******************************************************************************** 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/491/491.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9040 1.0000 500 36531 1.0000 500 46926 1.0000 500 29309 1.0000 500 43556 1.0000 500 55102 1.0000 500 40672 1.0000 500 16606 1.0000 500 18693 1.0000 500 44884 1.0000 500 45569 1.0000 500 38627 1.0000 500 46662 1.0000 500 36724 1.0000 500 37916 1.0000 500 49015 1.0000 500 40996 1.0000 500 50159 1.0000 500 47950 1.0000 500 46119 1.0000 500 49779 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/491/491.seqs.fa -oc motifs/491 -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= 21 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= 10500 N= 21 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.247 G 0.221 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.247 G 0.221 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 16 llr = 180 E-value = 2.6e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :19:6:::9434 pos.-specific C :21a:::2::13 probability G :8:::a:8:622 matrix T a:::4:a:1:51 bits 2.2 * 2.0 * * ** 1.7 * * ** 1.5 * ** **** Relative 1.3 * ** **** Entropy 1.1 **** ***** (16.2 bits) 0.9 ********** 0.7 ********** 0.4 ********** 0.2 ************ 0.0 ------------ Multilevel TGACAGTGAGTA consensus T AAC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 36724 343 1.11e-07 TGATGTTGTG TGACTGTGAGTA ATCGATGTCA 44884 422 3.26e-07 ACGGCACGAA TGACAGTGAGTG ACTCTCACTT 55102 441 3.26e-07 ATGACAAGTT TGACAGTGAGAA GAAATCGCTT 49015 452 3.71e-07 CTACTCTCTC TGACAGTGAGGA ACACAAATAC 36531 388 8.49e-07 CATGGACCTT TGACAGTGAGTT GCATTCTTTT 46926 224 1.16e-06 CTCACCTTCC TGACAGTGAAGA TCACAAGCTC 50159 262 1.34e-06 ACTTTCGAGC TGACTGTGAGAC GTTTGTCTTT 43556 331 1.34e-06 ATCATCGACC TGACTGTGAATC ACAGTCAGTT 45569 336 1.61e-06 GTCAGCTGAC TGACTGTGAATG ATGCAACAAA 16606 87 4.14e-06 GCGATAATGA TGACAGTGAACA ATGATTCACA 38627 243 5.06e-06 AGCTGTGATG TCACAGTGAAAA CACTCCGACT 37916 119 1.20e-05 CATGTTGACA TCACTGTCAGTC CAGATCAAAA 47950 265 1.43e-05 GCGCCGGGCA TGACAGTCTGTA CCTCGACCCA 40996 219 1.43e-05 TTTTGGTATT TGCCTGTGAGTT TCTACCACGC 40672 382 1.66e-05 AAGTATTACT TCACAGTCAGAG TAAATTGAAC 46662 189 2.23e-05 AGAGTAGCAC TAACTGTGAAGC GTAAGCATAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36724 1.1e-07 342_[+1]_146 44884 3.3e-07 421_[+1]_67 55102 3.3e-07 440_[+1]_48 49015 3.7e-07 451_[+1]_37 36531 8.5e-07 387_[+1]_101 46926 1.2e-06 223_[+1]_265 50159 1.3e-06 261_[+1]_227 43556 1.3e-06 330_[+1]_158 45569 1.6e-06 335_[+1]_153 16606 4.1e-06 86_[+1]_402 38627 5.1e-06 242_[+1]_246 37916 1.2e-05 118_[+1]_370 47950 1.4e-05 264_[+1]_224 40996 1.4e-05 218_[+1]_270 40672 1.7e-05 381_[+1]_107 46662 2.2e-05 188_[+1]_300 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=16 36724 ( 343) TGACTGTGAGTA 1 44884 ( 422) TGACAGTGAGTG 1 55102 ( 441) TGACAGTGAGAA 1 49015 ( 452) TGACAGTGAGGA 1 36531 ( 388) TGACAGTGAGTT 1 46926 ( 224) TGACAGTGAAGA 1 50159 ( 262) TGACTGTGAGAC 1 43556 ( 331) TGACTGTGAATC 1 45569 ( 336) TGACTGTGAATG 1 16606 ( 87) TGACAGTGAACA 1 38627 ( 243) TCACAGTGAAAA 1 37916 ( 119) TCACTGTCAGTC 1 47950 ( 265) TGACAGTCTGTA 1 40996 ( 219) TGCCTGTGAGTT 1 40672 ( 382) TCACAGTCAGAG 1 46662 ( 189) TAACTGTGAAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 10269 bayes= 10.0616 E= 2.6e-010 -1064 -1064 -1064 189 -206 -40 176 -1064 184 -198 -1064 -1064 -1064 202 -1064 -1064 110 -1064 -1064 69 -1064 -1064 218 -1064 -1064 -1064 -1064 189 -1064 -40 188 -1064 184 -1064 -1064 -211 52 -1064 150 -1064 -7 -198 -23 89 74 2 -23 -111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 16 E= 2.6e-010 0.000000 0.000000 0.000000 1.000000 0.062500 0.187500 0.750000 0.000000 0.937500 0.062500 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.562500 0.000000 0.000000 0.437500 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.187500 0.812500 0.000000 0.937500 0.000000 0.000000 0.062500 0.375000 0.000000 0.625000 0.000000 0.250000 0.062500 0.187500 0.500000 0.437500 0.250000 0.187500 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TGAC[AT]GTGA[GA][TA][AC] -------------------------------------------------------------------------------- Time 3.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 99 E-value = 2.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 82:442:a2a42::628::a: pos.-specific C :::6::::2::2684::a::8 probability G 28a:68a:4:4:2::8::a:2 matrix T ::::::::2:2622::2:::: bits 2.2 * * * 2.0 * ** * *** 1.7 * ** * *** 1.5 * ** * *** Relative 1.3 *** *** * * ****** Entropy 1.1 ******** * ******** (28.6 bits) 0.9 ******** * ******** 0.7 ******** * ********** 0.4 ******** ************ 0.2 ********************* 0.0 --------------------- Multilevel AGGCGGGAGAATCCAGACGAC consensus GA AAA A GAGTCAT G sequence C TCT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36531 183 1.21e-10 ACCCAAAATG AGGAGGGAAAATCCAAACGAC GTTTCTTCGT 45569 280 1.50e-10 GTGCGTCGCC AGGCGGGATAGTGCAGACGAG ATACACGCAT 36724 403 6.85e-10 ATCAGCAACA AGGCGGGAGATCTCAGTCGAC TGTTTGCCCC 40996 142 8.62e-10 ACCGACCGGT AGGAAGGACAGACTCGACGAC GACATAAACA 46662 479 1.64e-09 ATTTTATTTT GAGCAAGAGAATCCCGACGAC A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36531 1.2e-10 182_[+2]_297 45569 1.5e-10 279_[+2]_200 36724 6.9e-10 402_[+2]_77 40996 8.6e-10 141_[+2]_338 46662 1.6e-09 478_[+2]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 36531 ( 183) AGGAGGGAAAATCCAAACGAC 1 45569 ( 280) AGGCGGGATAGTGCAGACGAG 1 36724 ( 403) AGGCGGGAGATCTCAGTCGAC 1 40996 ( 142) AGGAAGGACAGACTCGACGAC 1 46662 ( 479) GAGCAAGAGAATCCCGACGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 10080 bayes= 11.2282 E= 2.3e+001 161 -897 -14 -897 -39 -897 186 -897 -897 -897 218 -897 61 128 -897 -897 61 -897 144 -897 -39 -897 186 -897 -897 -897 218 -897 193 -897 -897 -897 -39 -31 86 -43 193 -897 -897 -897 61 -897 86 -43 -39 -31 -897 115 -897 128 -14 -43 -897 169 -897 -43 119 69 -897 -897 -39 -897 186 -897 161 -897 -897 -43 -897 201 -897 -897 -897 -897 218 -897 193 -897 -897 -897 -897 169 -14 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 2.3e+001 0.800000 0.000000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.400000 0.200000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.400000 0.200000 0.200000 0.200000 0.000000 0.600000 0.000000 0.600000 0.200000 0.200000 0.000000 0.800000 0.000000 0.200000 0.600000 0.400000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AG][GA]G[CA][GA][GA]GA[GACT]A[AGT][TAC][CGT][CT][AC][GA][AT]CGA[CG] -------------------------------------------------------------------------------- Time 7.47 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 14 sites = 7 llr = 96 E-value = 1.