******************************************************************************** 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/440/440.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 24748 1.0000 500 9576 1.0000 500 47428 1.0000 500 48028 1.0000 500 14998 1.0000 500 48556 1.0000 500 43596 1.0000 500 49633 1.0000 500 5718 1.0000 500 51714 1.0000 500 35644 1.0000 500 50209 1.0000 500 34949 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/440/440.seqs.fa -oc motifs/440 -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 0.264 C 0.229 G 0.235 T 0.272 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.229 G 0.235 T 0.272 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 8 llr = 122 E-value = 8.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :11:194:55:5a4:1:994: pos.-specific C 1543:13::16::4:::1::8 probability G 94389:185145:148a::33 matrix T ::3:::33:3:::161::14: bits 2.1 * 1.9 * * 1.7 * * 1.5 * ** * ** Relative 1.3 * *** * * *** * Entropy 1.1 * *** ** *** ***** * (21.9 bits) 0.9 * *** ** *** ***** * 0.6 ** *** ** *** ***** * 0.4 ** *** ** *** ******* 0.2 ****** ************** 0.0 --------------------- Multilevel GCCGGAAGAACAAATGGAAAC consensus GGC CTGTGG CG TG sequence T T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 34949 32 6.94e-10 TTATAAGGAG GGTGGAAGGTCAACTGGAAGC AATGGTAATG 5718 238 1.36e-08 TGGCAGGCTG GGCGGATTGAGGAATGGAATG CGACCATGAG 43596 165 3.63e-08 TTTTGGTCTC GCCGGCAGGTCGACGAGAAAC GTTTCTTTGC 51714 110 5.62e-08 CTGCGGGAAT GCTGGACGACGAAAGTGAAAC TGTGGCCGGA 48028 184 8.43e-08 TCACGTATTC GGGCGATTGACAAATGGCATC ATCGCCAAAA 47428 446 1.06e-07 TGCAACGGAT GAAGGAAGAGCGATGGGAATC AGAGTGTTGC 49633 451 1.33e-07 GCACTATTCA CCGGAAGGAAGGACTGGAAAC GTGCGAAATC 14998 140 1.42e-07 TCGGATCGCT GCCCGACGAACAAGTGGATGG AGAAGAAGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34949 6.9e-10 31_[+1]_448 5718 1.4e-08 237_[+1]_242 43596 3.6e-08 164_[+1]_315 51714 5.6e-08 109_[+1]_370 48028 8.4e-08 183_[+1]_296 47428 1.1e-07 445_[+1]_34 49633 1.3e-07 450_[+1]_29 14998 1.4e-07 139_[+1]_340 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=8 34949 ( 32) GGTGGAAGGTCAACTGGAAGC 1 5718 ( 238) GGCGGATTGAGGAATGGAATG 1 43596 ( 165) GCCGGCAGGTCGACGAGAAAC 1 51714 ( 110) GCTGGACGACGAAAGTGAAAC 1 48028 ( 184) GGGCGATTGACAAATGGCATC 1 47428 ( 446) GAAGGAAGAGCGATGGGAATC 1 49633 ( 451) CCGGAAGGAAGGACTGGAAAC 1 14998 ( 140) GCCCGACGAACAAGTGGATGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 9.60548 E= 8.5e+001 -965 -87 190 -965 -107 112 67 -965 -107 71 9 -12 -965 12 167 -965 -107 -965 190 -965 173 -87 -965 -965 51 12 -91 -12 -965 -965 167 -12 92 -965 109 -965 92 -87 -91 -12 -965 145 67 -965 92 -965 109 -965 192 -965 -965 -965 51 71 -91 -112 -965 -965 67 120 -107 -965 167 -112 -965 -965 209 -965 173 -87 -965 -965 173 -965 -965 -112 51 -965 9 46 -965 171 9 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 8.5e+001 0.000000 0.125000 0.875000 0.000000 0.125000 0.500000 0.375000 0.000000 0.125000 0.375000 0.250000 0.250000 0.000000 0.250000 0.750000 0.000000 0.125000 0.000000 0.875000 0.000000 0.875000 0.125000 0.000000 0.000000 0.375000 0.250000 0.125000 0.250000 0.000000 0.000000 0.750000 0.250000 0.500000 0.000000 0.500000 0.000000 0.500000 0.125000 0.125000 0.250000 0.000000 0.625000 0.375000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.375000 0.375000 0.125000 0.125000 0.000000 0.000000 0.375000 0.625000 0.125000 0.000000 0.750000 0.125000 0.000000 0.000000 1.