******************************************************************************** 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/170/170.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10535 1.0000 500 10598 1.0000 500 10928 1.0000 500 11327 1.0000 500 11721 1.0000 500 11865 1.0000 500 25552 1.0000 500 261307 1.0000 500 262570 1.0000 500 263487 1.0000 500 264303 1.0000 500 36909 1.0000 500 37458 1.0000 500 38180 1.0000 500 4263 1.0000 500 4725 1.0000 500 7513 1.0000 500 7768 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/170/170.seqs.fa -oc motifs/170 -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= 18 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= 9000 N= 18 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.230 G 0.244 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.230 G 0.244 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 14 llr = 177 E-value = 2.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::7:1211:2:4131321 pos.-specific C 1::2:14:3::1::2::::: probability G :9631:255:94166294:5 matrix T 9145293319139:15:384 bits 2.1 1.9 1.7 * * 1.5 ** ** * * Relative 1.3 ** * ** * * Entropy 1.1 *** * ** ** * * (18.2 bits) 0.8 *** ** ** ** * * 0.6 *** ** ** ** * ** 0.4 ****** **** ******** 0.2 ****** ************* 0.0 -------------------- Multilevel TGGTATCGGTGGTGGTGGTG consensus TGT TTC T ACA AAT sequence C GA A G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 4725 324 5.99e-10 TGTAATGGAC TGGGATGGGTGGTAGTGGTG GCAAGGAGGG 36909 27 1.13e-08 TCCGCCACGT TGGTATCTGTGGTGGGGGAT GGTGTTCAAG 264303 351 2.66e-08 ACGTTGATAT TGGTTTTGGTGATGGGGTTG CCCTTGGTGG 11721 142 1.77e-07 TCGCTCAGCG TTGTTTCTGTGGTGGTGTTG AGAGTGGTTT 261307 294 2.40e-07 ATGTATTACA TGGTATCGATGATACTGAAG TCTATTTAGA 25552 260 2.65e-07 TTGCTCAAAG CGGCATCGCTGTTGGGGTTG TATCAATGAT 263487 76 7.89e-07 GGTACAATGT TGTGATTGGTGAGAGTGATT TCAGTTTGGA 4263 54 1.09e-06 CGGTGAGTGA TGTGTTTTGTTGTGCTGTTG CTTCGCATGC 262570 12 1.18e-06 ATGTCTCAAA TGTTATCAATGGTGAAGGTA TGACGAGAGT 10928 274 1.73e-06 ATGAATTTTA TGGGACAGCTGCTGTTGGTT TCGGTGAGTG 7513 243 2.15e-06 GACAACTCAC TGGCATGACTTGTAGAGATA GAGGGCTGTG 11327 69 2.84e-06 CGTCTCGTTG TGGTGTGAGTGTTGGAAGTT ACATTTGAAT 10535 126 5.06e-06 AATAGTTGAT TGTCACAGTTGTTACAGGTG TATCTATAAT 7768 318 6.42e-06 AAAACGTTTT TGTTATTTCAGTTGTTGAAT TTAACACCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4725 6e-10 323_[+1]_157 36909 1.1e-08 26_[+1]_454 264303 2.7e-08 350_[+1]_130 11721 1.8e-07 141_[+1]_339 261307 2.4e-07 293_[+1]_187 25552 2.6e-07 259_[+1]_221 263487 7.9e-07 75_[+1]_405 4263 1.1e-06 53_[+1]_427 262570 1.2e-06 11_[+1]_469 10928 1.7e-06 273_[+1]_207 7513 2.2e-06 242_[+1]_238 11327 2.8e-06 68_[+1]_412 10535 5.1e-06 125_[+1]_355 7768 6.4e-06 317_[+1]_163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=14 4725 ( 324) TGGGATGGGTGGTAGTGGTG 1 36909 ( 27) TGGTATCTGTGGTGGGGGAT 1 264303 ( 351) TGGTTTTGGTGATGGGGTTG 1 11721 ( 142) TTGTTTCTGTGGTGGTGTTG 1 261307 ( 294) TGGTATCGATGATACTGAAG 1 25552 ( 260) CGGCATCGCTGTTGGGGTTG 1 263487 ( 