******************************************************************************** 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/452/452.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10046 1.0000 500 10585 1.0000 500 11539 1.0000 500 12209 1.0000 500 261825 1.0000 500 2632 1.0000 500 263338 1.0000 500 263840 1.0000 500 33377 1.0000 500 4405 1.0000 500 6722 1.0000 500 8231 1.0000 500 9230 1.0000 500 9280 1.0000 500 9310 1.0000 500 943 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/452/452.seqs.fa -oc motifs/452 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.269 C 0.239 G 0.226 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.239 G 0.226 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 10 llr = 145 E-value = 8.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 169:a7291895385:91:61 pos.-specific C 631a::6:71:16:45:1515 probability G 3::::::1:1:4:2:3:11:4 matrix T :1:::32:2:1:1:121743: bits 2.1 * 1.9 ** 1.7 ** 1.5 *** * * * Relative 1.3 *** * * * * Entropy 1.1 **** * ** * * (21.0 bits) 0.9 * **** **** * * 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CAACAACACAAACAACATCAC consensus GC TA T GAGCG TTG sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6722 145 6.42e-10 CAGTCCTTCA CAACAACACAAACAAGAGTAC CACTCACACA 33377 13 3.17e-09 TAGTTTGCTC GAACATCACAAGAAATATCAG AATAGCATCA 10046 295 3.74e-08 CGTTGCATGA CAACAACATGTGCAACATCAC GAAGTCGATT 9280 429 5.89e-08 CACCGTAATG GAACAACAAAAACAATAACAG ATTCCAGTAC 8231 237 9.89e-08 CTGTCGTATT GCACAACACAAACGTGACCAC CCATCATGCT 263840 43 1.16e-07 CCCGTCGGTT CCACAATGTAAACACCATTTG ACGGGGCAAG 9230 119 2.34e-07 CTGCACTCAA CCACATAACAAGAGCCATCTA AGCATTATTG 9310 480 2.71e-07 CAACATCAAT CAACAATACCAAAACCATGCC 2632 236 3.13e-07 ACGACTTTCG ATACATAACAAGCACGATTTG TCAGACAAGA 943 470 4.13e-07 ACAACTGAAC CACCAACACAACTAACTTTAC TTCTACAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6722 6.4e-10 144_[+1]_335 33377 3.2e-09 12_[+1]_467 10046 3.7e-08 294_[+1]_185 9280 5.9e-08 428_[+1]_51 8231 9.9e-08 236_[+1]_243 263840 1.2e-07 42_[+1]_437 9230 2.3e-07 118_[+1]_361 9310 2.7e-07 479_[+1] 2632 3.1e-07 235_[+1]_244 943 4.1e-07 469_[+1]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=10 6722 ( 145) CAACAACACAAACAAGAGTAC 1 33377 ( 13) GAACATCACAAGAAATATCAG 1 10046 ( 295) CAACAACATGTGCAACATCAC 1 9280 ( 429) GAACAACAAAAACAATAACAG 1 8231 ( 237) GCACAACACAAACGTGACCAC 1 263840 ( 43) CCACAATGTAAACACCATTTG 1 9230 ( 119) CCACATAACAAGAGCCATCTA 1 9310 ( 480) CAACAATACCAAAACCATGCC 1 2632 ( 236) ATACATAACAAGCACGATTTG 1 943 ( 470) CACCAACACAACTAACTTTAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 9.83492 E= 8.4e+001 -143 133 41 -997 116 33 -997 -141 174 -126 -997 -997 -997 206 -997 -997 189 -997 -997 -997 138 -997 -997 17 -43 133 -997 -41 174 -997 -117 -997 -143 155 -997 -41 157 -126 -117 -997 174 -997 -997 -141 89 -126 83 -997 16 133 -997 -141 157 -997 -17 -997 89 74 -997 -141 -997 106 41 -41 174 -997 -997 -141 -143 -126 -117 139 -997 106 -117 59 116 -126 -997 17 -143 106 83 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 10 E= 8.4e+001 0.100000 0.600000 0.300000 