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.375000 0.000000 0.250000 0.375000 0.000000 0.750000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[CG][CGT][GC]GA[ACT][GT][AG][AT][CG][AG]A[AC][TG]GGAA[ATG][CG] -------------------------------------------------------------------------------- Time 1.50 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 8 llr = 99 E-value = 1.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :46:::9:::::9: pos.-specific C 8:19:4191::6:6 probability G :131:4:::a1414 matrix T 35::a3:19:9::: bits 2.1 * 1.9 * * 1.7 * * 1.5 ** ** * * Relative 1.3 * ** ***** * Entropy 1.1 * ** ******** (17.9 bits) 0.9 * ** ******** 0.6 * *** ******** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel CTACTCACTGTCAC consensus TAG G G G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 50209 86 6.92e-09 AAATGGTCAC CTACTCACTGTCAC ATGAAGTTGG 34949 318 5.57e-08 ACAATTTTCG CAACTGACTGTGAC TGTTGAAAAG 47428 51 6.75e-07 GCTTCGACTC TTGCTCACTGTCAG TGATTTACAT 51714 244 1.14e-06 GGTATACTCA CTGCTTACTGTCGC ATTTGGGAAG 43596 445 2.20e-06 TCGCCACCAT CGACTGATTGTGAC ACGGACTGCT 35644 449 2.66e-06 GCAGTCCTTT TTACTGCCTGTGAG ATTTGGGATT 48028 150 2.77e-06 AATGGGAATT CACGTCACTGTCAG GAACCGTAAA 9576 384 3.21e-06 TATCAATAGG CAACTTACCGGCAC TCCGAGTCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50209 6.9e-09 85_[+2]_401 34949 5.6e-08 317_[+2]_169 47428 6.8e-07 50_[+2]_436 51714 1.1e-06 243_[+2]_243 43596 2.2e-06 444_[+2]_42 35644 2.7e-06 448_[+2]_38 48028 2.8e-06 149_[+2]_337 9576 3.2e-06 383_[+2]_103 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=8 50209 ( 86) CTACTCACTGTCAC 1 34949 ( 318) CAACTGACTGTGAC 1 47428 ( 51) TTGCTCACTGTCAG 1 51714 ( 244) CTGCTTACTGTCGC 1 43596 ( 445) CGACTGATTGTGAC 1 35644 ( 449) TTACTGCCTGTGAG 1 48028 ( 150) CACGTCACTGTCAG 1 9576 ( 384) CAACTTACCGGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 6331 bayes= 9.62639 E= 1.5e+002 -965 171 -965 -12 51 -965 -91 88 124 -87 9 -965 -965 193 -91 -965 -965 -965 -965 187 -965 71 67 -12 173 -87 -965 -965 -965 193 -965 -112 -965 -87 -965 168 -965 -965 209 -965 -965 -965 -91 168 -965 145 67 -965 173 -965 -91 -965 -965 145 67 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 8 E= 1.5e+002 0.000000 0.750000 0.000000 0.250000 0.375000 0.000000 0.125000 0.500000 0.625000 0.125000 0.250000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.375000 0.375000 0.250000 0.875000 0.125000 0.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.625000 0.375000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 0.625000 0.375000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][TA][AG]CT[CGT]ACTGT[CG]A[CG] -------------------------------------------------------------------------------- Time 2.97 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 4 llr = 78 E-value = 1.