******************************************************************************** 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/442/442.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11168 1.0000 500 11199 1.0000 500 11858 1.0000 500 15972 1.0000 500 17095 1.0000 500 22560 1.0000 500 4191 1.0000 500 7282 1.0000 500 8215 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/442/442.seqs.fa -oc motifs/442 -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= 9 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= 4500 N= 9 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.251 G 0.210 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.251 G 0.210 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 8 llr = 107 E-value = 4.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :1:34:13:833:::: pos.-specific C :::::133::1:1::: probability G ::a1:911a13:5:3a matrix T a9:66:54:1484a8: bits 2.2 * * * 2.0 * * * 1.8 * * * * * 1.6 * * * * * * Relative 1.3 *** * * * * Entropy 1.1 *** * * * *** (19.3 bits) 0.9 *** ** ** * *** 0.7 ****** ** ***** 0.4 ****** ** ***** 0.2 ******* ** ***** 0.0 ---------------- Multilevel TTGTTGTTGATTGTTG consensus AA CA AAT G sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11858 153 2.12e-10 GCTGTTGGAT TTGTTGTTGATTGTTG TGTTGCTGAC 22560 237 5.61e-09 GTCTCCGTCG TTGTTGCCGATTGTTG AATCATGATT 11199 248 9.21e-08 TTCTCCAAAA TTGTTCTTGAATGTTG TCCCCCACTT 15972 156 1.15e-07 AGAGTAAAGG TTGTAGTTGAAATTTG TGAAGGGTTG 4191 59 3.56e-07 AGAGTGACAT TTGAAGGAGATTTTTG GAAGGAGATA 17095 16 1.63e-06 GCTTTTAGTT TTGATGACGAGTCTGG CTGTTCTGCG 8215 479 1.92e-06 ATTGCACTGA TAGGTGTAGTGTGTTG CTTCCA 7282 36 4.31e-06 TGGAAACCTT TTGTAGCGGGCATTGG GGAGAGATAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11858 2.1e-10 152_[+1]_332 22560 5.6e-09 236_[+1]_248 11199 9.2e-08 247_[+1]_237 15972 1.2e-07 155_[+1]_329 4191 3.6e-07 58_[+1]_426 17095 1.6e-06 15_[+1]_469 8215 1.9e-06 478_[+1]_6 7282 4.3e-06 35_[+1]_449 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=8 11858 ( 153) TTGTTGTTGATTGTTG 1 22560 ( 237) TTGTTGCCGATTGTTG 1 11199 ( 248) TTGTTCTTGAATGTTG 1 15972 ( 156) TTGTAGTTGAAATTTG 1 4191 ( 59) TTGAAGGAGATTTTTG 1 17095 ( 16) TTGATGACGAGTCTGG 1 8215 ( 479) TAGGTGTAGTGTGTTG 1 7282 ( 36) TTGTAGCGGGCATTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4365 bayes= 9.08912 E= 4.5e-002 -965 -965 -965 190 -111 -965 -965 171 -965 -965 225 -965 -12 -965 -75 122 47 -965 -965 122 -965 -100 206 -965 -111 0 -75 90 -12 0 -75 48 -965 -965 225 -965 147 -965 -75 -110 -12 -100 25 48 -12 -965 -965 148 -965 -100 125 48 -965 -965 -965 190 -965 -965 25 148 -965 -965 225 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 4.5e-002 0.000000 0.000000 0.000000 1.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.125000 0.625000 0.375000 0.000000 0.000000 0.625000 0.000000 0.125000 0.875000 0.000000 0.125000 0.250000 0.125000 0.500000 0.250000 0.250000 0.125000 0.375000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.125000 0.125000 0.250000 0.125000 0.250000 0.375000 0.250000 0.000000 0.000000 0.750000 0.000000 0.125000 0.500000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTG[TA][TA]G[TC][TAC]GA[TAG][TA][GT]T[TG]G -------------------------------------------------------------------------------- Time 0.