******************************************************************************** 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/263/263.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10616 1.0000 500 17439 1.0000 500 20248 1.0000 500 22643 1.0000 500 23689 1.0000 500 262607 1.0000 500 263191 1.0000 500 263720 1.0000 500 263984 1.0000 500 263996 1.0000 500 264240 1.0000 500 264868 1.0000 500 33194 1.0000 500 34055 1.0000 500 6459 1.0000 500 8035 1.0000 500 9804 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/263/263.seqs.fa -oc motifs/263 -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= 17 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= 8500 N= 17 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.244 G 0.234 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.244 G 0.234 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 8 llr = 116 E-value = 1.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::1:531:9:11::3: pos.-specific C ::3::3:11::1:::: probability G 966a::99:95:a96a matrix T 14::55:::148:11: bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 * * **** ** * Relative 1.3 * * **** ** * Entropy 1.0 ** * **** ** * (20.8 bits) 0.8 ***** **** ***** 0.6 ***** ********** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel GGGGATGGAGGTGGGG consensus TC TA T A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 264868 245 7.09e-09 AAGTAGTAGT GGAGTTGGAGGTGGGG GAGGAAGGAG 9804 100 1.90e-08 TCGTTTGGAT GGGGATAGAGTTGGGG CAGAAGTAGA 262607 95 2.59e-08 ATTGGTTGCT GGGGTAGCAGGTGGGG AGGAGCAAAC 8035 236 3.96e-08 CACCACAGAG TTGGTTGGAGTTGGGG TTGTTCTTTA 10616 152 1.15e-07 GACGACGACG GTGGACGGAGGCGGAG CGACGGGGAG 23689 228 1.60e-07 TGGTAGAGTT GTGGACGGAGGTGTAG TGGAGTGGTG 263720 54 3.44e-07 TGTTGGCTGC GGCGTTGGATTTGGTG CTCTGCGTCG 264240 60 1.17e-06 ATCAACAGGA GGCGAAGGCGAAGGGG CCGCAGACGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 264868 7.1e-09 244_[+1]_240 9804 1.9e-08 99_[+1]_385 262607 2.6e-08 94_[+1]_390 8035 4e-08 235_[+1]_249 10616 1.1e-07 151_[+1]_333 23689 1.6e-07 227_[+1]_257 263720 3.4e-07 53_[+1]_431 264240 1.2e-06 59_[+1]_425 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=8 264868 ( 245) GGAGTTGGAGGTGGGG 1 9804 ( 100) GGGGATAGAGTTGGGG 1 262607 ( 95) GGGGTAGCAGGTGGGG 1 8035 ( 236) TTGGTTGGAGTTGGGG 1 10616 ( 152) GTGGACGGAGGCGGAG 1 23689 ( 228) GTGGACGGAGGTGTAG 1 263720 ( 54) GGCGTTGGATTTGGTG 1 264240 ( 60) GGCGAAGGCGAAGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 11.3307 E= 1.5e-001 -965 -965 190 -106 -965 -965 142 52 -106 3 142 -965 -965 -965 209 -965 94 -965 -965 94 -6 3 -965 94 -106 -965 190 -965 -965 -97 190 -965 175 -97 -965 -965 -965 -965 190 -106 -106 -965 109 52 -106 -97 -965 152 -965 -965 209 -965 -965 -965 190 -106 -6 -965 142 -106 -965 -965 209 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 1.5e-001 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.625000 0.375000 0.125000 0.250000 