******************************************************************************** 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/246/246.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31841 1.0000 500 8945 1.0000 500 14176 1.0000 500 54960 1.0000 500 15294 1.0000 500 43564 1.0000 500 50058 1.0000 500 44859 1.0000 500 35698 1.0000 500 36149 1.0000 500 12799 1.0000 500 31713 1.0000 500 45227 1.0000 500 50349 1.0000 500 48169 1.0000 500 34241 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/246/246.seqs.fa -oc motifs/246 -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 0.271 C 0.246 G 0.223 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.246 G 0.223 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 12 llr = 157 E-value = 7.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::7:::143a88733:66 pos.-specific C 2:4::1323313::132:443 probability G 32:2a1226152::2:386:2 matrix T 5868:26725:3:3::3:::: bits 2.2 * 1.9 * * 1.7 * * 1.5 * * Relative 1.3 * ** * * Entropy 1.1 **** ** * ** (18.9 bits) 0.9 **** **** *** 0.6 ***** *** * **** **** 0.4 *********** **** **** 0.2 *********** **** **** 0.0 --------------------- Multilevel TTTTGATTGTGAAAAAAGGAA consensus G C C CCAC T CGACCC sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 35698 438 1.49e-10 CGAGATACTG TTCTGATTGTGTAAACGGGAA CGCCAGTTGT 31841 26 5.37e-08 AAACGGCAGT TTTTGATTTGATAAAAAGCAA TTGATCTTGT 31713 127 1.69e-07 GCTTAGTGCT TTCTGACTCTACAAAAGAGAG CAAGCAACGA 48169 436 2.54e-07 TCACTTTTTT GTTTGAGTGTGGAAGACAGCA GTACTCTACC 45227 422 4.10e-07 CCTACACCCC CTTTGACTGTGCATACCAGCA GTAAGCACAA 43564 4 5.36e-07 CAG TGTTGACTGAGTATAATGCAA CAGAAAAATC 54960 5 5.85e-07 TTGC GTCGGATTGTAGAAGCAGGCG ACCTAAAGGC 50058 264 6.37e-07 TCGAGATTCC GTTGGTTTTCGAAAAATGGCC AACCATCGAT 50349 128 8.85e-07 ACTTCACTGT TGCTGAGCCCAAAAACGGGAA CTGCATAAGG 14176 406 8.85e-07 CGGACGTGTC CTTTGGTCCCACAAAAAGCAA TTGGCAGTAT 8945 36 1.21e-06 TCTGGTACGG TTCTGCTGGTCAAAAATGCAC AAGCAAGTGT 15294 94 2.55e-06 GCGAATTCAA GTTTGTTGGCGAATCAAGCCC CGTCGATGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35698 1.5e-10 437_[+1]_42 31841 5.4e-08 25_[+1]_454 31713 1.7e-07 126_[+1]_353 48169 2.5e-07 435_[+1]_44 45227 4.1e-07 421_[+1]_58 43564 5.4e-07 3_[+1]_476 54960 5.8e-07 4_[+1]_475 50058 6.4e-07 263_[+1]_216 50349 8.9e-07 127_[+1]_352 14176 8.9e-07 405_[+1]_74 8945 1.2e-06 35_[+1]_444 15294 2.6e-06 93_[+1]_386 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=12 35698 ( 438) TTCTGATTGTGTAAACGGGAA 1 31841 ( 26) TTTTGATTTGATAAAAAGCAA 1 31713 ( 127) TTCTGACTCTACAAAAGAGAG 1 48169 ( 436) GTTTGAGTGTGGAAGACAGCA 1 45227 ( 422) CTTTGACTGTGCATACCAGCA 1 43564 ( 4) TGTTGACTGAGTATAATGCAA 1 54960 ( 5) GTCGGATTGTAGAAGCAGGCG 1 50058 ( 264) GTTGGTTTTCGAAAAATGGCC 1 50349 ( 128) TGCTGAGCCCAAAAACGGGAA 1 14176 ( 406) CTTTGGTCCCACAAAAAGCAA 1 8945 ( 36) TTCTGCTGGTCAAAAATGCAC 1 15294 ( 94) GTTTGTTGGCGAATCAAGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 9.76773 E= 7.3e+001 -1023 -56 58 94 -1023 -1023 -42 168 -1023 76 -1023 116 -1023 -1023 -42 168 -1023 -1023 216 -1023 130 -156 -142 -64 -1023 3 -42 116 -1023 -56 -42 136 -1023 3 138 -64 -170 44 -142 94 62 -156 116 -1023 30 3 -42 -6 188 -1023 -1023 -1023 147 -1023 -1023 -6 147 -156 -42 -1023 130 44 -1023 -1023 30 -56 16 -6 -11 -1023 175 -1023 -1023 76 138 -1023 111 76 -1023 -1023 111 3 -42 