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 9 llr = 108 E-value = 2.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3:714621::23:: pos.-specific C :3::23::::6:::3 probability G a182722:1a4:7:7 matrix T :221::288::8:a: bits 2.2 * * 2.0 * * 1.8 * * * 1.6 * * * Relative 1.3 * * * ** Entropy 1.1 * * * ****** (17.3 bits) 0.9 * * * ******** 0.7 * *** ******** 0.4 * ************* 0.2 * ************* 0.0 --------------- Multilevel GAGAGAATTGCTGTG consensus CTGCCGA GAA C sequence T GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 11858 118 5.55e-10 CGTCTCCCGA GCGAGAATTGCTGTG CCATGGTATT 17095 39 2.86e-07 TGGCTGTTCT GCGAGCTATGGTGTG CGTTCGTCGG 8215 291 5.05e-07 GCAAACGGCA GAGAAAGTTGGTGTG TCTACGCAAG 11199 369 7.91e-07 GGTTTGCTAT GTGGGCATGGCTGTG GGCCCGGAAT 15972 29 1.54e-06 GTGTAGCACA GCGACGATTGCAGTC TCCTCTCAAG 4191 238 2.78e-06 CCATCACTTT GATGGCATTGCTATC ACTCGCGAAT 22560 423 3.22e-06 CTCAGGTTCG GTGACATTTGGTATC ACCTCCCGAG 11168 393 3.73e-06 AAGTATCTTA GAGTGAGTTGCAATG ATTGGATGCG 7282 117 1.03e-05 AGAGCCACCG GGTAGGAAAGGTGTG ACATCTGTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11858 5.5e-10 117_[+2]_368 17095 2.9e-07 38_[+2]_447 8215 5e-07 290_[+2]_195 11199 7.9e-07 368_[+2]_117 15972 1.5e-06 28_[+2]_457 4191 2.8e-06 237_[+2]_248 22560 3.2e-06 422_[+2]_63 11168 3.7e-06 392_[+2]_93 7282 1e-05 116_[+2]_369 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=9 11858 ( 118) GCGAGAATTGCTGTG 1 17095 ( 39) GCGAGCTATGGTGTG 1 8215 ( 291) GAGAAAGTTGGTGTG 1 11199 ( 369) GTGGGCATGGCTGTG 1 15972 ( 29) GCGACGATTGCAGTC 1 4191 ( 238) GATGGCATTGCTATC 1 22560 ( 423) GTGACATTTGGTATC 1 11168 ( 393) GAGTGAGTTGCAATG 1 7282 ( 117) GGTAGGAAAGGTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4374 bayes= 9.05641 E= 2.3e+000 -982 -982 225 -982 30 41 -92 -27 -982 -982 189 -27 130 -982 8 -127 -128 -17 166 -982 71 41 8 -982 103 -982 8 -27 -29 -982 -982 154 -128 -982 -92 154 -982 -982 225 -982 -982 115 108 -982 -29 -982 -982 154 30 -982 166 -982 -982 -982 -982 190 -982 41 166 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.3e+000 0.000000 0.000000 1.000000 0.000000 0.333333 0.333333 0.111111 0.222222 0.000000 0.000000 0.777778 0.222222 0.666667 0.000000 0.222222 0.111111 0.111111 0.222222 0.666667 0.000000 0.444444 0.333333 0.222222 0.000000 0.555556 0.000000 0.222222 0.222222 0.222222 0.000000 0.000000 0.777778 0.111111 0.000000 0.111111 0.777778 0.000000 0.000000 1.000000 0.000000 0.000000 0.555556 0.444444 0.000000 0.222222 0.000000 0.000000 0.777778 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[ACT][GT][AG][GC][ACG][AGT][TA]TG[CG][TA][GA]T[GC] -------------------------------------------------------------------------------- Time 1.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 95 E-value = 2.8e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::22:2:42::::22:::44: pos.