******************************************************************************** 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/355/355.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11075 1.0000 500 11076 1.0000 500 11823 1.0000 500 14555 1.0000 500 1771 1.0000 500 262312 1.0000 500 33497 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/355/355.seqs.fa -oc motifs/355 -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= 7 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= 3500 N= 7 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.291 C 0.213 G 0.258 T 0.238 Background letter frequencies (from dataset with add-one prior applied): A 0.291 C 0.213 G 0.258 T 0.238 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 17 sites = 7 llr = 97 E-value = 4.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :4:::::31:aa:3:3: pos.-specific C 71:4::71:9::7161: probability G :3:441:4:1:::::3: matrix T 31a169319:::3643a bits 2.2 2.0 * * 1.8 * ** * 1.6 * * *** * Relative 1.3 * * ** ***** * Entropy 1.1 * * *** ***** * * (19.9 bits) 0.9 * * *** ***** * * 0.7 * ***** ******* * 0.4 * ***** ******* * 0.2 * ************* * 0.0 ----------------- Multilevel CATCTTCGTCAACTCAT consensus TG GG TA TATG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------- 11076 480 2.35e-09 TCATCGAAAC CATCGTCATCAACTCAT CATC 14555 453 3.13e-08 AAATCTCATG CATCGTCCTCAACTTCT CCTACACCGC 1771 370 7.50e-08 GCAACGCACG TGTCTTCATCAACACGT GGAGGCGATC 11823 228 2.67e-07 AACTCTTTTT CATTTTTGTCAATTTAT ATTCTCCTCT 33497 319 4.30e-07 ATTGTGATGG CTTGTGCTTCAACTTTT GCTGTAGGAA 11075 161 7.48e-07 AAAGTACGAA TCTGTTCGACAACACTT GACAGAAAAG 262312 101 1.83e-06 TTGGCGTCGT CGTGGTTGTGAATCCGT CAACAGCTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11076 2.4e-09 479_[+1]_4 14555 3.1e-08 452_[+1]_31 1771 7.5e-08 369_[+1]_114 11823 2.7e-07 227_[+1]_256 33497 4.3e-07 318_[+1]_165 11075 7.5e-07 160_[+1]_323 262312 1.8e-06 100_[+1]_383 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=17 seqs=7 11076 ( 480) CATCGTCATCAACTCAT 1 14555 ( 453) CATCGTCCTCAACTTCT 1 1771 ( 370) TGTCTTCATCAACACGT 1 11823 ( 228) CATTTTTGTCAATTTAT 1 33497 ( 319) CTTGTGCTTCAACTTTT 1 11075 ( 161) TCTGTTCGACAACACTT 1 262312 ( 101) CGTGGTTGTGAATCCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 17 n= 3388 bayes= 10.14 E= 4.9e-001 -945 174 -945 26 56 -57 15 -74 -945 -945 -945 207 -945 101 73 -74 -945 -945 73 126 -945 -945 -85 185 -945 174 -945 26 -3 -57 73 -74 -102 -945 -945 185 -945 201 -85 -945 178 -945 -945 -945 178 -945 -945 -945 -945 174 -945 26 -3 -57 -945 126 -945 142 -945 85 -3 -57 15 26 -945 -945 -945 207 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 17 nsites= 7 E= 4.9e-001 0.000000 0.714286 0.000000 0.285714 0.428571 0.142857 0.285714 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.428571 0.142857 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.142857 0.857143 0.000000 0.714286 0.000000 0.285714 0.285714 0.142857 0.428571 0.142857 0.142857 0.000000 0.000000 0.857143 0.000000 0.857143 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.285714 0.285714 0.142857 0.000000 0.571429 0.000000 0.571429 0.000000 0.428571 0.285714 0.142857 0.285714 0.285714 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][AG]T[CG][TG]T[CT][GA]TCAA[CT][TA][CT][AGT]T -------------------------------------------------------------------------------- Time 0.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 108 E-value = 1.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::6:14137:33691:77: pos.-specific C ::4:44::4::a16::411:a probability G a:1a::93333:113147:3: matrix T :a4::6:314::4:1::11:: bits 2.2 * * 2.0 ** * * * 1.8 ** * * * 1.6 ** * * * Relative 1.3 ** * * * * Entropy 1.1 ** * ** * * * (22.3 bits) 0.9 ** **** ** * * ** 0.7 ******* ** * ****** 0.4 ******** *** ******** 0.2 ********************* 0.0 --------------------- Multilevel GTCGATGACTACTCAACGAAC consensus T CC GGAG AAG G G sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 11823 417 2.89e-09 AGAAGCTGTT GTTGATGGCTGCAAAACGAAC AGTGGAGCTT 14555 46 3.32e-08 TGTGTCGCTT GTCGACGTCGACCCGACGCGC AAAGGACCTT 33497 358 3.64e-08 TGGTTGCGAG GTCGCCGGGAGCGCAAGGAGC TGAAAGTCGC 11075 19 4.77e-08 CTCTTGGAGC GTGGCTAATGACTCAACGAAC AGAGTACCGA 1771 247 6.70e-08 