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 12 E= 7.3e+001 0.000000 0.166667 0.333333 0.500000 0.000000 0.000000 0.166667 0.833333 0.000000 0.416667 0.000000 0.583333 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.666667 0.083333 0.083333 0.166667 0.000000 0.250000 0.166667 0.583333 0.000000 0.166667 0.166667 0.666667 0.000000 0.250000 0.583333 0.166667 0.083333 0.333333 0.083333 0.500000 0.416667 0.083333 0.500000 0.000000 0.333333 0.250000 0.166667 0.250000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.750000 0.083333 0.166667 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.166667 0.250000 0.250000 0.250000 0.000000 0.750000 0.000000 0.000000 0.416667 0.583333 0.000000 0.583333 0.416667 0.000000 0.000000 0.583333 0.250000 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG]T[TC]TGA[TC]T[GC][TC][GA][ACT]A[AT]A[AC][AGT][GA][GC][AC][AC] -------------------------------------------------------------------------------- Time 2.16 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 7 llr = 94 E-value = 4.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :9:17::16a73a: pos.-specific C a:a9::a64::7:7 probability G ::::31:1::1::3 matrix T :1:::9:1::1::: bits 2.2 1.9 * * * * * 1.7 * * * * * 1.5 * ** * * * Relative 1.3 **** ** * ** Entropy 1.1 ******* * *** (19.5 bits) 0.9 ******* ****** 0.6 ******* ****** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel CACCATCCAAACAC consensus G C A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 31713 295 5.61e-09 TAACGCCGAG CACCATCCAAACAC TCCCTCGAAC 44859 424 9.15e-08 CTATCAAGAC CACCATCTCAACAC AAAGCTACAA 48169 406 1.26e-07 GAAGGGTAAA CACCAGCCCAACAC CATCTGTCAC 50058 50 2.93e-07 TGTCCGATGT CACCGTCCAAAAAG GCCTCCAGTC 31841 247 8.55e-07 TTTGGATTGG CTCAATCCAAACAC GGAACGACAT 54960 416 1.25e-06 GATCCATATC CACCATCACATCAG TATAGGCGTC 36149 132 1.55e-06 TTTGCATGTT CACCGTCGAAGAAC TGCGACGGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31713 5.6e-09 294_[+2]_192 44859 9.1e-08 423_[+2]_63 48169 1.3e-07 405_[+2]_81 50058 2.9e-07 49_[+2]_437 31841 8.6e-07 246_[+2]_240 54960 1.2e-06 415_[+2]_71 36149 1.5e-06 131_[+2]_355 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=7 31713 ( 295) CACCATCCAAACAC 1 44859 ( 424) CACCATCTCAACAC 1 48169 ( 406) CACCAGCCCAACAC 1 50058 ( 50) CACCGTCCAAAAAG 1 31841 ( 247) CTCAATCCAAACAC 1 54960 ( 416) CACCATCACATCAG 1 36149 ( 132) CACCGTCGAAGAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 7792 bayes= 9.96286 E= 4.5e+002 -945 202 -945 -945 166 -945 -945 -86 -945 202 -945 -945 -92 180 -945 -945 140 -945 36 -945 -945 -945 -64 172 -945 202 -945 -945 -92 122 -64 -86 108 80 -945 -945 188 -945 -945 -945 140 -945 -64 -86 8 154 -945 -945 188 -945 -945 -945 -945 154 36 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 7 E= 4.5e+002 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.714286 0.000000 0.285714 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 1.000000 0.000000 0.000000 0.142857 0.571429 0.142857 0.142857 0.571429 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.142857 0.142857 0.285714 0.714286 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CACC[AG]TCC[AC]AA[CA]A[CG] -------------------------------------------------------------------------------- Time 4.50 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 9 llr = 100 E-value = 1.