76) TGTGATTGGTGAGAGTGATT 1 4263 ( 54) TGTGTTTTGTTGTGCTGTTG 1 262570 ( 12) TGTTATCAATGGTGAAGGTA 1 10928 ( 274) TGGGACAGCTGCTGTTGGTT 1 7513 ( 243) TGGCATGACTTGTAGAGATA 1 11327 ( 69) TGGTGTGAGTGTTGGAAGTT 1 10535 ( 126) TGTCACAGTTGTTACAGGTG 1 7768 ( 318) TGTTATTTCAGTTGTTGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8658 bayes= 9.11374 E= 2.8e-002 -1045 -168 -1045 178 -1045 -1045 193 -191 -1045 -1045 140 41 -1045 -10 23 89 147 -1045 -177 -33 -1045 -68 -1045 167 -85 64 -18 8 -26 -1045 104 8 -85 31 104 -191 -185 -1045 -1045 178 -1045 -1045 181 -92 -26 -168 81 8 -1045 -1045 -177 178 47 -1045 140 -1045 -185 -10 123 -92 15 -1045 -18 89 -185 -1045 193 -1045 15 -1045 81 8 -26 -1045 -1045 154 -85 -1045 104 41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 14 E= 2.8e-002 0.000000 0.071429 0.000000 0.928571 0.000000 0.000000 0.928571 0.071429 0.000000 0.000000 0.642857 0.357143 0.000000 0.214286 0.285714 0.500000 0.714286 0.000000 0.071429 0.214286 0.000000 0.142857 0.000000 0.857143 0.142857 0.357143 0.214286 0.285714 0.214286 0.000000 0.500000 0.285714 0.142857 0.285714 0.500000 0.071429 0.071429 0.000000 0.000000 0.928571 0.000000 0.000000 0.857143 0.142857 0.214286 0.071429 0.428571 0.285714 0.000000 0.000000 0.071429 0.928571 0.357143 0.000000 0.642857 0.000000 0.071429 0.214286 0.571429 0.142857 0.285714 0.000000 0.214286 0.500000 0.071429 0.000000 0.928571 0.000000 0.285714 0.000000 0.428571 0.285714 0.214286 0.000000 0.000000 0.785714 0.142857 0.000000 0.500000 0.357143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TG[GT][TGC][AT]T[CTG][GTA][GC]TG[GTA]T[GA][GC][TAG]G[GAT][TA][GT] -------------------------------------------------------------------------------- Time 3.73 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 8 llr = 112 E-value = 1.8e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::153141:91:1:68 pos.-specific C ::9::5:3a:99:a:3 probability G a9:48141:::1::4: matrix T :1:1:335:1::9::: bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 *** **** * Relative 1.3 *** * ****** * Entropy 1.1 *** * ******** (20.1 bits) 0.8 *** * ******** 0.6 ***** ******** 0.4 ***** * ******** 0.2 **************** 0.0 ---------------- Multilevel GGCAGCATCACCTCAA consensus GATGC GC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 25552 389 7.10e-09 GTTCCCGCTT GGCAGTTTCACCTCAA CTCTCAAGCT 38180 174 3.03e-08 CACAACATTG GTCGGCATCACCTCAA CGCGCGCCAT 36909 389 3.31e-08 CATTACGACC GGCAGCGTCACCACGA GCAGCGTCAA 261307 350 9.29e-08 TCAAAGAATT GGCAAGACCACCTCAA AGTGCTAGAA 4725 368 1.51e-07 GGAGGGGAAA GGCGGTGTCACGTCGA CAGGAACGTC 37458 1 5.61e-07 . GGATGCTCCACCTCGA GAGATTTCAA 7513 227 1.04e-06 AAGAGGAGAT GGCGACGACAACTCAC TGGCATGACT 11327 180 1.04e-06 GTACACTCGG GGCAGAAGCTCCTCAC CATCTCCCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25552 7.1e-09 388_[+2]_96 38180 3e-08 173_[+2]_311 36909 3.3e-08 388_[+2]_96 261307 9.3e-08 349_[+2]_135 4725 1.5e-07 367_[+2]_117 37458 5.6e-07 [+2]_484 7513 1e-06 226_[+2]_258 11327 1e-06 179_[+2]_305 