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::1:::7:9:: pos.-specific C :1:a39:11:91:: probability G 1:1:::::1:::9: matrix T 999:7:a9731:1a bits 2.2 2.0 * * * 1.7 * * * 1.5 * * ** Relative 1.3 **** *** **** Entropy 1.1 ******** ***** (19.7 bits) 0.9 ************** 0.7 ************** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel TTTCTCTTTACAGT consensus C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 16606 151 6.46e-09 CGTCTTCTCC TTTCTCTTTACAGT TTTACTGTCA 36531 321 7.16e-08 CCATATTGAA TTTCTATTTACAGT ACCAAGTCAC 44884 389 2.39e-07 GAACTTCATT TCTCTCTTGACAGT CAAATGTAAA 36724 107 2.60e-07 GTCCACTCTC TTTCTCTCCACAGT CTAGCTCGAG 49015 28 3.61e-07 TGAAGCGTGG GTTCCCTTTTCAGT CGTATTTTTG 29309 429 6.58e-07 TTACCAACCC TTGCCCTTTACCGT CGATCAAGTA 18693 87 1.23e-06 TCGTATGGGG TTTCTCTTTTTATT GACCCTAGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16606 6.5e-09 150_[+3]_336 36531 7.2e-08 320_[+3]_166 44884 2.4e-07 388_[+3]_98 36724 2.6e-07 106_[+3]_380 49015 3.6e-07 27_[+3]_459 29309 6.6e-07 428_[+3]_58 18693 1.2e-06 86_[+3]_400 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=14 seqs=7 16606 ( 151) TTTCTCTTTACAGT 1 36531 ( 321) TTTCTATTTACAGT 1 44884 ( 389) TCTCTCTTGACAGT 1 36724 ( 107) TTTCTCTCCACAGT 1 49015 ( 28) GTTCCCTTTTCAGT 1 29309 ( 429) TTGCCCTTTACCGT 1 18693 ( 87) TTTCTCTTTTTATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 10227 bayes= 10.3555 E= 1.0e+003 -945 -945 -63 166 -945 -79 -945 166 -945 -945 -63 166 -945 201 -945 -945 -945 21 -945 140 -87 179 -945 -945 -945 -945 -945 189 -945 -79 -945 166 -945 -79 -63 140 145 -945 -945 8 -945 179 -945 -92 171 -79 -945 -945 -945 -945 196 -92 -945 -945 -945 189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 7 E= 1.0e+003 0.000000 0.000000 0.142857 0.857143 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 0.142857 0.857143 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.000000 0.714286 0.142857 0.857143 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.142857 0.142857 0.714286 0.714286 0.000000 0.000000 0.285714 0.000000 0.857143 0.000000 0.142857 0.857143 0.142857 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TTTC[TC]CTTT[AT]CAGT -------------------------------------------------------------------------------- Time 11.29 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9040 4.44e-01 500 36531 5.38e-13 182_[+2(1.21e-10)]_117_\ [+3(7.16e-08)]_53_[+1(8.49e-07)]_101 46926 1.17e-02 223_[+1(1.16e-06)]_265 29309 1.20e-02 428_[+3(6.58e-07)]_58 43556 1.72e-03 330_[+1(1.34e-06)]_158 55102 1.52e-03 440_[+1(3.26e-07)]_48 40672 4.73e-02 381_[+1(1.66e-05)]_107 16606 4.24e-07 86_[+1(4.14e-06)]_52_[+3(6.46e-09)]_\ 336 18693 1.33e-02 86_[+3(1.23e-06)]_400 44884 1.34e-06 388_[+3(2.39e-07)]_19_\ [+1(3.26e-07)]_67 45569 1.38e-08 279_[+2(1.50e-10)]_20_\ [+1(4.49e-05)]_3_[+1(1.61e-06)]_153 38627 2.70e-02 242_[+1(5.06e-06)]_246 46662 8.17e-07 188_[+1(2.23e-05)]_278_\ [+2(1.64e-09)]_1 36724 1.36e-12 106_[+3(2.60e-07)]_222_\ [+1(1.11e-07)]_48_[+2(6.85e-10)]_77 37916 2.31e-02 118_[+1(1.20e-05)]_370 49015 3.41e-06 27_[+3(3.61e-07)]_410_\ [+1(3.71e-07)]_37 40996 1.76e-07 141_[+2(8.62e-10)]_56_\ [+1(1.43e-05)]_270 50159 3.31e-03 22_[+1(5.48e-05)]_227_\ [+1(1.34e-06)]_227 47950 4.32e-02 264_[+1(1.43e-05)]_224 46119 2.86e-01 500 49779 2.55e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************