******************************************************************************** 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/437/437.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42521 1.0000 500 42971 1.0000 500 42975 1.0000 500 43067 1.0000 500 43258 1.0000 500 52110 1.0000 500 47122 1.0000 500 21379 1.0000 500 52260 1.0000 500 38005 1.0000 500 48658 1.0000 500 48888 1.0000 500 43382 1.0000 500 43530 1.0000 500 16632 1.0000 500 24120 1.0000 500 44591 1.0000 500 44608 1.0000 500 45780 1.0000 500 36257 1.0000 500 46425 1.0000 500 47721 1.0000 500 34846 1.0000 500 49837 1.0000 500 49709 1.0000 500 41548 1.0000 500 44878 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/437/437.seqs.fa -oc motifs/437 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.225 G 0.226 T 0.272 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.225 G 0.226 T 0.272 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 22 llr = 220 E-value = 3.1e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 51::a:6:::95 pos.-specific C :6:3:8:::31: probability G 3::6:::a:5:5 matrix T 13a1:14:a2:: bits 2.2 * 1.9 * * ** 1.7 * * ** 1.5 * * ** * Relative 1.3 * ** ** * Entropy 1.1 * ** ** ** (14.4 bits) 0.9 **** ** ** 0.6 ******** ** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACTGACAGTGAA consensus GT C T C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43382 93 1.26e-07 TTCGATATTG ACTGACAGTGAG AGAGTTTGGG 45780 45 4.79e-07 TCCTGACTCT GCTGACAGTGAG AGGAAACGTG 44591 83 9.55e-07 GACGCACGCG ACTCACAGTCAA GAAACGGCTC 49709 232 1.21e-06 GTATAGGGGA ATTGACAGTGAG GCCTCGGCGA 43258 229 2.99e-06 AGCTAGGTAA GCTGACAGTTAG TCGAGCGTTT 21379 285 3.69e-06 ATTGTCGGTG AATGACAGTGAA AAACGAGTTT 42971 303 4.19e-06 TTGCCCTCGT GTTGACTGTGAA TCGTCTCCGA 16632 126 6.25e-06 TAGCTCATAA ACTGACAGTGCA CGAGCGTTTT 44608 264 6.80e-06 TCACAGGCAC ATTCACTGTCAA AAAGATCATC 48888 125 6.80e-06 CCGAGCATCT ATTCACTGTCAG CTGGCTCGTT 42521 448 7.35e-06 TTCTTTTCCA TTTGACAGTGAG TTCACAATGT 44878 187 9.41e-06 CGTCGGGCTG GCTGATAGTGAG ATTGCCGTCG 47721 394 1.04e-05 GAAGGAAACG GATGACTGTGAA CCTTTTACAC 34846 306 1.12e-05 TAGTCTGGCA TCTCACTGTCAG GATATGACGC 43530 288 1.61e-05 TATGTAAACT TCTCACAGTTAG ATACGCAATC 43067 77 1.73e-05 CGAGATTGGG ACTGAAAGTGAA TGTGTGTGTT 41548 173 2.51e-05 TACTTTTGCA CCTCACTGTCAA CTTACCTACC 47122 132 2.51e-05 GAACCTGTTT ACTGATTGTTAA CTGAGCGAAC 42975 272 3.12e-05 CAATTTTGAT ATTGACTGTAAA GCTGATGTGA 49837 261 5.91e-05 CTGTAATTAG AATTACAGTTAA TACAAGGTAG 24120 247 6.19e-05 ATTCAGGATG GCTTACAGTCCA GCGCGGTACG 38005 204 7.67e-05 CTCAACAGGG ACTCATGGTCAG GTTCTAGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43382 1.3e-07 92_[+1]_396 45780 4.8e-07 44_[+1]_444 44591 9.6e-07 82_[+1]_406 49709 1.2e-06 231_[+1]_257 43258 3e-06 228_[+1]_260 21379 3.7e-06 284_[+1]_204 42971 4.2e-06 302_[+1]_186 16632 6.2e-06 125_[+1]_363 44608 6.8e-06 263_[+1]_225 48888 6.8e-06 124_[+1]_364 42521 7.4e-06 447_[+1]_41 44878 