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=8 25552 ( 389) GGCAGTTTCACCTCAA 1 38180 ( 174) GTCGGCATCACCTCAA 1 36909 ( 389) GGCAGCGTCACCACGA 1 261307 ( 350) GGCAAGACCACCTCAA 1 4725 ( 368) GGCGGTGTCACGTCGA 1 37458 ( 1) GGATGCTCCACCTCGA 1 7513 ( 227) GGCGACGACAACTCAC 1 11327 ( 180) GGCAGAAGCTCCTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8730 bayes= 10.0904 E= 1.8e+000 -965 -965 204 -965 -965 -965 184 -111 -104 193 -965 -965 96 -965 62 -111 -4 -965 162 -965 -104 112 -96 -11 54 -965 62 -11 -104 12 -96 89 -965 212 -965 -965 177 -965 -965 -111 -104 193 -965 -965 -965 193 -96 -965 -104 -965 -965 170 -965 212 -965 -965 128 -965 62 -965 154 12 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 1.8e+000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.875000 0.125000 0.125000 0.875000 0.000000 0.000000 0.500000 0.000000 0.375000 0.125000 0.250000 0.000000 0.750000 0.000000 0.125000 0.500000 0.125000 0.250000 0.375000 0.000000 0.375000 0.250000 0.125000 0.250000 0.125000 0.500000 0.000000 1.000000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.125000 0.875000 0.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.125000 0.000000 0.000000 0.875000 0.000000 1.000000 0.000000 0.000000 0.625000 0.000000 0.375000 0.000000 0.750000 0.250000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GGC[AG][GA][CT][AGT][TC]CACCTC[AG][AC] -------------------------------------------------------------------------------- Time 7.42 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 17 llr = 154 E-value = 1.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :18::582::11 pos.-specific C 1:1113:2::1: probability G 19:192:1:816 matrix T 8:19::25a273 bits 2.1 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * ** * ** Entropy 1.1 ** ** * ** (13.1 bits) 0.8 ***** * ** 0.6 ******* **** 0.4 ******* **** 0.2 ************ 0.0 ------------ Multilevel TGATGAATTGTG consensus C A T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 37458 188 4.15e-07 CGTTGCCCGT TGATGAACTGTG AGTTGCAAAA 25552 286 1.24e-06 GTTGTATCAA TGATGAATTGTA TCGTCGGTGC 261307 180 1.48e-06 ATGAGGAAAG TGCTGAATTGTG CACCATCATC 11721 172 1.74e-06 AGAGTGGTTT GGATGAATTGTG TTGACGAACG 264303 219 9.47e-06 AAACCTCTCG TGATGGAGTGTG GACGGATTCT 7513 306 1.43e-05 TGAACGGATG CGATGGATTGTG ACTCTGTGAC 10535 100 1.90e-05 TGTACATAAT TGATCCATTTTG TCATAATAGT 263487 230 2.07e-05 CATTCTTGGC TGATGCTTTGAG AGCTACGATG 10928 251 2.44e-05 AGAATGTGGC TAATGCAATGTG TATGAATTTT 4725 26 2.91e-05 TCGGCTGGGT TGACGAATTGCG ATCCATCGCC 11327 10 4.16e-05 TGCGTTTGA TGATGATCTTTT TTTGTCGAGC 36909 206 5.62e-05 TAACTTTGCG TGATCAACTTTT ACCGTGAGCA 262570 456 6.57e-05 TAGTCTAAGG TGATGCAATTAT CGTGTCGCTA 4263 297 7.64e-05 TATGTTGGTG GGCTGAATTGCG TATCAATGCG 10598 33 8.21e-05 CGACAACGCT TGTTGGAATGTA CGGATCATGA 7768 439 1.08e-04 ACAGTAGAAC TGAGGATATGTT GACCCTGAGA 38180 329 1.08e-04 GCTTGGCCTG TGTTGCATTGGT GTCACTCAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37458 4.1e-07 187_[+3]_301 25552 1.2e-06 285_[+3]_203 261307 1.5e-06 179_[+3]_309 11721 1.7e-06 171_[+3]_317 