0.625000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.500000 0.125000 0.000000 0.875000 0.000000 0.000000 0.125000 0.875000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 0.000000 0.875000 0.125000 0.125000 0.000000 0.500000 0.375000 0.125000 0.125000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.875000 0.125000 0.250000 0.000000 0.625000 0.125000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[GT][GC]G[AT][TAC]GGAG[GT]TGG[GA]G -------------------------------------------------------------------------------- Time 2.60 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 17 llr = 176 E-value = 2.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 649149:622956358 pos.-specific C 4518619338:11342 probability G ::::::::5::41311 matrix T :111:111::1:211: bits 2.1 1.9 1.7 * * 1.5 * * Relative 1.3 ** ** ** Entropy 1.0 * ***** ** * (14.9 bits) 0.8 ******* ** * 0.6 ************ * 0.4 ************* ** 0.2 ************* ** 0.0 ---------------- Multilevel ACACCACAGCAAAAAA consensus CA A CCA GTCC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 263996 326 8.58e-09 CCTTGAGAGT ACACCACCGCAAAGAA AAGAGCCACC 9804 23 2.33e-07 GAACGAGATC CAACAACAGCAGTGAA CTCATCCGTG 23689 430 3.90e-07 CCGAGCTGCA CCACAACAGCACAGCA ACTACACACC 17439 251 7.93e-07 TTCTCCGCTC ACACAACAACAAACAC AACGCCAACC 8035 478 1.24e-06 CTCTGGTACC ACACCACACAAACCAA CAACAAA 10616 296 1.53e-06 CAAACCACAC CCACCCCAGCAGACCA CAGCGCAAAC 264868 8 2.81e-06 CCACCAA CAACAACACCAGGCAA GCTACAGTAC 263984 118 5.36e-06 CAACCAACAA CAACCACCACAATAAC GAGGGATGCG 22643 475 8.24e-06 ATATCAACAT ACATCACACAAAATCA ATACCCAACC 264240 352 9.71e-06 TTTCACCGGT AAATCACCGCACATAA CTTACTCTTC 33194 126 1.14e-05 AGCAAGAAGT ACACCACCGCTAAAGA GACCTTCCAC 263191 307 1.33e-05 CTACCACCAT ACCCAACACCAACACA CTTGTTTCAT 262607 422 1.68e-05 GCAGTAGCGA AAACAACAACAGTCCG AACAGGGTAG 6459 344 2.25e-05 TCAACATTTA AATCCACACAAAAAAC GTACCTTGAC 263720 442 2.25e-05 CCTTTCTCTT CCAAAACTGAAAAAAA TCTAACGAAC 20248 275 4.44e-05 TCTATTAGTA ATACCTCTGCAGAGCA AGTCCTCACA 34055 207 5.04e-05 GGGACTTCGC CAACCATCGCAGTGTA CTTTTTGTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263996 8.6e-09 325_[+2]_159 9804 2.3e-07 22_[+2]_462 23689 3.9e-07 429_[+2]_55 17439 7.9e-07 250_[+2]_234 8035 1.2e-06 477_[+2]_7 10616 1.5e-06 295_[+2]_189 264868 2.8e-06 7_[+2]_477 263984 5.4e-06 117_[+2]_367 22643 8.2e-06 474_[+2]_10 264240 9.7e-06 351_[+2]_133 33194 1.1e-05 125_[+2]_359 263191 1.3e-05 306_[+2]_178 262607 1.7e-05 421_[+2]_63 6459 2.2e-05 343_[+2]_141 263720 2.2e-05 441_[+2]_43 20248 4.4e-05 274_[+2]_210 34055 5e-05 206_[+2]_278 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=17 263996 ( 326) ACACCACCGCAAAGAA 1 9804 ( 23) CAACAACAGCAGTGAA 1 23689 ( 430) CCACAACAGCACAGCA 1 17439 ( 251) ACACAACAACAAACAC 1 8035 ( 478) ACACCACACAAACCAA 1 10616 ( 296) CCACCCCAGCAGACCA 1 264868 ( 8) CAACAACACCAGGCAA 1 263984 ( 118) CAACCACCACAATAAC 1 22643 ( 475) ACATCACACAAAATCA 1 264240 ( 352) AAATCACCGCACATAA 1 