******************************************************************************** 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/362/362.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42542 1.0000 500 17683 1.0000 500 43150 1.0000 500 36608 1.0000 500 37711 1.0000 500 21996 1.0000 500 52444 1.0000 500 3676 1.0000 500 49017 1.0000 500 6292 1.0000 500 49462 1.0000 500 50123 1.0000 500 18469 1.0000 500 44111 1.0000 500 44112 1.0000 500 41450 1.0000 500 2808 1.0000 500 45163 1.0000 500 45223 1.0000 500 45401 1.0000 500 36001 1.0000 500 48257 1.0000 500 47469 1.0000 500 49720 1.0000 500 45579 1.0000 500 45635 1.0000 500 47863 1.0000 500 35909 1.0000 500 46048 1.0000 500 48144 1.0000 500 38535 1.0000 500 39968 1.0000 500 46308 1.0000 500 49361 1.0000 500 46030 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/362/362.seqs.fa -oc motifs/362 -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= 35 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= 17500 N= 35 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.270 C 0.228 G 0.228 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.270 C 0.228 G 0.228 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 14 llr = 180 E-value = 1.9e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :313141::::::a:8 pos.-specific C 129:73:37:12::9: probability G 91:7226:19::9:11 matrix T :41::12721981::1 bits 2.1 1.9 * 1.7 ** 1.5 * ** *** Relative 1.3 * ** ****** Entropy 1.1 * *** ********* (18.5 bits) 0.9 * *** ********** 0.6 * *** ********** 0.4 * *** ********** 0.2 ***** ********** 0.0 ---------------- Multilevel GTCGCAGTCGTTGACA consensus A AGCTCT C sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 46030 292 3.02e-09 CCGTTCGCCA GACGCAGCCGTTGACA TGAGTCCTGA 38535 387 3.02e-09 AATCGGTTCG GTCACCGTCGTTGACA GAGCTGAACC 35909 292 3.02e-09 CCGTTCGCCA GACGCAGCCGTTGACA TGAGTCCTGA 48257 55 8.84e-08 AAATCCTGTT GTCGCCATCGTTGACG GAGAAAGTCG 45635 190 1.80e-07 CAGGATATAC CCCGCGTTCGTTGACA GAATAGCTGT 49361 238 5.89e-07 CGCGAGGCCC CACACGGTTGTTGACA CGACTGTTAG 43150 216 6.98e-07 GTAGTCTTTG GTCGCGGTTGTCGACT TTATTAATAT 42542 384 6.98e-07 TTTGCCTGTG GGCGCTTTTGTTGACA GTGATCAATA 45579 130 8.88e-07 ACTTGCCAAC GAAGGCGTCGTCGACA ATGGTGTCGT 47469 191 1.12e-06 TTTATGTGTT GCCGAAGCCTTTGACA AAGGAACAGA 36608 51 1.41e-06 CATCGTTTTC GTCGCCATCGCTGAGA TCCATTGACC 18469 447 3.45e-06 TACCGCTGGT GTTGGTGTGGTTGACA GTTTTTCGGG 37711 379 3.45e-06 GCATCATCGC GCCAGAGTCGTTTACG AGCAAGAGCA 46308 458 6.68e-06 CCAGTCCATC GTCACATCCTTCGAGA ACAGAGAACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46030 3e-09 291_[+1]_193 38535 3e-09 386_[+1]_98 35909 3e-09 291_[+1]_193 48257 8.8e-08 54_[+1]_430 45635 1.8e-07 189_[+1]_295 49361 5.9e-07 237_[+1]_247 43150 7e-07 215_[+1]_269 42542 7e-07 383_[+1]_101 45579 8.9e-07 129_[+1]_355 47469 1.1e-06 190_[+1]_294 36608 1.4e-06 50_[+1]_434 18469 3.4e-06 446_[+1]_38 37711 3.4e-06 378_[+1]_106 46308 6.7e-06 457_[+1]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=14 46030 ( 292) GACGCAGCCGTTGACA 1 38535 ( 387) GTCACCGTCGTTGACA 