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::38a:a::5::38::3:3: pos.-specific C 3a83:8::3::a:38::::8 probability G 8::::3::85::3:385:83 matrix T :::::::a::a:5::33a:: bits 2.1 * * 1.9 * * ** ** * 1.7 * * ** ** * 1.5 * * ** ** * Relative 1.3 *** ***** ** ** *** Entropy 1.1 ************ *** *** (28.2 bits) 0.9 ************ *** *** 0.6 ************ *** *** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GCCAACATGATCTACGGTGC consensus C AC G CG ACGTA AG sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 14998 432 1.91e-10 CAGTTTTTAC GCCAACATGATCGACGTTGG AAACACAGCG 35644 86 2.78e-10 TTGCGTAATA GCCCAGATGGTCTACGATGC TTTGCAAAAG 34949 270 1.21e-09 AGAACGCTGC GCCAACATGATCACGTGTGC ACGAAAAGAT 48556 96 2.06e-09 TGATTTCCAA CCAAACATCGTCTACGGTAC ACTTTTGCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14998 1.9e-10 431_[+3]_49 35644 2.8e-10 85_[+3]_395 34949 1.2e-09 269_[+3]_211 48556 2.1e-09 95_[+3]_385 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=4 14998 ( 432) GCCAACATGATCGACGTTGG 1 35644 ( 86) GCCCAGATGGTCTACGATGC 1 34949 ( 270) GCCAACATGATCACGTGTGC 1 48556 ( 96) CCAAACATCGTCTACGGTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 6253 bayes= 10.6094 E= 1.1e+003 -865 12 167 -865 -865 212 -865 -865 -8 171 -865 -865 151 12 -865 -865 192 -865 -865 -865 -865 171 9 -865 192 -865 -865 -865 -865 -865 -865 187 -865 12 167 -865 92 -865 109 -865 -865 -865 -865 187 -865 212 -865 -865 -8 -865 9 87 151 12 -865 -865 -865 171 9 -865 -865 -865 167 -12 -8 -865 109 -12 -865 -865 -865 187 -8 -865 167 -865 -865 171 9 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 4 E= 1.1e+003 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.250000 0.500000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.750000 0.250000 0.250000 0.000000 0.500000 0.250000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.750000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC]C[CA][AC]A[CG]AT[GC][AG]TC[TAG][AC][CG][GT][GAT]T[GA][CG] -------------------------------------------------------------------------------- Time 4.57 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24748 8.71e-02 244_[+3(5.36e-05)]_236 9576 5.90e-03 383_[+2(3.21e-06)]_103 47428 2.04e-06 50_[+2(6.75e-07)]_381_\ [+1(1.06e-07)]_34 48028 5.27e-06 149_[+2(2.77e-06)]_20_\ [+1(8.43e-08)]_296 14998 1.02e-09 139_[+1(1.42e-07)]_271_\ [+3(1.91e-10)]_49 48556 3.81e-05 95_[+3(2.06e-09)]_385 43596 1.13e-06 164_[+1(3.63e-08)]_259_\ [+2(2.20e-06)]_42 49633 4.77e-04 450_[+1(1.33e-07)]_29 5718 3.79e-05 237_[+1(1.36e-08)]_242 51714 1.33e-06 109_[+1(5.62e-08)]_113_\ [+2(1.14e-06)]_98_[+2(7.29e-05)]_131 35644 4.20e-08 48_[+2(6.59e-05)]_23_[+3(2.78e-10)]_\ 343_[+2(2.66e-06)]_38 50209 1.09e-04 85_[+2(6.92e-09)]_401 34949 4.39e-15 31_[+1(6.94e-10)]_217_\ [+3(1.21e-09)]_28_[+2(5.57e-08)]_169 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************