33194 ( 126) ACACCACCGCTAAAGA 1 263191 ( 307) ACCCAACACCAACACA 1 262607 ( 422) AAACAACAACAGTCCG 1 6459 ( 344) AATCCACACAAAAAAC 1 263720 ( 442) CCAAAACTGAAAAAAA 1 20248 ( 275) ATACCTCTGCAGAGCA 1 34055 ( 207) CAACCATCGCAGTGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 8.91886 E= 2.5e-001 117 75 -1073 -1073 66 111 -1073 -215 176 -205 -1073 -215 -214 175 -1073 -115 66 127 -1073 -1073 176 -205 -1073 -215 -1073 194 -1073 -215 117 27 -1073 -115 -56 27 118 -1073 -15 164 -1073 -1073 185 -1073 -1073 -215 102 -105 59 -1073 117 -105 -199 -15 18 27 33 -115 102 53 -199 -215 155 -47 -199 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 17 E= 2.5e-001 0.588235 0.411765 0.000000 0.000000 0.411765 0.529412 0.000000 0.058824 0.882353 0.058824 0.000000 0.058824 0.058824 0.823529 0.000000 0.117647 0.411765 0.588235 0.000000 0.000000 0.882353 0.058824 0.000000 0.058824 0.000000 0.941176 0.000000 0.058824 0.588235 0.294118 0.000000 0.117647 0.176471 0.294118 0.529412 0.000000 0.235294 0.764706 0.000000 0.000000 0.941176 0.000000 0.000000 0.058824 0.529412 0.117647 0.352941 0.000000 0.588235 0.117647 0.058824 0.235294 0.294118 0.294118 0.294118 0.117647 0.529412 0.352941 0.058824 0.058824 0.764706 0.176471 0.058824 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC][CA]AC[CA]AC[AC][GC][CA]A[AG][AT][ACG][AC]A -------------------------------------------------------------------------------- Time 5.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 136 E-value = 1.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :44:633:82223:a4:32:7 pos.-specific C :::::1::2::44::4:1:1: probability G a36a3439:782:a:194291 matrix T :2::1131:1:12:::116:2 bits 2.1 * * * 1.9 * * ** 1.7 * * * ** * * 1.5 * * * ** * * Relative 1.3 * * ** * ** * * Entropy 1.0 * ** ** * ** * * (21.9 bits) 0.8 * ** **** ** * * 0.6 * *** **** **** *** 0.4 ***** ***** ***** *** 0.2 ********************* 0.0 --------------------- Multilevel GAGGAGAGAGGCCGAAGGTGA consensus GA GAG CAAAA C AA T sequence T T GT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 23689 264 3.09e-11 GCCGGGCGAA GGAGAGAGAGGCCGACGATGA GCTGACGGAC 263720 218 1.20e-08 TTGTAGAGGA GAGGGCGGAGGCCGACGTGGA CTGGCAACAG 262607 12 1.84e-08 GCCGGTGATG GTGGAAAGAAGAAGAAGGGGA CTGTGGGGAA 263984 421 2.03e-08 TTGAAATGTT GGAGAGTGATGATGAAGATGA AGTGATTCAG 9804 176 2.73e-08 ACCATGATGC GAGGAGGTCGACCGACGGTGA CTCTTTTTTT 22643 109 8.49e-08 CGTCGTCCGT GTAGAAAGAGGGCGAAGCTCA GCTCATCGAT 263996 55 1.34e-07 GGAAGCGAGT GAAGGATGAAAGTGAAGGTGT CATTGACAGT 10616 20 2.45e-07 TGGTGCAGAA GAGGTGTGAGGCAGACTGAGG CTGCTGGCAC 264868 218 8.29e-07 GTCTTCTCGT GGGGGTGGCGGTAGAGGAAGT AGTAGTGGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23689 3.1e-11 263_[+3]_216 263720 1.2e-08 217_[+3]_262 262607 1.8e-08 11_[+3]_468 263984 2e-08 420_[+3]_59 9804 2.7e-08 175_[+3]_304 22643 8.5e-08 108_[+3]_371 263996 1.3e-07 54_[+3]_425 10616 2.5e-07 19_[+3]_460 264868 8.3e-07 217_[+3]_262 