TTGCACTTAT GTCGATGAATACAAGAGGTAC GAAGGGACCA 262312 290 7.27e-08 GTCTGTCGTT GTTGCCGTCTACTGAGGCAAC GATCAGTGGC 11076 320 8.51e-08 GCTCCAAGGT GTTGATGAGAACTCTAATAAC GCTGCATGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11823 2.9e-09 416_[+2]_63 14555 3.3e-08 45_[+2]_434 33497 3.6e-08 357_[+2]_122 11075 4.8e-08 18_[+2]_461 1771 6.7e-08 246_[+2]_233 262312 7.3e-08 289_[+2]_190 11076 8.5e-08 319_[+2]_160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 11823 ( 417) GTTGATGGCTGCAAAACGAAC 1 14555 ( 46) GTCGACGTCGACCCGACGCGC 1 33497 ( 358) GTCGCCGGGAGCGCAAGGAGC 1 11075 ( 19) GTGGCTAATGACTCAACGAAC 1 1771 ( 247) GTCGATGAATACAAGAGGTAC 1 262312 ( 290) GTTGCCGTCTACTGAGGCAAC 1 11076 ( 320) GTTGATGAGAACTCTAATAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 8.90388 E= 1.6e+001 -945 -945 195 -945 -945 -945 -945 207 -945 101 -85 85 -945 -945 195 -945 97 101 -945 -945 -945 101 -945 126 -102 -945 173 -945 56 -945 15 26 -102 101 15 -74 -3 -945 15 85 130 -945 15 -945 -945 223 -945 -945 -3 -57 -85 85 -3 142 -85 -945 97 -945 15 -74 156 -945 -85 -945 -102 101 73 -945 -945 -57 147 -74 130 -57 -945 -74 130 -945 15 -945 -945 223 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.6e+001 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.142857 0.428571 0.000000 0.000000 1.000000 0.000000 0.571429 0.428571 0.000000 0.000000 0.000000 0.428571 0.000000 0.571429 0.142857 0.000000 0.857143 0.000000 0.428571 0.000000 0.285714 0.285714 0.142857 0.428571 0.285714 0.142857 0.285714 0.000000 0.285714 0.428571 0.714286 0.000000 0.285714 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.142857 0.142857 0.428571 0.285714 0.571429 0.142857 0.000000 0.571429 0.000000 0.285714 0.142857 0.857143 0.000000 0.142857 0.000000 0.142857 0.428571 0.428571 0.000000 0.000000 0.142857 0.714286 0.142857 0.714286 0.142857 0.000000 0.142857 0.714286 0.000000 0.285714 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GT[CT]G[AC][TC]G[AGT][CG][TAG][AG]C[TA][CA][AG]A[CG]GA[AG]C -------------------------------------------------------------------------------- Time 0.96 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 3 llr = 56 E-value = 3.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::7:::::::::a::a pos.-specific C a:37a:3a::7a::a: probability G :::::3::a7:::7:: matrix T :a:3:77::33::3:: bits 2.2 * * * * * 2.0 ** * ** * * 1.8 ** * ** ** ** 1.6 ** * ** ** ** Relative 1.3 ** ** ** *** ** Entropy 1.1 **************** (26.7 bits) 0.9 **************** 0.7 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CTACCTTCGGCCAGCA consensus CT GC TT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11076 97 1.67e-09 CGAGGCCACA CTACCTTCGTCCATCA GCCCTTTCTG 1771 172 3.26e-09 CCTTCGATAA CTATCTTCGGTCAGCA GTAACAACAA 33497 435 3.57e-09 AACGGACATC CTCCCGCCGGCCAGCA CACCCTGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11076 1.7e-09 96_[+3]_388 1771 3.3e-09 171_[+3]_313 33497 3.6e-09 434_[+3]_50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=3 11076 ( 97) CTACCTTCGTCCATCA 1 1771 ( 172) CTATCTTCGGTCAGCA 1 33497 ( 435) CTCCCGCCGGCCAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 3395 bayes= 9.80158 E= 3.1e+002 -823 223 -823 -823 -823 -823 -823 207 119 65 -823 -823 -823 164 -823 48 -823 223 -823 -823 -823 -823 37 148 -823 65 -823 148 -823 223 -823 -823 -823 -823 195 -823 -823 -823 137 48 -823 164 -823 48 -823 223 -823 -823 178 -823 -823 -823 -823 -823 137 48 -823 223 -823 -823 178 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 3 E= 3.1e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CT[AC][CT]C[TG][TC]CG[GT][CT]CA[GT]CA -------------------------------------------------------------------------------- Time 1.35 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11075 1.13e-06 18_[+2(4.77e-08)]_121_\ [+1(7.48e-07)]_323 11076 2.84e-14 96_[+3(1.67e-09)]_207_\ [+2(8.51e-08)]_139_[+1(2.35e-09)]_4 11823 4.89e-08 227_[+1(2.67e-07)]_172_\ [+2(2.89e-09)]_63 14555 9.17e-09 45_[+2(3.32e-08)]_386_\ [+1(3.13e-08)]_31 1771 1.13e-12 171_[+3(3.26e-09)]_59_\ [+2(6.70e-08)]_102_[+1(7.50e-08)]_114 262312 1.87e-06 100_[+1(1.83e-06)]_172_\ [+2(7.27e-08)]_190 33497 3.58e-12 318_[+1(4.30e-07)]_22_\ [+2(3.64e-08)]_56_[+3(3.57e-09)]_50 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************