0.000000 0.600000 0.300000 0.000000 0.100000 0.900000 0.100000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.700000 0.000000 0.000000 0.300000 0.200000 0.600000 0.000000 0.200000 0.900000 0.000000 0.100000 0.000000 0.100000 0.700000 0.000000 0.200000 0.800000 0.100000 0.100000 0.000000 0.900000 0.000000 0.000000 0.100000 0.500000 0.100000 0.400000 0.000000 0.300000 0.600000 0.000000 0.100000 0.800000 0.000000 0.200000 0.000000 0.500000 0.400000 0.000000 0.100000 0.000000 0.500000 0.300000 0.200000 0.900000 0.000000 0.000000 0.100000 0.100000 0.100000 0.100000 0.700000 0.000000 0.500000 0.100000 0.400000 0.600000 0.100000 0.000000 0.300000 0.100000 0.500000 0.400000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][AC]ACA[AT][CAT]A[CT]AA[AG][CA][AG][AC][CGT]AT[CT][AT][CG] -------------------------------------------------------------------------------- Time 1.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 6 llr = 77 E-value = 2.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::3:2:::a: pos.-specific C :::::2:::2:: probability G 22aa788558:a matrix T 88:::::55::: bits 2.1 ** * 1.9 ** ** 1.7 ** ** 1.5 ** ** *** Relative 1.3 **** ** *** Entropy 1.1 ************ (18.6 bits) 0.9 ************ 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTGGGGGGGGAG consensus A TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 943 358 2.93e-08 GTCATCTGAC TTGGGGGGGGAG TTCGCCCTTT 33377 150 3.04e-07 TTTAAACGAT TTGGAGGTTGAG TAAATTCACA 10046 10 3.54e-07 TAGGGGGGT GTGGGGGGGGAG GCGAGCTTCT 12209 87 9.50e-07 CACTCAGCGT TTGGGCGTTGAG GCCGTGTACT 10585 95 9.50e-07 GTTGTTGTTC TTGGGGAGTGAG TGTTTGCCAA 8231 416 3.86e-06 TCTTACAATG TGGGAGGTGCAG TCAATGCTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 943 2.9e-08 357_[+2]_131 33377 3e-07 149_[+2]_339 10046 3.5e-07 9_[+2]_479 12209 9.5e-07 86_[+2]_402 10585 9.5e-07 94_[+2]_394 8231 3.9e-06 415_[+2]_73 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=6 943 ( 358) TTGGGGGGGGAG 1 33377 ( 150) TTGGAGGTTGAG 1 10046 ( 10) GTGGGGGGGGAG 1 12209 ( 87) TTGGGCGTTGAG 1 10585 ( 95) TTGGGGAGTGAG 1 8231 ( 416) TGGGAGGTGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 11.4477 E= 2.0e+002 -923 -923 -44 165 -923 -923 -44 165 -923 -923 215 -923 -923 -923 215 -923 31 -923 156 -923 -923 -52 188 -923 -69 -923 188 -923 -923 -923 115 91 -923 -923 115 91 -923 -52 188 -923 189 -923 -923 -923 -923 -923 215 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 6 E= 2.0e+002 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.166667 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TTGG[GA]GG[GT][GT]GAG -------------------------------------------------------------------------------- Time 3.79 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 10 llr = 108 E-value = 2.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :993:::::1:: pos.