******************************************************************************** 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/286/286.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 36501 1.0000 500 37232 1.0000 500 47258 1.0000 500 47529 1.0000 500 47945 1.0000 500 38406 1.0000 500 14805 1.0000 500 48519 1.0000 500 18096 1.0000 500 49297 1.0000 500 49567 1.0000 500 44251 1.0000 500 44521 1.0000 500 45524 1.0000 500 35734 1.0000 500 54505 1.0000 500 20504 1.0000 500 46296 1.0000 500 32645 1.0000 500 43633 1.0000 500 46610 1.0000 500 49184 1.0000 500 46118 1.0000 500 47521 1.0000 500 34247 1.0000 500 43391 1.0000 500 50597 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/286/286.seqs.fa -oc motifs/286 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.246 G 0.236 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.246 G 0.236 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 17 llr = 206 E-value = 1.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 7584538389299341:9728 pos.-specific C 32122222211::12391112 probability G ::1222:5:16:::2:1:251 matrix T :4:213::::211626:::2: bits 2.1 1.9 1.7 ** 1.5 ** ** Relative 1.3 * ** ** ** Entropy 1.0 * * ** ** ** * (17.5 bits) 0.8 * * * ** ** **** * 0.6 * * **** *** **** * 0.4 *** * ******** **** * 0.2 *** * ******** ****** 0.0 --------------------- Multilevel AAAAAAAGAAGAATATCAAGA consensus CT CCT A ATC G sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 50597 325 1.94e-10 GATTCTACGG AAAAATAGAAGAATATCAACA TGATTTCGCT 38406 265 5.33e-09 AAGGAACCTT ATCCAAAGAAGAATGTCAAGA GATCGGTGAC 37232 428 5.33e-09 AAGGAACCTT ATCCAAAGAAGAATGTCAAGA GATCGGTGAC 36501 450 8.93e-08 TTCCCCGCCA AAATAAAGAGTAAAATCAAGA CTGACTGTGA 46118 251 1.26e-07 TCAAATAAAT ACACATCGAAGAATATCAATC AATAAAAACA 47521 119 7.08e-07 TTCTTCTGTC CTAAATAAAATAATTTCCAAA AGTCCTTAGT 49297 89 1.11e-06 ATTTATAGGT CAATGAAGACGAACACCAAGA GTGTTCGTGT 49567 91 1.21e-06 TCCTTTCCTG CTACCAAGCAGAAACTCAGTA GTGCTCTCTA 43391 306 1.70e-06 CATTCTGTCA AAGAGGCAAAAAATATCAATA TTCTCTGAGC 46296 369 2.35e-06 TCGGTTCAAC AAAGATAGCAGTAAGCCAGGA TCGTCAGAGT 43633 200 2.75e-06 GGTCATCCAG ATAAACACAACATTATCAAAA CTAGTAGGTA 44251 188 2.97e-06 TTGCTGGTGG AAAAGTAAAAGAATCAGAAGC CTATGAGAAG 45524 453 3.45e-06 ATTATTTTGC AAATCGACAAAAAACCCAAGG ACGTCCCTAC 18096 179 6.16e-06 GGGGGAGAAC CAAAAGACAATAAATTGACGA GCCCTCACCG 44521 210 7.56e-06 ACAGCGAAGA CCAGCCAAAAAAACTCCAGGA AGACTTATAT 35734 418 8.64e-06 TAGATTTTTC ACAGTCAACAGAATACCAAAC AGCGACAAAG 47529 74 9.84e-06 GGTGTTCGGC ATGTCGCGAAGAATTTCCGCA TCGTCTACGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50597 1.9e-10 324_[+1]_155 38406 5.3e-09 264_[+1]_215 37232 5.3e-09 427_[+1]_52 36501 8.9e-08 449_[+1]_30 46118 1.3e-07 250_[+1]_229 47521 7.1e-07 118_[+1]_361 49297 1.1e-06 88_[+1]_391 49567 1.2e-06 90_[+1]_389 43391 1.7e-06 305_[+1]_174 46296 2.3e-06 368_[+1]_111 43633 2.7e-06 199_[+1]_280 44251 3e-06 187_[+1]_292 45524 3.5e-06 452_[+1]_27 18096 6.2e-06 178_[+1]_301 44521 7.6e-06 209_[+1]_270 35734 8.6e-06 417_[+1]_62 47529 9.8e-06 73_[+1]_406 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=17 50597 ( 325) AAAAATAGAAGAATATCAACA 1 38406 ( 265) ATCCAAAGAAGAATGTCAAGA 1 37232 ( 428) ATCCAAAGAAGAATGTCAAGA 1 36501 ( 450) AAATAAAGAGTAAAATCAAGA 1 46118 ( 251) ACACATCGAAGAATATCAATC 1 47521 ( 119) CTAAATAAAATAATTTCCAAA 1 49297 ( 89) CAATGAAGACGAACACCAAGA 1 49567 ( 91) CTACCAAGCAGAAACTCAGTA 1 43391 ( 306) AAGAGGCAAAAAATATCAATA 1 46296 ( 369) AAAGATAGCAGTAAGCCAGGA 1 43633 ( 200) ATAAACACAACATTATCAAAA 1 44251 ( 188) AAAAGTAAAAGAATCAGAAGC 1 45524 ( 453) AAATCGACAAAAAACCCAAGG 1 18096 ( 179) CAAAAGACAATAAATTGACGA 1 44521 ( 210) CCAGCCAAAAAAACTCCAGGA 1 35734 ( 418) ACAGTCAACAGAATACCAAAC 1 47529 ( 74) ATGTCGCGAAGAATTTCCGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 