1 35909 ( 292) GACGCAGCCGTTGACA 1 48257 ( 55) GTCGCCATCGTTGACG 1 45635 ( 190) CCCGCGTTCGTTGACA 1 49361 ( 238) CACACGGTTGTTGACA 1 43150 ( 216) GTCGCGGTTGTCGACT 1 42542 ( 384) GGCGCTTTTGTTGACA 1 45579 ( 130) GAAGGCGTCGTCGACA 1 47469 ( 191) GCCGAAGCCTTTGACA 1 36608 ( 51) GTCGCCATCGCTGAGA 1 18469 ( 447) GTTGGTGTGGTTGACA 1 37711 ( 379) GCCAGAGTCGTTTACG 1 46308 ( 458) GTCACATCCTTCGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16975 bayes= 10.8487 E= 1.9e-003 -1045 -67 191 -1045 8 -9 -167 65 -191 191 -1045 -194 8 -1045 164 -1045 -191 165 -9 -1045 40 33 -9 -94 -92 -1045 149 -35 -1045 33 -1045 138 -1045 165 -167 -35 -1045 -1045 191 -94 -1045 -167 -1045 176 -1045 -9 -1045 152 -1045 -1045 202 -194 189 -1045 -1045 -1045 -1045 191 -68 -1045 154 -1045 -68 -194 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 14 E= 1.9e-003 0.000000 0.142857 0.857143 0.000000 0.285714 0.214286 0.071429 0.428571 0.071429 0.857143 0.000000 0.071429 0.285714 0.000000 0.714286 0.000000 0.071429 0.714286 0.214286 0.000000 0.357143 0.285714 0.214286 0.142857 0.142857 0.000000 0.642857 0.214286 0.000000 0.285714 0.000000 0.714286 0.000000 0.714286 0.071429 0.214286 0.000000 0.000000 0.857143 0.142857 0.000000 0.071429 0.000000 0.928571 0.000000 0.214286 0.000000 0.785714 0.000000 0.000000 0.928571 0.071429 1.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.785714 0.000000 0.142857 0.071429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[TAC]C[GA][CG][ACG][GT][TC][CT]GT[TC]GACA -------------------------------------------------------------------------------- Time 10.07 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 15 llr = 168 E-value = 1.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::6:852:9a33 pos.-specific C 1a:a:::a::13 probability G ::4::5::1:13 matrix T 9:::2:8:::51 bits 2.1 * * * 1.9 * * * * 1.7 * * * * 1.5 ** * *** Relative 1.3 ** * *** Entropy 1.1 ********** (16.2 bits) 0.9 ********** 0.6 ********** 0.4 ********** 0.2 ************ 0.0 ------------ Multilevel TCACAGTCAATA consensus G TAA AG sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 47469 218 2.04e-07 AGGAACAGAT TCACAGTCAATA GATTCTCTTC 49017 238 3.38e-07 TGTGAGTGTG TCACAGTCAATC AAAGCAACCT 45223 163 6.76e-07 CTACACATGT TCACAGTCAAAA GGAAATTGTT 45163 59 6.76e-07 GGGGTGTGCT TCACAGTCAAAA CACCTAAAAA 21996 238 6.76e-07 AATTGTTCCT TCGCAGTCAAAG AAAATGTCGC 50123 279 9.05e-07 ACACTCACAC TCACAGTCAAAC TTCGGCAGAA 49361 57 2.20e-06 CTGTTAATCG TCACTGTCAATG TGCGGTTTCC 46030 8 2.79e-06 TAGAAAG TCGCAATCAAGG CTGGCGACGT 35909 11 2.79e-06 ACTTAGAAAG TCGCAATCAAGG CTGGCGACGT 3676 298 3.13e-06 GATGTCAGTC TCACAAACAATG GCTTTGGCAA 45579 254 4.15e-06 TTCGATTGGA TCACAAACAATA CGTATGTTTT 36001 471 1.33e-05 ATGGAAGAAA TCGCAGACAATT CCTGAAACTT 17683 416 1.39e-05 TTGACAAAAC CCGCAATCAAAA AACGAGTTTG 46308 228 1.77e-05 GCCCTTGTAT TCGCTATCAACC AGGCGACACT 39968 462 2.34e-05 TGGAGGTGTA TCACTATCGATC CTGCAGGCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47469 2e-07 217_[+2]_271 49017 3.4e-07 237_[+2]_251 45223 6.8e-07 