264303 9.5e-06 218_[+3]_270 7513 1.4e-05 305_[+3]_183 10535 1.9e-05 99_[+3]_389 263487 2.1e-05 229_[+3]_259 10928 2.4e-05 250_[+3]_238 4725 2.9e-05 25_[+3]_463 11327 4.2e-05 9_[+3]_479 36909 5.6e-05 205_[+3]_283 262570 6.6e-05 455_[+3]_33 4263 7.6e-05 296_[+3]_192 10598 8.2e-05 32_[+3]_456 7768 0.00011 438_[+3]_50 38180 0.00011 328_[+3]_160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=17 37458 ( 188) TGATGAACTGTG 1 25552 ( 286) TGATGAATTGTA 1 261307 ( 180) TGCTGAATTGTG 1 11721 ( 172) GGATGAATTGTG 1 264303 ( 219) TGATGGAGTGTG 1 7513 ( 306) CGATGGATTGTG 1 10535 ( 100) TGATCCATTTTG 1 263487 ( 230) TGATGCTTTGAG 1 10928 ( 251) TAATGCAATGTG 1 4725 ( 26) TGACGAATTGCG 1 11327 ( 10) TGATGATCTTTT 1 36909 ( 206) TGATCAACTTTT 1 262570 ( 456) TGATGCAATTAT 1 4263 ( 297) GGCTGAATTGCG 1 10598 ( 33) TGTTGGAATGTA 1 7768 ( 439) TGAGGATATGTT 1 38180 ( 329) TGTTGCATTGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8802 bayes= 9.80923 E= 1.5e+002 -1073 -196 -105 161 -213 -1073 195 -1073 157 -96 -1073 -120 -1073 -196 -205 171 -1073 -96 186 -1073 104 36 -46 -1073 168 -1073 -1073 -61 -13 -38 -205 97 -1073 -1073 -1073 189 -1073 -1073 165 -20 -113 -96 -205 139 -113 -1073 127 13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 1.5e+002 0.000000 0.058824 0.117647 0.823529 0.058824 0.000000 0.941176 0.000000 0.764706 0.117647 0.000000 0.117647 0.000000 0.058824 0.058824 0.882353 0.000000 0.117647 0.882353 0.000000 0.529412 0.294118 0.176471 0.000000 0.823529 0.000000 0.000000 0.176471 0.235294 0.176471 0.058824 0.529412 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.764706 0.235294 0.117647 0.117647 0.058824 0.705882 0.117647 0.000000 0.588235 0.294118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TGATG[AC]A[TA]T[GT]T[GT] -------------------------------------------------------------------------------- Time 11.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10535 4.46e-04 99_[+3(1.90e-05)]_14_[+1(5.06e-06)]_\ 355 10598 2.22e-01 32_[+3(8.21e-05)]_456 10928 3.39e-04 250_[+3(2.44e-05)]_11_\ [+1(1.73e-06)]_207 11327 2.54e-06 9_[+3(4.16e-05)]_47_[+1(2.84e-06)]_\ 91_[+2(1.04e-06)]_305 11721 4.03e-06 141_[+1(1.77e-07)]_10_\ [+3(1.74e-06)]_317 11865 9.76e-01 500 25552 1.20e-10 259_[+1(2.65e-07)]_6_[+3(1.24e-06)]_\ 91_[+2(7.10e-09)]_96 261307 1.41e-09 179_[+3(1.48e-06)]_102_\ [+1(2.40e-07)]_36_[+2(9.29e-08)]_135 262570 5.93e-04 11_[+1(1.18e-06)]_424_\ [+3(6.57e-05)]_33 263487 3.24e-05 75_[+1(7.89e-07)]_134_\ [+3(2.07e-05)]_259 264303 1.82e-06 218_[+3(9.47e-06)]_120_\ [+1(2.66e-08)]_130 36909 9.13e-10 26_[+1(1.13e-08)]_159_\ [+3(5.62e-05)]_171_[+2(3.31e-08)]_96 37458 2.04e-06 [+2(5.61e-07)]_171_[+3(4.15e-07)]_\ 301 38180 1.35e-05 173_[+2(3.03e-08)]_311 4263 3.83e-04 53_[+1(1.09e-06)]_223_\ [+3(7.64e-05)]_192 4725 1.33e-10 25_[+3(2.91e-05)]_286_\ [+1(5.99e-10)]_24_[+2(1.51e-07)]_117 7513 7.62e-07 226_[+2(1.04e-06)]_[+1(2.15e-06)]_\ 43_[+3(1.43e-05)]_183 7768 5.11e-03 317_[+1(6.42e-06)]_163 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************