10.3679 E= 1.9e+000 141 26 -1073 -1073 83 -48 -1073 48 153 -106 -100 -1073 41 -6 -42 -10 99 -6 -42 -210 15 -48 0 22 163 -48 -1073 -1073 15 -48 117 -1073 163 -48 -1073 -1073 173 -206 -200 -1073 -59 -206 132 -52 182 -1073 -1073 -210 182 -1073 -1073 -210 15 -106 -1073 122 63 -48 -42 -10 -217 26 -1073 136 -1073 184 -100 -1073 173 -106 -1073 -1073 141 -206 0 -1073 -59 -106 117 -52 153 -48 -200 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 1.9e+000 0.705882 0.294118 0.000000 0.000000 0.470588 0.176471 0.000000 0.352941 0.764706 0.117647 0.117647 0.000000 0.352941 0.235294 0.176471 0.235294 0.529412 0.235294 0.176471 0.058824 0.294118 0.176471 0.235294 0.294118 0.823529 0.176471 0.000000 0.000000 0.294118 0.176471 0.529412 0.000000 0.823529 0.176471 0.000000 0.000000 0.882353 0.058824 0.058824 0.000000 0.176471 0.058824 0.588235 0.176471 0.941176 0.000000 0.000000 0.058824 0.941176 0.000000 0.000000 0.058824 0.294118 0.117647 0.000000 0.588235 0.411765 0.176471 0.176471 0.235294 0.058824 0.294118 0.000000 0.647059 0.000000 0.882353 0.117647 0.000000 0.882353 0.117647 0.000000 0.000000 0.705882 0.058824 0.235294 0.000000 0.176471 0.117647 0.529412 0.176471 0.764706 0.176471 0.058824 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC][AT]A[ACT][AC][ATG]A[GA]AAGAA[TA][AT][TC]CA[AG]GA -------------------------------------------------------------------------------- Time 6.17 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 103 E-value = 7.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :6a4:6:::::a82::::28a pos.-specific C ::::2:222:2:::a2:a8:: probability G a4:6842::a8::8:26::2: matrix T ::::::688:::2::64:::: bits 2.1 * * * * 1.9 * * * * * * * 1.7 * * * * * * * 1.5 * * * * * * * Relative 1.3 * * * ******** **** Entropy 1.0 ****** ******** ***** (29.7 bits) 0.8 ****** ******** ***** 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GAAGGATTTGGAAGCTGCCAA consensus G ACGCCC C TA CT AG sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 38406 316 1.17e-12 AAAGCTACAA GAAGGATTTGGAAGCTTCCAA GATGTATGTG 37232 479 1.17e-12 AAAGCTACGA GAAGGATTTGGAAGCTTCCAA G 20504 104 1.54e-10 CCGATGCTCC GGAAGATTTGCAAGCCGCCAA GTCCTTGAGA 49184 102 2.11e-09 GACAAGGAAA GGAACGGTTGGAAGCTGCAGA CACTGTCAGG 49567 392 4.48e-09 AAACCGTAAA GAAGGGCCCGGATACGGCCAA CGTTGATGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38406 1.2e-12 315_[+2]_164 37232 1.2e-12 478_[+2]_1 20504 1.5e-10 103_[+2]_376 49184 2.1e-09 101_[+2]_378 49567 4.5e-09 391_[+2]_88 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 38406 ( 316) GAAGGATTTGGAAGCTTCCAA 1 37232 ( 479) GAAGGATTTGGAAGCTTCCAA 1 20504 ( 104) GGAAGATTTGCAAGCCGCCAA 1 49184 ( 102) GGAACGGTTGGAAGCTGCAGA 1 49567 ( 392) GAAGGGCCCGGATACGGCCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 11.5909 E= 7.6e+001 -897 -897 208 -897 117 -897 76 -897 191 -897 -897 -897 59 -897 135 -897 -897 -30 176 -897 117 -897 76 -897 -897 -30 -24 125 -897 -30 -897 166 -897 -30 -897 166 -897 -897 208 -897 -897 -30 176 -897 191 -897 -897 -897 159 -897 -897 -34 -41 -897 176 -897 -897 202 -897 -897 -897 -30 -24 125 -897 -897 135 66 -897 202 -897 -897 -41 170 -897 -897 159 -897 -24 -897 191 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 7.6e+001 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.200000 0.800000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.200000 0.200000 0.600000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.200000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.600000 0.000000 0.000000 0.600000 0.400000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AG]A[GA][GC][AG][TCG][TC][TC]G[GC]A[AT][GA]C[TCG][GT]C[CA][AG]A -------------------------------------------------------------------------------- Time 12.16 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 6 llr = 114 E-value = 6.