******************************************************************************** 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/233/233.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 51430 1.0000 500 24922 1.0000 500 12989 1.0000 500 28568 1.0000 500 47293 1.0000 500 43387 1.0000 500 51214 1.0000 500 40349 1.0000 500 16615 1.0000 500 44011 1.0000 500 6457 1.0000 500 7893 1.0000 500 44572 1.0000 500 11131 1.0000 500 45108 1.0000 500 35002 1.0000 500 12106 1.0000 500 12925 1.0000 500 36383 1.0000 500 34358 1.0000 500 34363 1.0000 500 44978 1.0000 500 33892 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/233/233.seqs.fa -oc motifs/233 -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 0.267 C 0.240 G 0.240 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.240 G 0.240 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 17 llr = 165 E-value = 4.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 11:22::::::: pos.-specific C 2991:1:::8:7 probability G ::123::1517: matrix T 7:1459a95133 bits 2.1 * 1.9 * 1.6 * * 1.4 ** *** Relative 1.2 ** *** *** Entropy 1.0 ** ******* (14.0 bits) 0.8 *** ******* 0.6 *** ******* 0.4 *** ******** 0.2 ************ 0.0 ------------ Multilevel TCCTTTTTTCGC consensus AG G TT sequence GA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 34363 351 5.28e-08 CATTGTAAAA TCCTTTTTTCGC TACTCAAAAA 34358 351 5.28e-08 CATTGTAAAA TCCTTTTTTCGC TACTCAAAAA 16615 130 5.16e-07 TTCTTCATAC TCCTATTTGCGC GTGCCGTTCT 11131 298 8.78e-07 AACAATGCTT TCCGGTTTGCGC AATCGGCAAG 36383 440 5.99e-06 CCGTAATTAC TCCATTTTTTGC AAATCAAGAG 24922 64 8.08e-06 TCGTTCGCCT CCCGTTTTTCGT TTTGGTCGTT 6457 34 1.24e-05 CGTCATCATA TCGTGTTTGCGC AGCTCGTCTT 12925 63 1.40e-05 CTGCCGCCGA TCCAATTTTTGC GTGTCCAATT 7893 289 1.55e-05 ACTTTACCGT ACCATTTTTCTC ACGACGACGC 51214 195 1.81e-05 ATGTAAAGTA TCCATTTGTCGT CGCGTTGCGT 45108 112 2.47e-05 TTATTGTCGG TACGGTTTGCGC GTTGACCTGT 44978 306 3.05e-05 ACTTACATTC ACCGATTTGCTC TACCTCTCTC 28568 210 4.06e-05 ATCCCACGTA CCCCTCTTTCGC GGAAAACCCG 12106 83 4.35e-05 CTGGTTGTGG TCCTTTTTGGTT CTCATGCTGT 43387 302 4.67e-05 GGCAACCGCT TCCTACTTTCTT AAGTATCGGA 51430 378 4.67e-05 CGTTGCGGCG TCCCGTTGGCTC TCAATGATGG 33892 440 8.12e-05 CACGTAGATT CCTTGTTTGCGT ACGGAGAGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34363 5.3e-08 350_[+1]_138 34358 5.3e-08 350_[+1]_138 16615 5.2e-07 129_[+1]_359 11131 8.8e-07 297_[+1]_191 36383 6e-06 439_[+1]_49 24922 8.1e-06 63_[+1]_425 6457 1.2e-05 33_[+1]_455 12925 1.4e-05 62_[+1]_426 7893 1.5e-05 288_[+1]_200 51214 1.8e-05 194_[+1]_294 45108 2.5e-05 111_[+1]_377 44978 3e-05 305_[+1]_183 28568 4.1e-05 209_[+1]_279 12106 4.3e-05 82_[+1]_406 43387 4.7e-05 301_[+1]_187 51430 4.7e-05 377_[+1]_111 33892 8.1e-05 439_[+1]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=17 34363 ( 351) TCCTTTTTTCGC 1 34358 ( 351) TCCTTTTTTCGC 1 16615 ( 130) TCCTATTTGCGC 1 11131 ( 298) TCCGGTTTGCGC 1 36383 ( 440) TCCATTTTTTGC 1 24922 ( 64) CCCGTTTTTCGT 1 6457 ( 34) TCGTGTTTGCGC 1 12925 ( 63) TCCAATTTTTGC 1 