-specific C 8a2:a8:48:a2:8822a4:a probability G 2:44::42:2::a::8:::6: matrix T ::24::6::8:8::::8:2:: bits 2.2 * 2.0 * * * * * * 1.8 * * * * * * 1.6 * * * * * * * Relative 1.3 ** ** *** **** * * Entropy 1.1 ** *** ********** ** (27.4 bits) 0.9 ** *** ********** ** 0.7 ** *** ********** ** 0.4 ** ****************** 0.2 ********************* 0.0 --------------------- Multilevel CCGGCCTACTCTGCCGTCAGC consensus G AT AGCAG C AACC CA sequence CA G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 4191 388 1.88e-12 TGACCCCTCT CCGTCCTACTCTGCCGTCAGC GGCCTCCCTC 11858 401 1.88e-12 CTGCCCCTCT CCGTCCTACTCTGCCGTCAGC AGCTCGCAGT 11168 223 6.63e-09 CTTTATTCAT CCAGCATCATCTGACGTCCAC TCTCTTGCTC 17095 452 8.54e-09 TTTCCCCAAC CCTACCGGCTCTGCACTCTGC AGACAAAGAC 11199 101 1.03e-08 GATCCTCGCC GCCGCCGCCGCCGCCGCCCAC TAACGACACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4191 1.9e-12 387_[+3]_92 11858 1.9e-12 400_[+3]_79 11168 6.6e-09 222_[+3]_257 17095 8.5e-09 451_[+3]_28 11199 1e-08 100_[+3]_379 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 4191 ( 388) CCGTCCTACTCTGCCGTCAGC 1 11858 ( 401) CCGTCCTACTCTGCCGTCAGC 1 11168 ( 223) CCAGCATCATCTGACGTCCAC 1 17095 ( 452) CCTACCGGCTCTGCACTCTGC 1 11199 ( 101) GCCGCCGCCGCCGCCGCCCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4320 bayes= 10.005 E= 2.8e+000 -897 167 -7 -897 -897 199 -897 -897 -44 -33 93 -42 -44 -897 93 58 -897 199 -897 -897 -44 167 -897 -897 -897 -897 93 116 56 67 -7 -897 -44 167 -897 -897 -897 -897 -7 158 -897 199 -897 -897 -897 -33 -897 158 -897 -897 225 -897 -44 167 -897 -897 -44 167 -897 -897 -897 -33 193 -897 -897 -33 -897 158 -897 199 -897 -897 56 67 -897 -42 56 -897 151 -897 -897 199 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 2.8e+000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.200000 0.400000 0.200000 0.200000 0.000000 0.400000 0.400000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.400000 0.400000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.400000 0.400000 0.000000 0.200000 0.400000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CG]C[GACT][GTA]C[CA][TG][ACG][CA][TG]C[TC]G[CA][CA][GC][TC]C[ACT][GA]C -------------------------------------------------------------------------------- Time 2.27 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11168 6.50e-07 222_[+3(6.63e-09)]_149_\ [+2(3.73e-06)]_93 11199 4.09e-11 100_[+3(1.03e-08)]_126_\ [+1(9.21e-08)]_105_[+2(7.91e-07)]_117 11858 3.50e-20 117_[+2(5.55e-10)]_20_\ [+1(2.12e-10)]_232_[+3(1.88e-12)]_79 15972 1.72e-06 28_[+2(1.54e-06)]_112_\ [+1(1.15e-07)]_107_[+1(8.41e-05)]_206 17095 1.95e-10 15_[+1(1.63e-06)]_7_[+2(2.86e-07)]_\ 398_[+3(8.54e-09)]_28 22560 8.55e-07 236_[+1(5.61e-09)]_170_\ [+2(3.22e-06)]_63 4191 1.44e-13 58_[+1(3.56e-07)]_163_\ [+2(2.78e-06)]_135_[+3(1.88e-12)]_92 7282 7.71e-04 35_[+1(4.31e-06)]_65_[+2(1.03e-05)]_\ 369 8215 2.78e-05 290_[+2(5.05e-07)]_173_\ [+1(1.92e-06)]_6 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************