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :23:::a82:a: pos.-specific C 8:44:a:12::6 probability G 2826a::149:4 matrix T ::::::::11:: bits 2.2 * 1.9 *** * 1.7 *** ** 1.5 *** ** Relative 1.3 ** *** ** Entropy 1.1 ** **** *** (16.1 bits) 0.9 ** ***** *** 0.6 ** ***** *** 0.4 ******** *** 0.2 ************ 0.0 ------------ Multilevel CGCGGCAAGGAC consensus GAAC A G sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43564 301 7.66e-08 CTCTTGTAAT CGCGGCAAGGAG GGACAGAAAG 34241 59 1.12e-06 CGACTCTCTC CGCCGCAAAGAG AATAAGATTC 31841 313 1.12e-06 GAAACATCCC CGAGGCAACGAG CAATTTCCAT 14176 389 2.52e-06 GTAACACAAG CGCGGCACGGAC GTGTCCTTTG 15294 381 5.53e-06 ACTGAGTCAG GGACGCAACGAC GGCTTGGCAA 12799 104 5.95e-06 ACACACGCGT CGCCGCAAGTAG TCGATCCTCC 35698 179 8.70e-06 CTGGACGGAA GAGGGCAAGGAC ACGAAAGTGA 8945 342 8.70e-06 TTTCCTTCGG CAGCGCAAAGAC AATGTTAAGA 31713 17 1.26e-05 ACATTTCCTC CGAGGCAGTGAC ATCCCAGGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43564 7.7e-08 300_[+3]_188 34241 1.1e-06 58_[+3]_430 31841 1.1e-06 312_[+3]_176 14176 2.5e-06 388_[+3]_100 15294 5.5e-06 380_[+3]_108 12799 5.9e-06 103_[+3]_385 35698 8.7e-06 178_[+3]_310 8945 8.7e-06 341_[+3]_147 31713 1.3e-05 16_[+3]_472 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=9 43564 ( 301) CGCGGCAAGGAG 1 34241 ( 59) CGCCGCAAAGAG 1 31841 ( 313) CGAGGCAACGAG 1 14176 ( 389) CGCGGCACGGAC 1 15294 ( 381) GGACGCAACGAC 1 12799 ( 104) CGCCGCAAGTAG 1 35698 ( 179) GAGGGCAAGGAC 1 8945 ( 342) CAGCGCAAAGAC 1 31713 ( 17) CGAGGCAGTGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 10.6108 E= 1.6e+003 -982 166 -1 -982 -28 -982 180 -982 30 85 -1 -982 -982 85 131 -982 -982 -982 216 -982 -982 202 -982 -982 188 -982 -982 -982 152 -114 -101 -982 -28 -14 99 -123 -982 -982 199 -123 188 -982 -982 -982 -982 118 99 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 1.6e+003 0.000000 0.777778 0.222222 0.000000 0.222222 0.000000 0.777778 0.000000 0.333333 0.444444 0.222222 0.000000 0.000000 0.444444 0.555556 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 0.777778 0.111111 0.111111 0.000000 0.222222 0.222222 0.444444 0.111111 0.000000 0.000000 0.888889 0.111111 1.000000 0.000000 0.000000 0.000000 0.000000 0.555556 0.444444 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG][GA][CAG][GC]GCAA[GAC]GA[CG] -------------------------------------------------------------------------------- Time 6.81 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31841 2.11e-09 25_[+1(5.37e-08)]_200_\ [+2(8.55e-07)]_52_[+3(1.12e-06)]_176 8945 2.11e-04 35_[+1(1.21e-06)]_285_\ [+3(8.70e-06)]_147 14176 4.31e-06 388_[+3(2.52e-06)]_5_[+1(8.85e-07)]_\ 74 54960 2.24e-05 4_[+1(5.85e-07)]_390_[+2(1.25e-06)]_\ 71 15294 2.41e-04 93_[+1(2.55e-06)]_266_\ [+3(5.53e-06)]_108 43564 7.03e-07 3_[+1(5.36e-07)]_276_[+3(7.66e-08)]_\ 188 50058 5.42e-06 49_[+2(2.93e-07)]_200_\ [+1(6.37e-07)]_216 44859 9.71e-04 423_[+2(9.15e-08)]_63 35698 6.20e-08 178_[+3(8.70e-06)]_247_\ [+1(1.49e-10)]_42 36149 8.46e-03 131_[+2(1.55e-06)]_355 12799 4.96e-03 103_[+3(5.95e-06)]_385 31713 5.48e-10 16_[+3(1.26e-05)]_98_[+1(1.69e-07)]_\ 147_[+2(5.61e-09)]_192 45227 1.21e-03 421_[+1(4.10e-07)]_58 50349 3.94e-03 127_[+1(8.85e-07)]_352 48169 9.88e-07 405_[+2(1.26e-07)]_16_\ [+1(2.54e-07)]_44 34241 8.41e-03 58_[+3(1.12e-06)]_430 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************