******************************************************************************** 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/497/497.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11609 1.0000 500 21152 1.0000 500 24115 1.0000 500 24478 1.0000 500 25726 1.0000 500 262803 1.0000 500 264269 1.0000 500 268976 1.0000 500 2759 1.0000 500 6796 1.0000 500 9031 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/497/497.seqs.fa -oc motifs/497 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.294 C 0.232 G 0.225 T 0.249 Background letter frequencies (from dataset with add-one prior applied): A 0.294 C 0.232 G 0.225 T 0.249 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 9 llr = 137 E-value = 1.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :16417763::311:2111:7 pos.-specific C :11::1::2::::::4:13:: probability G :73:7232:3a:9972882a3 matrix T a1:62::247:7::311:3:: bits 2.2 * * 1.9 * * * 1.7 * * * 1.5 * * ** * Relative 1.3 * * *** * Entropy 1.1 * * ****** ** ** (21.9 bits) 0.9 * ** * ****** ** ** 0.6 ******* ****** ** ** 0.4 *************** ** ** 0.2 ********************* 0.0 --------------------- Multilevel TGATGAAATTGTGGGCGGCGA consensus GATGGGAG A TA T G sequence TC G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 11609 255 2.12e-12 AAGGTTACAT TGAAGAAATTGTGGGCGGCGA GAAGTGGAAA 25726 268 1.70e-09 GTAGATGGAT TGATGAATTGGAGGGGGGTGG GTATCTTCTC 21152 9 2.89e-08 GACGAAGA TGAATCAGCGGTGGGCGGTGG GGCGGCGTGA 24115 69 3.46e-08 GACTGATTGA TGATGAAATTGTGAGAGATGA TGAATCGCAG 268976 293 5.79e-08 ACGAGAATGA TGCAGAGAATGAGGTTGGGGA AGATAAAATG 9031 322 9.35e-08 GTGAGCGCGG TAGTGGGAAGGTGGGGGGAGA ATTTGACCTA 2759 428 2.21e-07 GTCTTTGGGC TTGATAAACTGTGGGAGCGGA TCGGCGGGCC 262803 31 2.69e-07 CATCAACGCC TCGTGGAGATGAGGTCAGCGA TTCTACCGAA 6796 52 5.81e-07 AACTGGCTTG TGATAAGTTTGTAGTCTGCGG TATCGGAGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11609 2.1e-12 254_[+1]_225 25726 1.7e-09 267_[+1]_212 21152 2.9e-08 8_[+1]_471 24115 3.5e-08 68_[+1]_411 268976 5.8e-08 292_[+1]_187 9031 9.4e-08 321_[+1]_158 2759 2.2e-07 427_[+1]_52 262803 2.7e-07 30_[+1]_449 6796 5.8e-07 51_[+1]_428 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=9 11609 ( 255) TGAAGAAATTGTGGGCGGCGA 1 25726 ( 268) TGATGAATTGGAGGGGGGTGG 1 21152 ( 9) TGAATCAGCGGTGGGCGGTGG 1 24115 ( 69) TGATGAAATTGTGAGAGATGA 1 268976 ( 293) TGCAGAGAATGAGGTTGGGGA 1 9031 ( 322) TAGTGGGAAGGTGGGGGGAGA 1 2759 ( 428) TTGATAAACTGTGGGAGCGGA 1 262803 ( 31) TCGTGGAGATGAGGTCAGCGA 1 6796 ( 52) TGATAAGTTTGTAGTCTGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 9.32846 E= 1.0e-001 -982 -982 -982 200 -140 -106 157 -116 92 -106 57 -982 60 -982 -982 116 -140 -982 157 -17 118 -106 -2 -982 118 -982 57 -982 92 -982 -2 -17 18 -6 -982 83 -982 -982 57 142 -982 -982 215 -982 18 -982 -982 142 -140 -982 198 -982 -140 -982 198 -982 -982 -982 157 42 -40 94 -2 -116 -140 -982 179 -116 -140 -106 179 -982 -140 52 -2 42 -982 -982 215 -982 118 -982 57 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 1.0e-001 0.000000 0.000000 0.000000 1.000000 0.111111 0.111111 0.666667 0.111111 0.555556 0.111111 0.333333 0.000000 0.444444 0.000000 0.000000 0.555556 0.111111 0.000000 0.666667 0.222222 0.666667 0.111111 0.222222 0.000000 0.666667 0.000000 0.333333 0.000000 0.555556 0.000000 0.222222 0.222222 0.333333 0.222222 0.000000 0.444444 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.000000 0.666667 0.333333 0.222222 0.444444 0.222222 0.111111 0.111111 0.000000 0.777778 0.111111 0.111111 0.111111 0.777778 0.000000 0.111111 0.333333 0.222222 0.333333 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TG[AG][TA][GT][AG][AG][AGT][TAC][TG]G[TA]GG[GT][CAG]GG[CTG]G[AG] -------------------------------------------------------------------------------- Time 1.