7893 ( 289) ACCATTTTTCTC 1 51214 ( 195) TCCATTTGTCGT 1 45108 ( 112) TACGGTTTGCGC 1 44978 ( 306) ACCGATTTGCTC 1 28568 ( 210) CCCCTCTTTCGC 1 12106 ( 83) TCCTTTTTGGTT 1 43387 ( 302) TCCTACTTTCTT 1 51430 ( 378) TCCCGTTGGCTC 1 33892 ( 440) CCTTGTTTGCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 11247 bayes= 10.1632 E= 4.1e+000 -118 -44 -1073 148 -218 197 -1073 -1073 -1073 188 -203 -210 -18 -103 -3 70 -18 -1073 29 90 -1073 -103 -1073 180 -1073 -1073 -1073 198 -1073 -1073 -103 180 -1073 -1073 97 107 -1073 178 -203 -110 -1073 -1073 155 22 -1073 156 -1073 22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 4.1e+000 0.117647 0.176471 0.000000 0.705882 0.058824 0.941176 0.000000 0.000000 0.000000 0.882353 0.058824 0.058824 0.235294 0.117647 0.235294 0.411765 0.235294 0.000000 0.294118 0.470588 0.000000 0.117647 0.000000 0.882353 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.117647 0.882353 0.000000 0.000000 0.470588 0.529412 0.000000 0.823529 0.058824 0.117647 0.000000 0.000000 0.705882 0.294118 0.000000 0.705882 0.000000 0.294118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TCC[TAG][TGA]TTT[TG]C[GT][CT] -------------------------------------------------------------------------------- Time 4.61 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 8 llr = 132 E-value = 5.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::11:1::683:4:483::: pos.-specific C ::1::::::::::1:41511: probability G ::9414819:36:4a1::5:3 matrix T aa:5861914:1a1:113498 bits 2.1 ** * * 1.9 ** * * 1.6 ** * * 1.4 *** ** * * * Relative 1.2 *** ** * * * ** Entropy 1.0 *** ****** * * ** (23.8 bits) 0.8 *** ******* * * * ** 0.6 ************* * * *** 0.4 ************* * ***** 0.2 ********************* 0.0 --------------------- Multilevel TTGTTTGTGAAGTAGAACGTT consensus G G TGA G C AT G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 34363 405 1.58e-11 TTCATCTCAT TTGGTTGTGAAGTAGCAAGTT CGAAGCGAAA 34358 405 1.58e-11 TTCATCTCAT TTGGTTGTGAAGTAGCAAGTT CGAAGCGAAA 51430 469 4.35e-09 GAAGCTGTCT TTGATGGTGAAATGGAACCTT TGGTTTCGGG 35002 3 1.19e-08 CT TTGTGTGTGTAGTTGAATGTG CCGCAAATTT 40349 10 4.70e-08 AGCAATACA TTGGTTGGGAAGTCGAACTCG TTTCACCTTC 24922 38 5.38e-08 AAGCAGCTTT TTCTTGGTGAATTGGTTCGTT CGCCTCCCGT 33892 256 1.00e-07 CCGCGTTGTT TTGTTGTTTTGGTGGCCCTTT CGCTAGACCT 7893 108 1.64e-07 TATACCTTCA TTGTATATGTGATAGGATTTT CCACGAAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34363 1.6e-11 404_[+2]_75 34358 1.6e-11 404_[+2]_75 51430 4.4e-09 468_[+2]_11 35002 1.2e-08 2_[+2]_477 40349 4.7e-08 9_[+2]_470 24922 5.4e-08 37_[+2]_442 33892 1e-07 255_[+2]_224 7893 1.6e-07 107_[+2]_372 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=8 34363 ( 405) TTGGTTGTGAAGTAGCAAGTT 1 34358 ( 405) TTGGTTGTGAAGTAGCAAGTT 1 51430 ( 469) TTGATGGTGAAATGGAACCTT 1 35002 ( 3) TTGTGTGTGTAGTTGAATGTG 1 40349 ( 10) TTGGTTGGGAAGTCGAACTCG 1 24922 ( 38) TTCTTGGTGAATTGGTTCGTT 1 33892 ( 256) TTGTTGTTTTGGTGGCCCTTT 1 7893 ( 108) TTGTATATGTGATAGGATTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11040 