9.4e-06 186_[+1]_302 47721 1e-05 393_[+1]_95 34846 1.1e-05 305_[+1]_183 43530 1.6e-05 287_[+1]_201 43067 1.7e-05 76_[+1]_412 41548 2.5e-05 172_[+1]_316 47122 2.5e-05 131_[+1]_357 42975 3.1e-05 271_[+1]_217 49837 5.9e-05 260_[+1]_228 24120 6.2e-05 246_[+1]_242 38005 7.7e-05 203_[+1]_285 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=22 43382 ( 93) ACTGACAGTGAG 1 45780 ( 45) GCTGACAGTGAG 1 44591 ( 83) ACTCACAGTCAA 1 49709 ( 232) ATTGACAGTGAG 1 43258 ( 229) GCTGACAGTTAG 1 21379 ( 285) AATGACAGTGAA 1 42971 ( 303) GTTGACTGTGAA 1 16632 ( 126) ACTGACAGTGCA 1 44608 ( 264) ATTCACTGTCAA 1 48888 ( 125) ATTCACTGTCAG 1 42521 ( 448) TTTGACAGTGAG 1 44878 ( 187) GCTGATAGTGAG 1 47721 ( 394) GATGACTGTGAA 1 34846 ( 306) TCTCACTGTCAG 1 43530 ( 288) TCTCACAGTTAG 1 43067 ( 77) ACTGAAAGTGAA 1 41548 ( 173) CCTCACTGTCAA 1 47122 ( 132) ACTGATTGTTAA 1 42975 ( 272) ATTGACTGTAAA 1 49837 ( 261) AATTACAGTTAA 1 24120 ( 247) GCTTACAGTCCA 1 38005 ( 204) ACTCATGGTCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13203 bayes= 10.2544 E= 3.1e-008 98 -231 27 -100 -102 139 -1110 0 -1110 -1110 -1110 188 -1110 50 138 -158 186 -1110 -1110 -1110 -260 186 -1110 -100 110 -1110 -231 42 -1110 -1110 214 -1110 -1110 -1110 -1110 188 -260 50 101 -58 172 -131 -1110 -1110 98 -1110 101 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 22 E= 3.1e-008 0.545455 0.045455 0.272727 0.136364 0.136364 0.590909 0.000000 0.272727 0.000000 0.000000 0.000000 1.000000 0.000000 0.318182 0.590909 0.090909 1.000000 0.000000 0.000000 0.000000 0.045455 0.818182 0.000000 0.136364 0.590909 0.000000 0.045455 0.363636 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.045455 0.318182 0.454545 0.181818 0.909091 0.090909 0.000000 0.000000 0.545455 0.000000 0.454545 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AG][CT]T[GC]AC[AT]GT[GC]A[AG] -------------------------------------------------------------------------------- Time 6.02 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 15 llr = 154 E-value = 1.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :111179:17aa pos.-specific C 2:17311::1:: probability G ::73621792:: matrix T 891::::3:::: bits 2.2 1.9 ** 1.7 * ** 1.5 * ** Relative 1.3 ** *** ** Entropy 1.1 ** * *** ** (14.8 bits) 0.9 ************ 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTGCGAAGGAAA consensus C GCG T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 24120 57 4.06e-07 GGAAGAACGT TTGCGAAGGGAA CGGCAACGCG 47721 380 7.02e-07 CCTACAAGGA TTTCGAAGGAAA CGGATGACTG 43382 110 1.23e-06 GTGAGAGAGT TTGGGGAGGAAA AGAGCTAATT 44878 53 1.58e-06 ATTTCCCATA TTGCGGAGGGAA AACTTTATCT 49837 8 3.07e-06 ACTGTTT CTGGCAAGGAAA AGGAATCAAA 44591 477 4.65e-06 TCGCCGTCGC CAGCGAAGGAAA AAACTCTCCG 41548 300 5.08e-06 CGCTTCAAAT TTCGGAAGGAAA CCGCAATAAA 52110 352 6.38e-06 TGTTGAGAAA TTGCGACTGAAA CACTTTGCAA 47122 89 8.84e-06 CTCTGTATTG TTGGCAAGGCAA TTCCTCTGCG 52260 377 1.16e-05 CGTGCGAGAA TTGCAAGGGAAA