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 7 llr = 113 E-value = 5.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::73194:61371:a9:aa: pos.-specific C a611911719::96::7::7 probability G :3:4:::::::3:1::3::3 matrix T :111::433:7::3:1:::: bits 2.2 * 1.9 * 1.7 * * ** 1.5 * * * * * ** Relative 1.3 * ** * * * ****** Entropy 1.1 * ** * **** ****** (23.3 bits) 0.9 * ** * **** ****** 0.6 *** ** * *********** 0.4 *** **************** 0.2 ******************** 0.0 -------------------- Multilevel CCAGCAACACTACCAACAAC consensus G A TTT AG T G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 25726 57 3.37e-11 CACACAAGAG CCACCATCACTACCAACAAC CTGACATATT 21152 179 2.18e-09 AGAAACACTT CCAGCATTTCTACTAACAAG TTTACAAGAG 268976 192 8.79e-09 ACCTCTTGCA CCAACACCACAGCCAAGAAC AACAACTCGT 262803 278 3.47e-08 TCGCATGTTG CCATAAACTCTACTAACAAG TCAACGATGA 9031 432 7.05e-08 ACAAACCAAG CGAGCCTCACTGACATCAAC GCTGTTGAAT 2759 470 9.11e-08 TTTGGACTCG CTCACAATCCTACCAAGAAC AATTATGAGT 11609 469 9.11e-08 CCGACAACGA CGTGCAACAAAACGAACAAC ACCTCGAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25726 3.4e-11 56_[+2]_424 21152 2.2e-09 178_[+2]_302 268976 8.8e-09 191_[+2]_289 262803 3.5e-08 277_[+2]_203 9031 7.1e-08 431_[+2]_49 2759 9.1e-08 469_[+2]_11 11609 9.1e-08 468_[+2]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=7 25726 ( 57) CCACCATCACTACCAACAAC 1 21152 ( 179) CCAGCATTTCTACTAACAAG 1 268976 ( 192) CCAACACCACAGCCAAGAAC 1 262803 ( 278) CCATAAACTCTACTAACAAG 1 9031 ( 432) CGAGCCTCACTGACATCAAC 1 2759 ( 470) CTCACAATCCTACCAAGAAC 1 11609 ( 469) CGTGCAACAAAACGAACAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 5291 bayes= 9.40372 E= 5.2e+000 -945 211 -945 -945 -945 130 34 -80 128 -70 -945 -80 -4 -70 93 -80 -104 188 -945 -945 154 -70 -945 -945 54 -70 -945 78 -945 162 -945 20 96 -70 -945 20 -104 188 -945 -945 -4 -945 -945 152 128 -945 34 -945 -104 188 -945 -945 -945 130 -65 20 176 -945 -945 -945 154 -945 -945 -80 -945 162 34 -945 176 -945 -945 -945 176 -945 -945 -945 -945 162 34 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 7 E= 5.2e+000 0.000000 1.000000 0.000000 0.000000 0.000000 0.571429 0.285714 0.142857 0.714286 0.142857 0.000000 0.142857 0.285714 0.142857 0.428571 0.142857 0.142857 0.857143 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.428571 0.142857 0.000000 0.428571 0.000000 0.714286 0.000000 0.285714 0.571429 0.142857 0.000000 0.285714 0.142857 0.857143 0.000000 0.000000 0.285714 0.000000 0.000000 0.714286 0.714286 0.000000 0.285714 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.571429 0.142857 0.285714 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 0.714286 0.285714 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[CG]A[GA]CA[AT][CT][AT]C[TA][AG]C[CT]AA[CG]AA[CG] -------------------------------------------------------------------------------- Time 2.43 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 9 llr = 115 E-value = 2.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::23::3:a:248 pos.