162_[+2]_326 45163 6.8e-07 58_[+2]_430 21996 6.8e-07 237_[+2]_251 50123 9e-07 278_[+2]_210 49361 2.2e-06 56_[+2]_432 46030 2.8e-06 7_[+2]_481 35909 2.8e-06 10_[+2]_478 3676 3.1e-06 297_[+2]_191 45579 4.1e-06 253_[+2]_235 36001 1.3e-05 470_[+2]_18 17683 1.4e-05 415_[+2]_73 46308 1.8e-05 227_[+2]_261 39968 2.3e-05 461_[+2]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=15 47469 ( 218) TCACAGTCAATA 1 49017 ( 238) TCACAGTCAATC 1 45223 ( 163) TCACAGTCAAAA 1 45163 ( 59) TCACAGTCAAAA 1 21996 ( 238) TCGCAGTCAAAG 1 50123 ( 279) TCACAGTCAAAC 1 49361 ( 57) TCACTGTCAATG 1 46030 ( 8) TCGCAATCAAGG 1 35909 ( 11) TCGCAATCAAGG 1 3676 ( 298) TCACAAACAATG 1 45579 ( 254) TCACAAACAATA 1 36001 ( 471) TCGCAGACAATT 1 17683 ( 416) CCGCAATCAAAA 1 46308 ( 228) TCGCTATCAACC 1 39968 ( 462) TCACTATCGATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 17115 bayes= 10.0798 E= 1.7e-002 -1055 -177 -1055 177 -1055 213 -1055 -1055 115 -1055 81 -1055 -1055 213 -1055 -1055 157 -1055 -1055 -45 79 -1055 122 -1055 -43 -1055 -1055 155 -1055 213 -1055 -1055 179 -1055 -177 -1055 189 -1055 -1055 -1055 30 -177 -78 77 30 23 55 -204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 1.7e-002 0.000000 0.066667 0.000000 0.933333 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.466667 0.000000 0.533333 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.933333 0.000000 0.066667 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.066667 0.133333 0.466667 0.333333 0.266667 0.333333 0.066667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TC[AG]C[AT][GA][TA]CAA[TA][AGC] -------------------------------------------------------------------------------- Time 20.12 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 11 llr = 134 E-value = 2.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 5::9a:a::99a pos.-specific C :78::7::3::: probability G 23:1:3:a61:: matrix T 3:2:::::1:1: bits 2.1 * 1.9 * ** * 1.7 * ** * 1.5 *** ** *** Relative 1.3 ******* *** Entropy 1.1 ******* *** (17.5 bits) 0.9 *********** 0.6 *********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACCAACAGGAAA consensus TG G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46030 103 6.44e-08 AAACAACAAA ACCAACAGGAAA GGCTTAACGC 35909 106 6.44e-08 AAACAACAAA ACCAACAGGAAA GGCTTTACGC 49462 466 5.74e-07 AACATACATC TCCAAGAGGAAA GCACTCAATT 3676 271 8.35e-07 CCGCTAATGC AGCAACAGCAAA ATGATGATGT 46308 26 1.19e-06 TATATTTTAC ACCAACAGTAAA AAATATGACG 45635 175 1.26e-06 ATAGCCTGTA ACCAACAGGATA TACCCCGCGT 45223 81 1.34e-06 GGCTTGTTAT TCTAACAGGAAA CCGGACGAAA 37711 395 2.01e-06 GTCGTTTACG AGCAAGAGCAAA CACAAGAAAA 42542 132 3.28e-06 TTAACATTAA TCTAACAGCAAA GTTTCAATTT 44111 478 5.79e-06 AAAAAAAATT GCCAAGAGGGAA ACTGAAGCGT 50123 136 5.79e-06 GCATCGTGGG GGCGACAGGAAA CAAAAAGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46030 6.4e-08 102_[+3]_386 35909 6.4e-08 105_[+3]_383 49462 5.7e-07 465_[+3]_23 3676 8.3e-07 270_[+3]_218 46308 1.2e-06 25_[+3]_463 45635 1.3e-06 174_[+3]_314 45223 1.3e-06 80_[+3]_408 37711 2e-06 394_[+3]_94 42542 3.3e-06 