bayes= 10.4294 E= 5.7e+001 -965 -965 -965 198 -965 -965 -965 198 -965 -94 186 -965 -109 -965 64 98 -109 -965 -94 157 -965 -965 64 130 -109 -965 164 -101 -965 -965 -94 179 -965 -965 186 -101 123 -965 -965 57 149 -965 6 -965 -9 -965 138 -101 -965 -965 -965 198 49 -94 64 -101 -965 -965 206 -965 49 64 -94 -101 149 -94 -965 -101 -9 106 -965 -2 -965 -94 106 57 -965 -94 -965 179 -965 -965 6 157 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 5.7e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.125000 0.875000 0.000000 0.125000 0.000000 0.375000 0.500000 0.125000 0.000000 0.125000 0.750000 0.000000 0.000000 0.375000 0.625000 0.125000 0.000000 0.750000 0.125000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.875000 0.125000 0.625000 0.000000 0.000000 0.375000 0.750000 0.000000 0.250000 0.000000 0.250000 0.000000 0.625000 0.125000 0.000000 0.000000 0.000000 1.000000 0.375000 0.125000 0.375000 0.125000 0.000000 0.000000 1.000000 0.000000 0.375000 0.375000 0.125000 0.125000 0.750000 0.125000 0.000000 0.125000 0.250000 0.500000 0.000000 0.250000 0.000000 0.125000 0.500000 0.375000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 0.250000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TTG[TG]T[TG]GTG[AT][AG][GA]T[AG]G[AC]A[CAT][GT]T[TG] -------------------------------------------------------------------------------- Time 8.94 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 16 llr = 160 E-value = 4.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 383:5:3a4:66 pos.-specific C :11:4a::61:3 probability G 7::a::7::941 matrix T 116:1::::::: bits 2.1 * * 1.9 * * * 1.6 * * * 1.4 * * * * Relative 1.2 * * * * Entropy 1.0 * ****** (14.4 bits) 0.8 **** ****** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GATGACGACGAA consensus A A C A A GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 28568 81 3.10e-07 CAGTGACGAT GATGACGAAGAA GAAGAAGAAG 7893 468 2.87e-06 TGCTGGCGTA GAAGACGACGGC GAGCCACCAG 34363 68 3.26e-06 AAAACTACGT GATGTCGAAGAA ACAATCGCCA 34358 68 3.26e-06 AAAACTACGT GATGTCGAAGAA ACAATCGCCA 12106 411 3.74e-06 TATCATGGCA GCTGACGACGAA TACGTTCCTC 12925 196 4.18e-06 GATACAATGA GATGCCAACGAC AAGCAACAAG 24922 435 4.18e-06 GCTGCCCGAA GAAGACGAAGAC GACGTTTTGG 36383 181 9.24e-06 TGCATGTATC GAAGCCGACGGG ATCGACCATT 47293 200 1.12e-05 CATGGTGTGG GATGCCAACGGG AACTTTTTTT 51214 43 1.77e-05 AATGTATCGC AATGACGACCAA ACAGGGAAAC 33892 50 2.08e-05 CGCCCGAATG GAAGCCGAACGA CAGGCCCGAG 44978 92 2.25e-05 ATTTTCTAGA TATGACAACGAA CTATTAGTAA 35002 270 2.25e-05 ATAGAGGAAA ACTGACGAAGGA CGAGCGAACG 40349 373 3.23e-05 AGTAGCAGTA AAAGCCAACGGC ATGCAGCTCC 16615 393 3.71e-05 TATAGAGGGC GTCGACGACGAA ATAAGCCAGC 12989 92 5.01e-05 TACTGATGAA ATTGCCAAAGGA TCAGTTTGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28568 3.1e-07 80_[+3]_408 7893 2.9e-06 467_[+3]_21 34363 3.3e-06 67_[+3]_421 34358 3.3e-06 67_[+3]_421 12106 3.7e-06 410_[+3]_78 12925 4.2e-06 195_[+3]_293 24922 4.2e-06 434_[+3]_54 36383 9.2e-06 180_[+3]_308 47293 1.1e-05 199_[+3]_289 51214 