-specific C 73::1::1:2::61:2 probability G 14::673:14a::66: matrix T 22aa31399:::41:: bits 2.2 * 1.9 ** * 1.7 ** ** 1.5 ** ** ** Relative 1.3 ** ** ** Entropy 1.1 ** ** *** ** (18.4 bits) 0.9 * ** * ** *** ** 0.6 ****** ** *** ** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CGTTGGATTGGACGGA consensus TC TAG A TAAC sequence T T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11609 1 1.01e-08 . CTTTGGTTTGGATGGA GAATAGTACC 24115 257 1.55e-07 GTGGACAGAG CCTTGGATTGGATTGA CGTCGGCCGG 6796 118 2.00e-07 AGGTAGAGTA CGTTTGGTGGGATGGA TTTTGTAGTT 262803 386 3.86e-07 CGATTGACAA CCTTTGATTGGACAGC CAAGCTTCGT 24478 189 4.71e-07 TATCAGGGGA CTTTGGTTTAGACCAA ACGTTTCCCC 264269 124 6.27e-07 ATGAGTATAA TGTTGATTTCGACGAA ACAACATCAG 2759 69 1.70e-06 TTGAGCAAGA GCTTGAGTTAGATGAA GACTTGGCTG 9031 271 2.71e-06 TGTGTCTGGG TGTTTTGTTCGACGGC TGTGTTGACG 25726 148 4.48e-06 CTTGTTGACA CGTTCGACTAGACAAA TTTCAATACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11609 1e-08 [+3]_484 24115 1.6e-07 256_[+3]_228 6796 2e-07 117_[+3]_367 262803 3.9e-07 385_[+3]_99 24478 4.7e-07 188_[+3]_296 264269 6.3e-07 123_[+3]_361 2759 1.7e-06 68_[+3]_416 9031 2.7e-06 270_[+3]_214 25726 4.5e-06 147_[+3]_337 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=9 11609 ( 1) CTTTGGTTTGGATGGA 1 24115 ( 257) CCTTGGATTGGATTGA 1 6796 ( 118) CGTTTGGTGGGATGGA 1 262803 ( 386) CCTTTGATTGGACAGC 1 24478 ( 189) CTTTGGTTTAGACCAA 1 264269 ( 124) TGTTGATTTCGACGAA 1 2759 ( 69) GCTTGAGTTAGATGAA 1 9031 ( 271) TGTTTTGTTCGACGGC 1 25726 ( 148) CGTTCGACTAGACAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5335 bayes= 10.058 E= 2.9e+001 -982 152 -102 -17 -982 52 98 -17 -982 -982 -982 200 -982 -982 -982 200 -982 -106 130 42 -40 -982 157 -116 18 -982 57 42 -982 -106 -982 183 -982 -982 -102 183 18 -6 98 -982 -982 -982 215 -982 177 -982 -982 -982 -982 126 -982 83 -40 -106 130 -116 60 -982 130 -982 140 -6 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 9 E= 2.9e+001 0.000000 0.666667 0.111111 0.222222 0.000000 0.333333 0.444444 0.222222 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.555556 0.333333 0.222222 0.000000 0.666667 0.111111 0.333333 0.000000 0.333333 0.333333 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.111111 0.888889 0.333333 0.222222 0.444444 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.555556 0.000000 0.444444 0.222222 0.111111 0.555556 0.111111 0.444444 0.000000 0.555556 0.000000 0.777778 0.222222 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][GCT]TT[GT][GA][AGT]TT[GAC]GA[CT][GA][GA][AC] -------------------------------------------------------------------------------- Time 3.44 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11609 2.12e-16 [+3(1.01e-08)]_90_[+3(2.20e-05)]_\ 132_[+1(2.12e-12)]_193_[+2(9.11e-08)]_12 21152 3.39e-09 8_[+1(2.89e-08)]_149_[+2(2.18e-09)]_\ 302 24115 2.90e-07 68_[+1(3.46e-08)]_167_\ [+3(1.55e-07)]_228 24478 1.77e-03 188_[+3(4.71e-07)]_296 25726 2.20e-14 56_[+2(3.37e-11)]_71_[+3(4.48e-06)]_\ 81_[+1(2.69e-07)]_2_[+1(1.70e-09)]_212 262803 1.77e-10 30_[+1(2.69e-07)]_226_\ [+2(3.47e-08)]_88_[+3(3.86e-07)]_99 264269 3.68e-03 123_[+3(6.27e-07)]_361 268976 1.03e-08 191_[+2(8.79e-09)]_81_\ [+1(5.79e-08)]_187 2759 1.43e-09 68_[+3(1.70e-06)]_343_\ [+1(2.21e-07)]_21_[+2(9.11e-08)]_11 6796 3.63e-06 51_[+1(5.81e-07)]_45_[+3(2.00e-07)]_\ 367 9031 7.81e-10 270_[+3(2.71e-06)]_35_\ [+1(9.35e-08)]_24_[+2(7.83e-05)]_45_[+2(7.05e-08)]_49 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************