131_[+3]_357 44111 5.8e-06 477_[+3]_11 50123 5.8e-06 135_[+3]_353 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=11 46030 ( 103) ACCAACAGGAAA 1 35909 ( 106) ACCAACAGGAAA 1 49462 ( 466) TCCAAGAGGAAA 1 3676 ( 271) AGCAACAGCAAA 1 46308 ( 26) ACCAACAGTAAA 1 45635 ( 175) ACCAACAGGATA 1 45223 ( 81) TCTAACAGGAAA 1 37711 ( 395) AGCAAGAGCAAA 1 42542 ( 132) TCTAACAGCAAA 1 44111 ( 478) GCCAAGAGGGAA 1 50123 ( 136) GGCGACAGGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 17115 bayes= 11.6296 E= 2.2e-001 101 -1010 -33 -1 -1010 167 26 -1010 -1010 184 -1010 -59 175 -1010 -133 -1010 189 -1010 -1010 -1010 -1010 167 26 -1010 189 -1010 -1010 -1010 -1010 -1010 213 -1010 -1010 26 148 -159 175 -1010 -133 -1010 175 -1010 -1010 -159 189 -1010 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 2.2e-001 0.545455 0.000000 0.181818 0.272727 0.000000 0.727273 0.272727 0.000000 0.000000 0.818182 0.000000 0.181818 0.909091 0.000000 0.090909 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.727273 0.272727 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.272727 0.636364 0.090909 0.909091 0.000000 0.090909 0.000000 0.909091 0.000000 0.000000 0.090909 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AT][CG]CAA[CG]AG[GC]AAA -------------------------------------------------------------------------------- Time 29.75 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42542 3.71e-05 39_[+3(4.29e-05)]_80_[+3(3.28e-06)]_\ 240_[+1(6.98e-07)]_101 17683 3.51e-02 415_[+2(1.39e-05)]_73 43150 1.79e-03 215_[+1(6.98e-07)]_269 36608 1.76e-02 50_[+1(1.41e-06)]_434 37711 5.91e-05 378_[+1(3.45e-06)]_[+3(2.01e-06)]_\ 94 21996 1.53e-03 237_[+2(6.76e-07)]_251 52444 6.30e-01 500 3676 3.61e-05 270_[+3(8.35e-07)]_15_\ [+2(3.13e-06)]_191 49017 2.11e-03 237_[+2(3.38e-07)]_251 6292 3.47e-01 500 49462 1.20e-03 465_[+3(5.74e-07)]_23 50123 1.20e-04 135_[+3(5.79e-06)]_131_\ [+2(9.05e-07)]_210 18469 2.64e-02 446_[+1(3.45e-06)]_38 44111 1.55e-02 477_[+3(5.79e-06)]_11 44112 1.69e-01 500 41450 3.09e-01 500 2808 5.69e-01 500 45163 2.65e-03 58_[+2(6.76e-07)]_430 45223 1.71e-05 80_[+3(1.34e-06)]_47_[+2(9.71e-05)]_\ 11_[+2(6.76e-07)]_326 45401 2.14e-01 274_[+1(9.85e-05)]_210 36001 2.46e-02 470_[+2(1.33e-05)]_18 48257 1.75e-03 54_[+1(8.84e-08)]_430 47469 4.13e-06 190_[+1(1.12e-06)]_11_\ [+2(2.04e-07)]_271 49720 2.14e-01 500 45579 9.38e-05 129_[+1(8.88e-07)]_108_\ [+2(4.15e-06)]_235 45635 1.61e-06 174_[+3(1.26e-06)]_3_[+1(1.80e-07)]_\ 68_[+3(8.66e-05)]_215 47863 7.31e-01 500 35909 3.10e-11 10_[+2(2.79e-06)]_83_[+3(6.44e-08)]_\ 103_[+1(8.39e-05)]_55_[+1(3.02e-09)]_193 46048 4.92e-01 500 48144 7.20e-01 500 38535 2.40e-05 128_[+1(9.54e-05)]_242_\ [+1(3.02e-09)]_98 39968 1.03e-01 461_[+2(2.34e-05)]_27 46308 2.92e-06 25_[+3(1.19e-06)]_190_\ [+2(1.77e-05)]_218_[+1(6.68e-06)]_27 49361 1.41e-05 56_[+2(2.20e-06)]_169_\ [+1(5.89e-07)]_116_[+2(6.87e-05)]_119 46030 3.10e-11 7_[+2(2.79e-06)]_83_[+3(6.44e-08)]_\ 106_[+1(8.39e-05)]_55_[+1(3.02e-09)]_193 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************