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 23689 ( 264) GGAGAGAGAGGCCGACGATGA 1 263720 ( 218) GAGGGCGGAGGCCGACGTGGA 1 262607 ( 12) GTGGAAAGAAGAAGAAGGGGA 1 263984 ( 421) GGAGAGTGATGATGAAGATGA 1 9804 ( 176) GAGGAGGTCGACCGACGGTGA 1 22643 ( 109) GTAGAAAGAGGGCGAAGCTCA 1 263996 ( 55) GAAGGATGAAAGTGAAGGTGT 1 10616 ( 20) GAGGTGTGAGGCAGACTGAGG 1 264868 ( 218) GGGGGTGGCGGTAGAGGAAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8160 bayes= 10.6715 E= 1.4e+000 -982 -982 209 -982 77 -982 51 -23 77 -982 125 -982 -982 -982 209 -982 109 -982 51 -123 36 -114 92 -123 36 -982 51 35 -982 -982 192 -123 158 -14 -982 -982 -23 -982 151 -123 -23 -982 173 -982 -23 86 -8 -123 36 86 -982 -23 -982 -982 209 -982 194 -982 -982 -982 77 86 -107 -982 -982 -982 192 -123 36 -114 92 -123 -23 -982 -8 109 -982 -114 192 -982 135 -982 -107 -23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 1.4e+000 0.000000 0.000000 1.000000 0.000000 0.444444 0.000000 0.333333 0.222222 0.444444 0.000000 0.555556 0.000000 0.000000 0.000000 1.000000 0.000000 0.555556 0.000000 0.333333 0.111111 0.333333 0.111111 0.444444 0.111111 0.333333 0.000000 0.333333 0.333333 0.000000 0.000000 0.888889 0.111111 0.777778 0.222222 0.000000 0.000000 0.222222 0.000000 0.666667 0.111111 0.222222 0.000000 0.777778 0.000000 0.222222 0.444444 0.222222 0.111111 0.333333 0.444444 0.000000 0.222222 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.444444 0.444444 0.111111 0.000000 0.000000 0.000000 0.888889 0.111111 0.333333 0.111111 0.444444 0.111111 0.222222 0.000000 0.222222 0.555556 0.000000 0.111111 0.888889 0.000000 0.666667 0.000000 0.111111 0.222222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AGT][GA]G[AG][GA][AGT]G[AC][GA][GA][CAG][CAT]GA[AC]G[GA][TAG]G[AT] -------------------------------------------------------------------------------- Time 7.67 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10616 1.78e-09 19_[+3(2.45e-07)]_111_\ [+1(1.15e-07)]_128_[+2(1.53e-06)]_189 17439 6.22e-03 250_[+2(7.93e-07)]_50_\ [+2(1.81e-05)]_168 20248 9.87e-02 274_[+2(4.44e-05)]_210 22643 6.79e-06 108_[+3(8.49e-08)]_345_\ [+2(8.24e-06)]_10 23689 1.50e-13 227_[+1(1.60e-07)]_20_\ [+3(3.09e-11)]_145_[+2(3.90e-07)]_55 262607 3.71e-10 11_[+3(1.84e-08)]_62_[+1(2.59e-08)]_\ 311_[+2(1.68e-05)]_63 263191 8.16e-02 306_[+2(1.33e-05)]_178 263720 3.61e-09 53_[+1(3.44e-07)]_148_\ [+3(1.20e-08)]_203_[+2(2.25e-05)]_43 263984 1.16e-06 117_[+2(5.36e-06)]_287_\ [+3(2.03e-08)]_59 263996 1.58e-08 54_[+3(1.34e-07)]_250_\ [+2(8.58e-09)]_159 264240 2.24e-04 59_[+1(1.17e-06)]_276_\ [+2(9.71e-06)]_133 264868 7.31e-10 7_[+2(2.81e-06)]_194_[+3(8.29e-07)]_\ 6_[+1(7.09e-09)]_240 33194 1.97e-02 125_[+2(1.14e-05)]_359 34055 1.41e-01 206_[+2(5.04e-05)]_278 6459 4.22e-02 343_[+2(2.25e-05)]_141 8035 6.15e-07 235_[+1(3.96e-08)]_226_\ [+2(1.24e-06)]_7 9804 7.40e-12 22_[+2(2.33e-07)]_61_[+1(1.90e-08)]_\ 60_[+3(2.73e-08)]_304 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************