-specific C a::11:7216:: probability G :11:2a1:9315 matrix T :::67:28::95 bits 2.1 * * 1.9 * * 1.7 * * * 1.5 *** * * * Relative 1.3 *** * ** * Entropy 1.1 *** * ** ** (15.6 bits) 0.9 *** ******** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CAATTGCTGCTG consensus AG TC G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 943 96 5.71e-08 TTTCTTCGTT CAATTGCTGCTG CAATTCAGAT 10585 114 1.24e-07 GAGTGTTTGC CAATTGCTGCTT CCAAGGTAGG 2632 67 5.79e-07 CAATCAGATA CAATGGCTGCTT TGAACCAAGT 8231 94 3.57e-06 TCTACATTTG CAAATGTTGGTG CACCCTCAAT 263840 229 3.57e-06 GACATTATAT CAATTGGTGGTT CTTTGCTGGA 10046 214 3.90e-06 TCGTGTGCTG CAGATGCTGCTG GCTCGTCTGT 33377 245 1.36e-05 ACATGACTTT CAAATGCCGATT CCCACTGGGC 6722 418 1.93e-05 CACCACCTCA CAACTGCTCGTG GACGTGAGAG 11539 305 1.93e-05 AGGAATAGTA CAATGGCCGCGT ATGTACGTAG 9230 6 3.01e-05 CACTG CGATCGTTGCTG TAATGTTGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 943 5.7e-08 95_[+3]_393 10585 1.2e-07 113_[+3]_375 2632 5.8e-07 66_[+3]_422 8231 3.6e-06 93_[+3]_395 263840 3.6e-06 228_[+3]_260 10046 3.9e-06 213_[+3]_275 33377 1.4e-05 244_[+3]_244 6722 1.9e-05 417_[+3]_71 11539 1.9e-05 304_[+3]_184 9230 3e-05 5_[+3]_483 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=10 943 ( 96) CAATTGCTGCTG 1 10585 ( 114) CAATTGCTGCTT 1 2632 ( 67) CAATGGCTGCTT 1 8231 ( 94) CAAATGTTGGTG 1 263840 ( 229) CAATTGGTGGTT 1 10046 ( 214) CAGATGCTGCTG 1 33377 ( 245) CAAATGCCGATT 1 6722 ( 418) CAACTGCTCGTG 1 11539 ( 305) CAATGGCCGCGT 1 9230 ( 6) CGATCGTTGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 9.86175 E= 2.2e+002 -997 206 -997 -997 174 -997 -117 -997 174 -997 -117 -997 16 -126 -997 117 -997 -126 -17 139 -997 -997 215 -997 -997 155 -117 -41 -997 -26 -997 159 -997 -126 199 -997 -143 133 41 -997 -997 -997 -117 176 -997 -997 115 91 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 2.2e+002 0.000000 1.000000 0.000000 0.000000 0.900000 0.000000 0.100000 0.000000 0.900000 0.000000 0.100000 0.000000 0.300000 0.100000 0.000000 0.600000 0.000000 0.100000 0.200000 0.700000 0.000000 0.000000 1.000000 0.000000 0.000000 0.700000 0.100000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 0.100000 0.900000 0.000000 0.100000 0.600000 0.300000 0.000000 0.000000 0.000000 0.100000 0.900000 0.000000 0.000000 0.500000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CAA[TA][TG]G[CT][TC]G[CG]T[GT] -------------------------------------------------------------------------------- Time 5.69 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10046 2.14e-09 9_[+2(3.54e-07)]_192_[+3(3.90e-06)]_\ 69_[+1(3.74e-08)]_185 10585 4.54e-06 94_[+2(9.50e-07)]_7_[+3(1.24e-07)]_\ 375 11539 1.88e-02 304_[+3(1.93e-05)]_184 12209 1.89e-03 86_[+2(9.50e-07)]_402 261825 6.19e-02 500 2632 6.77e-06 66_[+3(5.79e-07)]_157_\ [+1(3.13e-07)]_244 263338 8.57e-01 500 263840 1.20e-05 42_[+1(1.16e-07)]_165_\ [+3(3.57e-06)]_260 33377 5.98e-10 12_[+1(3.17e-09)]_116_\ [+2(3.04e-07)]_83_[+3(1.36e-05)]_244 4405 7.85e-01 500 6722 9.23e-08 144_[+1(6.42e-10)]_252_\ [+3(1.93e-05)]_71 8231 4.35e-08 93_[+3(3.57e-06)]_131_\ [+1(9.89e-08)]_158_[+2(3.86e-06)]_73 9230 2.26e-05 5_[+3(3.01e-05)]_101_[+1(2.34e-07)]_\ 361 9280 1.40e-04 428_[+1(5.89e-08)]_51 9310 4.11e-03 479_[+1(2.71e-07)] 943 3.85e-11 95_[+3(5.71e-08)]_250_\ [+2(2.93e-08)]_100_[+1(4.13e-07)]_10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************