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:37:22:8a33::aa::7: pos.-specific C ::7:7::72:72:a::::2: probability G ::::3:3::::5a::::7:2 matrix T 8a:3:853::::::::a328 bits 2.1 * ** * 1.9 * * ***** 1.7 * * ***** 1.5 * * ***** Relative 1.3 ** * ** ***** * Entropy 1.0 ****** **** ****** * (27.4 bits) 0.8 ****** **** ****** * 0.6 ******************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TTCACTTCAACGGCAATGAT consensus ATG GT AA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 38406 33 2.13e-12 TGCCCCATCT TTCACTGCAACGGCAATGAT CCCCTAGCAG 37232 196 2.13e-12 TGCCCCATCT TTCACTGCAACGGCAATGAT CCCCTAGCAG 44521 327 3.30e-10 TTTCTGAGGG TTCACTTCAACAGCAATTCT TTTCGCCATT 47945 224 4.79e-09 AGTCATGGGT TTATGTTTAAAGGCAATGAG ATTTTTGGCA 46118 358 9.53e-09 AATCGGGTCA TTCTGTTTCAAAGCAATGTT TTCTGTTGGT 50597 164 1.56e-08 GACGGAGGAT ATAACAACAACCGCAATTAT TCTTTGAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38406 2.1e-12 32_[+3]_448 37232 2.1e-12 195_[+3]_285 44521 3.3e-10 326_[+3]_154 47945 4.8e-09 223_[+3]_257 46118 9.5e-09 357_[+3]_123 50597 1.6e-08 163_[+3]_317 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=6 38406 ( 33) TTCACTGCAACGGCAATGAT 1 37232 ( 196) TTCACTGCAACGGCAATGAT 1 44521 ( 327) TTCACTTCAACAGCAATTCT 1 47945 ( 224) TTATGTTTAAAGGCAATGAG 1 46118 ( 358) TTCTGTTTCAAAGCAATGTT 1 50597 ( 164) ATAACAACAACCGCAATTAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 12987 bayes= 11.5268 E= 6.2e+001 -67 -923 -923 172 -923 -923 -923 198 33 144 -923 -923 133 -923 -923 40 -923 144 50 -923 -67 -923 -923 172 -67 -923 50 98 -923 144 -923 40 165 -56 -923 -923 191 -923 -923 -923 33 144 -923 -923 33 -56 108 -923 -923 -923 208 -923 -923 202 -923 -923 191 -923 -923 -923 191 -923 -923 -923 -923 -923 -923 198 -923 -923 150 40 133 -56 -923 -60 -923 -923 -50 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 6.2e+001 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 0.000000 1.000000 0.333333 0.666667 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.166667 0.000000 0.000000 0.833333 0.166667 0.000000 0.333333 0.500000 0.000000 0.666667 0.000000 0.333333 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.166667 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.666667 0.166667 0.000000 0.166667 0.000000 0.000000 0.166667 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TT[CA][AT][CG]T[TG][CT]AA[CA][GA]GCAAT[GT]AT -------------------------------------------------------------------------------- Time 17.78 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36501 4.08e-04 449_[+1(8.93e-08)]_30 37232 2.29e-21 195_[+3(2.13e-12)]_212_\ [+1(5.33e-09)]_30_[+2(1.17e-12)]_1 47258 9.51e-01 500 47529 5.11e-02 73_[+1(9.84e-06)]_406 47945 1.20e-04 162_[+3(8.59e-05)]_41_\ [+3(4.79e-09)]_257 38406 2.29e-21 32_[+3(2.13e-12)]_212_\ [+1(5.33e-09)]_30_[+2(1.17e-12)]_164 14805 3.81e-01 500 48519 9.72e-01 500 18096 1.55e-02 178_[+1(6.16e-06)]_301 49297 6.16e-03 88_[+1(1.11e-06)]_391 49567 6.66e-08 90_[+1(1.21e-06)]_280_\ [+2(4.48e-09)]_88 44251 6.07e-03 187_[+1(2.97e-06)]_292 44521 1.30e-07 209_[+1(7.56e-06)]_96_\ [+3(3.30e-10)]_154 45524 1.44e-02 452_[+1(3.45e-06)]_27 35734 2.48e-02 417_[+1(8.64e-06)]_62 54505 3.47e-02 500 20504 5.94e-06 103_[+2(1.54e-10)]_376 46296 1.93e-02 368_[+1(2.35e-06)]_111 32645 6.50e-01 500 43633 1.36e-02 199_[+1(2.75e-06)]_280 46610 7.62e-01 500 49184 6.64e-05 101_[+2(2.11e-09)]_378 46118 4.60e-08 250_[+1(1.26e-07)]_86_\ [+3(9.53e-09)]_123 47521 4.64e-03 118_[+1(7.08e-07)]_361 34247 3.08e-01 500 43391 1.06e-02 305_[+1(1.70e-06)]_174 50597 3.61e-11 163_[+3(1.56e-08)]_141_\ [+1(1.94e-10)]_155 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************