CACTCTCAGA 43067 238 1.26e-05 GCCAAGATGT TTGAAAAGGAAA TGCTCTTGGT 21379 243 1.40e-05 CTGATATTAA CAGCGAATGAAA TGCACACTTT 44608 489 2.01e-05 GTTTCTTGTC TTACGCAGGAAA 36257 99 2.32e-05 TTGAGATTCG TTTCCGATGAAA AATGTGGTTT 48658 195 4.82e-05 GCGTGGGGTA TTGCCAATAGAA GCGGTGACAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24120 4.1e-07 56_[+2]_432 47721 7e-07 379_[+2]_109 43382 1.2e-06 109_[+2]_379 44878 1.6e-06 52_[+2]_436 49837 3.1e-06 7_[+2]_481 44591 4.6e-06 476_[+2]_12 41548 5.1e-06 299_[+2]_189 52110 6.4e-06 351_[+2]_137 47122 8.8e-06 88_[+2]_400 52260 1.2e-05 376_[+2]_112 43067 1.3e-05 237_[+2]_251 21379 1.4e-05 242_[+2]_246 44608 2e-05 488_[+2] 36257 2.3e-05 98_[+2]_390 48658 4.8e-05 194_[+2]_294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=15 24120 ( 57) TTGCGAAGGGAA 1 47721 ( 380) TTTCGAAGGAAA 1 43382 ( 110) TTGGGGAGGAAA 1 44878 ( 53) TTGCGGAGGGAA 1 49837 ( 8) CTGGCAAGGAAA 1 44591 ( 477) CAGCGAAGGAAA 1 41548 ( 300) TTCGGAAGGAAA 1 52110 ( 352) TTGCGACTGAAA 1 47122 ( 89) TTGGCAAGGCAA 1 52260 ( 377) TTGCAAGGGAAA 1 43067 ( 238) TTGAAAAGGAAA 1 21379 ( 243) CAGCGAATGAAA 1 44608 ( 489) TTACGCAGGAAA 1 36257 ( 99) TTTCCGATGAAA 1 48658 ( 195) TTGCCAATAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13203 bayes= 9.705 E= 1.2e+003 -1055 -17 -1055 155 -105 -1055 -1055 167 -205 -175 170 -103 -205 156 24 -1055 -105 24 141 -1055 141 -175 -18 -1055 165 -175 -176 -1055 -1055 -1055 170 -3 -205 -1055 204 -1055 141 -175 -18 -1055 186 -1055 -1055 -1055 186 -1055 -1055 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 1.2e+003 0.000000 0.200000 0.000000 0.800000 0.133333 0.000000 0.000000 0.866667 0.066667 0.066667 0.733333 0.133333 0.066667 0.666667 0.266667 0.000000 0.133333 0.266667 0.600000 0.000000 0.733333 0.066667 0.200000 0.000000 0.866667 0.066667 0.066667 0.000000 0.000000 0.000000 0.733333 0.266667 0.066667 0.000000 0.933333 0.000000 0.733333 0.066667 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC]TG[CG][GC][AG]A[GT]G[AG]AA -------------------------------------------------------------------------------- Time 11.84 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 4 llr = 82 E-value = 1.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::3::53:::::::3:::: pos.-specific C 3:8:aa:338aa:5:::a:8 probability G 8:::::53:3:::3a:3::: matrix T :a38:::38:::a3:88:a3 bits 2.2 ** ** * * 1.9 * ** *** * ** 1.7 * ** *** * ** 1.5 * ** *** * ** Relative 1.3 *** ** **** * *** Entropy 1.1 ******* ***** ****** (29.7 bits) 0.9 ******* ***** ****** 0.6 ******* ************ 0.4 ******* ************ 0.2 ******* ************ 0.0 -------------------- Multilevel GTCTCCAATCCCTCGTTCTC consensus C TA GCCG G AG T sequence G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 16632 375 2.01e-11 TTTGCATTTC GTCTCCACTCCCTCGTGCTC GCAGACTTCT 38005 461 4.72e-11 GGATTCCTTT GTTTCCATTCCCTCGTTCTC TGTGCCCAGT 46425 233 3.22e-10 ATCATATAGT GTCACCGGTGCCTTGTTCTC CTAGAATTGT 43067 