACTGATGCGTTAC consensus C TT AT TG G TTCG T sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 518 7 1.56e-09 GATTTG TCGTTGGTAGTGATGCCTTAC ACCATTATTT 35085 7 1.56e-09 GATTTG TCGTTGGTAGTGATGCCTTAC ACCATTATTT 23810 125 1.56e-09 ATCGTCTCTT CTGATGTTAGTGATGGGTTGC TGTACATGAG 3779 424 4.81e-08 CTCCTTACTT TTGAAATTATTGGTTCGTTAC GCAAGGTTTG 2487 447 6.79e-08 AGTAGAATTA TTGAAAGTTCTGGTTTCTTTC AACCACCCAC 24680 421 3.22e-07 TATCATCTGC CTGATATTACTGATATCTTGA TGTGAATTCT 20911 50 1.44e-06 TTTGACATGT TGTATGGTTATGATGGTGTAC GTCCTCTCTC 3405 76 3.09e-06 ACGAGGACAC TTGTTGTCGATGCTGCATTTC ATGTCACGTA 2200 228 3.83e-06 ACGGCGCCGG TGGATGGTTGTGGTTTGGGTG GCATGATGAT 11907 174 5.78e-06 GGATTGGTAG TTTATGCTACTGCTCTGTAGA AATGTCTGAT 11177 45 8.00e-06 TCAGTTGGCA CTTCTGACACTGATACCGTAC TTTGTCTTCT 261059 239 1.63e-05 TTGAAACCGT TTGAGTCTTTTCGTCCGTTTC AACATGTCCC 25703 308 1.83e-05 CAAAATTATT TTCATAATAATATTGTGTTCC TCTGTATATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 518 1.6e-09 6_[+3]_473 35085 1.6e-09 6_[+3]_473 23810 1.6e-09 124_[+3]_355 3779 4.8e-08 423_[+3]_56 2487 6.8e-08 446_[+3]_33 24680 3.2e-07 420_[+3]_59 20911 1.4e-06 49_[+3]_430 3405 3.1e-06 75_[+3]_404 2200 3.8e-06 227_[+3]_252 11907 5.8e-06 173_[+3]_306 11177 8e-06 44_[+3]_435 261059 1.6e-05 238_[+3]_241 25703 1.8e-05 307_[+3]_172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=13 518 ( 7) TCGTTGGTAGTGATGCCTTAC 1 35085 ( 7) TCGTTGGTAGTGATGCCTTAC 1 23810 ( 125) CTGATGTTAGTGATGGGTTGC 1 3779 ( 424) TTGAAATTATTGGTTCGTTAC 1 2487 ( 447) TTGAAAGTTCTGGTTTCTTTC 1 24680 ( 421) CTGATATTACTGATATCTTGA 1 20911 ( 50) TGTATGGTTATGATGGTGTAC 1 3405 ( 76) TTGTTGTCGATGCTGCATTTC 1 2200 ( 228) TGGATGGTTGTGGTTTGGGTG 1 11907 ( 174) TTTATGCTACTGCTCTGTAGA 1 11177 ( 45) CTTCTGACACTGATACCGTAC 1 261059 ( 239) TTGAGTCTTTTCGTCCGTTTC 1 25703 ( 308) TTCATAATAATATTGTGTTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 8.90388 E= 8.1e-001 -1035 -5 -1035 151 -1035 -63 -51 136 -1035 -163 166 -23 135 -163 -1035 -23 -82 -1035 -151 151 18 -1035 149 -181 -82 -63 81 19 -1035 -63 -1035 165 118 -1035 -151 19 -24 36 49 -81 -1035 -1035 -1035 189 -182 -163 195 -1035 76 -63 49 -181 -1035 -1035 -1035 189 -82 -63 107 -23 -1035 95 -51 51 -182 69 107 -181 -1035 -1035 7 151 -182 -1035 -151 165 50 -163 7 19 -82 169 -151 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 8.1e-001 0.000000 0.230769 0.000000 0.769231 0.000000 0.153846 0.153846 0.692308 0.000000 0.076923 0.692308 0.230769 0.692308 0.076923 0.000000 0.230769 0.153846 0.000000 0.076923 0.769231 0.307692 0.000000 0.615385 0.076923 0.153846 0.153846 0.384615 0.307692 0.000000 0.153846 0.000000 0.846154 0.615385 0.000000 0.076923 0.307692 0.230769 0.307692 0.307692 0.153846 0.000000 0.000000 0.000000 1.000000 0.076923 0.076923 0.846154 0.000000 0.461538 0.153846 0.307692 0.076923 0.000000 0.000000 0.000000 1.000000 0.153846 0.153846 0.461538 0.230769 0.000000 0.461538 0.153846 0.384615 0.076923 0.384615 0.461538 0.076923 0.000000 0.000000 0.230769 0.769231 0.076923 0.000000 0.076923 0.846154 0.384615 0.076923 0.230769 0.307692 0.153846 0.769231 0.076923 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC]T[GT][AT]T[GA][GT]T[AT][CGA]TG[AG]T[GT][CT][GC][TG]T[ATG]C -------------------------------------------------------------------------------- Time 4.52 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11177 5.07e-08 44_[+3(8.00e-06)]_372_\ [+2(4.21e-06)]_19_[+1(4.88e-08)]_12 11907 1.05e-07 173_[+3(5.78e-06)]_126_\ [+1(8.59e-08)]_127_[+2(7.32e-06)]_21 20911 3.12e-04 49_[+3(1.44e-06)]_378_\ [+1(1.77e-05)]_32 2200 1.09e-07 104_[+3(4.28e-05)]_102_\ [+3(3.83e-06)]_146_[+2(3.26e-05)]_54_[+1(3.04e-08)]_20 23810 2.21e-08 124_[+3(1.56e-09)]_198_\ [+2(5.64e-07)]_145 24680 1.72e-10 25_[+2(1.81e-05)]_265_\ [+1(5.97e-10)]_98_[+3(3.22e-07)]_59 2487 3.48e-06 7_[+2(3.83e-05)]_147_[+2(8.41e-06)]_\ 268_[+3(6.79e-08)]_33 25703 1.52e-07 17_[+2(6.12e-07)]_278_\ [+3(1.83e-05)]_46_[+1(4.91e-07)]_106 261059 2.67e-05 238_[+3(1.63e-05)]_140_\ [+1(5.26e-08)]_81 3405 5.01e-06 75_[+3(3.09e-06)]_33_[+2(1.58e-07)]_\ 359 35085 1.48e-13 6_[+3(1.56e-09)]_77_[+2(1.53e-06)]_\ 168_[+1(8.03e-10)]_196 3779 9.60e-06 276_[+2(1.27e-05)]_135_\ [+3(4.81e-08)]_56 518 1.48e-13 6_[+3(1.56e-09)]_77_[+2(1.53e-06)]_\ 168_[+1(8.03e-10)]_196 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************