1.8e-05 42_[+3]_446 33892 2.1e-05 49_[+3]_439 44978 2.2e-05 91_[+3]_397 35002 2.2e-05 269_[+3]_219 40349 3.2e-05 372_[+3]_116 16615 3.7e-05 392_[+3]_96 12989 5e-05 91_[+3]_397 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=16 28568 ( 81) GATGACGAAGAA 1 7893 ( 468) GAAGACGACGGC 1 34363 ( 68) GATGTCGAAGAA 1 34358 ( 68) GATGTCGAAGAA 1 12106 ( 411) GCTGACGACGAA 1 12925 ( 196) GATGCCAACGAC 1 24922 ( 435) GAAGACGAAGAC 1 36383 ( 181) GAAGCCGACGGG 1 47293 ( 200) GATGCCAACGGG 1 51214 ( 43) AATGACGACCAA 1 33892 ( 50) GAAGCCGAACGA 1 44978 ( 92) TATGACAACGAA 1 35002 ( 270) ACTGACGAAGGA 1 40349 ( 373) AAAGCCAACGGC 1 16615 ( 393) GTCGACGACGAA 1 12989 ( 92) ATTGCCAAAGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 11247 bayes= 9.4552 E= 4.6e+001 -9 -1064 152 -201 149 -94 -1064 -102 23 -194 -1064 130 -1064 -1064 206 -1064 91 64 -1064 -102 -1064 206 -1064 -1064 23 -1064 152 -1064 191 -1064 -1064 -1064 71 123 -1064 -1064 -1064 -94 186 -1064 108 -1064 86 -1064 123 6 -94 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 16 E= 4.6e+001 0.250000 0.000000 0.687500 0.062500 0.750000 0.125000 0.000000 0.125000 0.312500 0.062500 0.000000 0.625000 0.000000 0.000000 1.000000 0.000000 0.500000 0.375000 0.000000 0.125000 0.000000 1.000000 0.000000 0.000000 0.312500 0.000000 0.687500 0.000000 1.000000 0.000000 0.000000 0.000000 0.437500 0.562500 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.562500 0.000000 0.437500 0.000000 0.625000 0.250000 0.125000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA]A[TA]G[AC]C[GA]A[CA]G[AG][AC] -------------------------------------------------------------------------------- Time 13.27 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 51430 6.33e-06 377_[+1(4.67e-05)]_79_\ [+2(4.35e-09)]_11 24922 5.64e-08 37_[+2(5.38e-08)]_5_[+1(8.08e-06)]_\ 359_[+3(4.18e-06)]_54 12989 1.76e-01 91_[+3(5.01e-05)]_397 28568 1.59e-04 80_[+3(3.10e-07)]_117_\ [+1(4.06e-05)]_279 47293 1.51e-02 199_[+3(1.12e-05)]_289 43387 5.86e-02 301_[+1(4.67e-05)]_187 51214 9.66e-04 42_[+3(1.77e-05)]_140_\ [+1(1.81e-05)]_294 40349 2.99e-05 9_[+2(4.70e-08)]_342_[+3(3.23e-05)]_\ 116 16615 3.75e-04 129_[+1(5.16e-07)]_251_\ [+3(3.71e-05)]_96 44011 4.10e-01 500 6457 4.64e-02 33_[+1(1.24e-05)]_455 7893 2.01e-07 107_[+2(1.64e-07)]_160_\ [+1(1.55e-05)]_167_[+3(2.87e-06)]_21 44572 7.77e-01 500 11131 4.33e-03 297_[+1(8.78e-07)]_191 45108 8.02e-02 111_[+1(2.47e-05)]_377 35002 7.47e-06 2_[+2(1.19e-08)]_246_[+3(2.25e-05)]_\ 219 12106 6.44e-04 82_[+1(4.35e-05)]_316_\ [+3(3.74e-06)]_78 12925 9.89e-04 62_[+1(1.40e-05)]_121_\ [+3(4.18e-06)]_293 36383 2.72e-04 180_[+3(9.24e-06)]_57_\ [+1(6.32e-05)]_178_[+1(5.99e-06)]_49 34358 2.11e-13 67_[+3(3.26e-06)]_271_\ [+1(5.28e-08)]_42_[+2(1.58e-11)]_75 34363 2.11e-13 67_[+3(3.26e-06)]_271_\ [+1(5.28e-08)]_42_[+2(1.58e-11)]_75 44978 4.12e-03 91_[+3(2.25e-05)]_202_\ [+1(3.05e-05)]_183 33892 3.36e-06 49_[+3(2.08e-05)]_194_\ [+2(1.00e-07)]_163_[+1(8.12e-05)]_49 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************