270 1.78e-09 CAACTTTGAC CTCTCCGACCCCTGGATCTT TCCGTAGCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16632 2e-11 374_[+3]_106 38005 4.7e-11 460_[+3]_20 46425 3.2e-10 232_[+3]_248 43067 1.8e-09 269_[+3]_211 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=4 16632 ( 375) GTCTCCACTCCCTCGTGCTC 1 38005 ( 461) GTTTCCATTCCCTCGTTCTC 1 46425 ( 233) GTCACCGGTGCCTTGTTCTC 1 43067 ( 270) CTCTCCGACCCCTGGATCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 12987 bayes= 11.6643 E= 1.3e+003 -865 15 173 -865 -865 -865 -865 187 -865 173 -865 -12 -14 -865 -865 146 -865 215 -865 -865 -865 215 -865 -865 85 -865 114 -865 -14 15 14 -12 -865 15 -865 146 -865 173 14 -865 -865 215 -865 -865 -865 215 -865 -865 -865 -865 -865 187 -865 115 14 -12 -865 -865 214 -865 -14 -865 -865 146 -865 -865 14 146 -865 215 -865 -865 -865 -865 -865 187 -865 173 -865 -12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 4 E= 1.3e+003 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.250000 0.000000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.250000 0.250000 0.250000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.250000 0.000000 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 0.500000 0.250000 0.250000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC]T[CT][TA]CC[AG][ACGT][TC][CG]CCT[CGT]G[TA][TG]CT[CT] -------------------------------------------------------------------------------- Time 18.16 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42521 3.43e-02 447_[+1(7.35e-06)]_41 42971 4.36e-03 302_[+1(4.19e-06)]_186 42975 1.52e-01 271_[+1(3.12e-05)]_217 43067 1.37e-08 71_[+2(1.52e-05)]_154_\ [+2(1.26e-05)]_20_[+3(1.78e-09)]_211 43258 3.57e-03 124_[+3(9.98e-05)]_84_\ [+1(2.99e-06)]_260 52110 3.23e-02 351_[+2(6.38e-06)]_137 47122 2.51e-03 88_[+2(8.84e-06)]_31_[+1(2.51e-05)]_\ 357 21379 6.47e-04 242_[+2(1.40e-05)]_30_\ [+1(3.69e-06)]_204 52260 3.97e-02 376_[+2(1.16e-05)]_112 38005 3.37e-08 203_[+1(7.67e-05)]_245_\ [+3(4.72e-11)]_20 48658 1.09e-01 194_[+2(4.82e-05)]_294 48888 8.50e-04 124_[+1(6.80e-06)]_364 43382 5.70e-06 92_[+1(1.26e-07)]_5_[+2(1.23e-06)]_\ 379 43530 4.22e-02 287_[+1(1.61e-05)]_201 16632 5.36e-09 125_[+1(6.25e-06)]_237_\ [+3(2.01e-11)]_106 24120 1.83e-04 56_[+2(4.06e-07)]_178_\ [+1(6.19e-05)]_242 44591 9.87e-05 82_[+1(9.55e-07)]_141_\ [+1(6.80e-06)]_229_[+2(4.65e-06)]_12 44608 1.93e-03 263_[+1(6.80e-06)]_213_\ [+2(2.01e-05)] 45780 5.06e-03 44_[+1(4.79e-07)]_444 36257 7.22e-02 98_[+2(2.32e-05)]_390 46425 1.58e-06 232_[+3(3.22e-10)]_248 47721 1.26e-04 379_[+2(7.02e-07)]_2_[+1(1.04e-05)]_\ 95 34846 4.95e-02 229_[+1(4.95e-05)]_64_\ [+1(1.12e-05)]_112_[+1(5.91e-05)]_59 49837 2.23e-03 7_[+2(3.07e-06)]_241_[+1(5.91e-05)]_\ 228 49709 4.37e-03 231_[+1(1.21e-06)]_257 41548 1.02e-03 172_[+1(2.51e-05)]_115_\ [+2(5.08e-06)]_189 44878 1.80e-04 52_[+2(1.58e-06)]_122_\ [+1(9.41e-06)]_302 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************