******************************************************************************** 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/345/345.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11727 1.0000 500 1586 1.0000 500 19637 1.0000 500 2047 1.0000 500 21991 1.0000 500 262000 1.0000 500 269547 1.0000 500 32015 1.0000 500 9299 1.0000 500 bd811 1.0000 500 bd828 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/345/345.seqs.fa -oc motifs/345 -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 0.278 C 0.238 G 0.231 T 0.253 Background letter frequencies (from dataset with add-one prior applied): A 0.278 C 0.238 G 0.231 T 0.253 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 124 E-value = 1.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 8:1a6:1a514:6a:: pos.-specific C 27::2a1:13:7::38 probability G ::5:1:8::52:4::1 matrix T :34:1:::4143::71 bits 2.1 * 1.9 * * * * 1.7 * * * * 1.5 * * * * Relative 1.3 * * * * * Entropy 1.1 ** * *** ***** (17.9 bits) 0.8 ** * *** ***** 0.6 **** **** ***** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel ACGAACGAAGACAATC consensus CTT C TCTTG C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- bd828 136 4.15e-08 AAAAGCGGCT ACTAACGAAGATGATC CGTTAGCATC 2047 268 4.15e-08 AAAAGCGGCT ACTAACGAAGATGATC CGTTAGCATC 21991 410 1.13e-07 TCGTTTGTAT ACTAACGATTTCAATC ATGTTTCGAA bd811 183 7.85e-07 GGCAGCGGTT CCGACCGAACTCGACC CTACCCTCCC 19637 385 9.35e-07 TCTTCTTTTC ATGAACGATGTCAACG GAAGCAAACA 11727 143 1.02e-06 TGGGAGGGAA ACGAACGACGACGATT CTGCCTCCTC 269547 256 1.43e-06 CGCCATTTGG ACTACCAATGGCAATC ATTCTCTCCA 262000 139 1.43e-06 ATTGTTCCCA ATGATCGATCATAATC TTGCAACGAT 1586 241 2.41e-06 GCCAATCTAA CCAAACGAACGCAACC GTAACAATAG 32015 60 7.53e-06 CGGTGGAATT ATGAGCCAAATCAATC AATCCAAAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd828 4.2e-08 135_[+1]_349 2047 4.2e-08 267_[+1]_217 21991 1.1e-07 409_[+1]_75 bd811 7.8e-07 182_[+1]_302 19637 9.4e-07 384_[+1]_100 11727 1e-06 142_[+1]_342 269547 1.4e-06 255_[+1]_229 262000 1.4e-06 138_[+1]_346 1586 2.4e-06 240_[+1]_244 32015 7.5e-06 59_[+1]_425 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 bd828 ( 136) ACTAACGAAGATGATC 1 2047 ( 268) ACTAACGAAGATGATC 1 21991 ( 410) ACTAACGATTTCAATC 1 bd811 ( 183) CCGACCGAACTCGACC 1 19637 ( 385) ATGAACGATGTCAACG 1 11727 ( 143) ACGAACGACGACGATT 1 269547 ( 256) ACTACCAATGGCAATC 1 262000 ( 139) ATGATCGATCATAATC 1 1586 ( 241) CCAAACGAACGCAACC 1 32015 ( 60) ATGAGCCAAATCAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5335 bayes= 8.94539 E= 1.1e+000 153 -25 -997 -997 -997 156 -997 24 -147 -997 111 66 185 -997 -997 -997 111 -25 -121 -134 -997 207 -997 -997 -147 -125 179 -997 185 -997 -997 -997 85 -125 -997 66 -147 33 111 -134 53 -997 -21 66 -997 156 -997 24 111 -997 79 -997 185 -997 -997 -997 -997 33 -997 146 -997 175 -121 -134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 1.1e+000 0.800000 0.200000 0.000000 0.000000 0.000000 0.700000 0.000000 0.300000 0.100000 0.000000 0.500000 0.400000 1.000000 0.000000 0.000000 0.000000 0.600000 0.200000 0.100000 0.100000 0.000000 1.000000 0.000000 0.000000 0.100000 0.100000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.100000 0.000000 0.400000 0.100000 0.300000 0.500000 0.100000 0.400000 0.000000 0.200000 0.400000 0.000000 0.700000 0.000000 0.300000 0.600000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.700000 0.000000 0.800000 0.100000 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC][CT][GT]A[AC]CGA[AT][GC][ATG][CT][AG]A[TC]C -------------------------------------------------------------------------------- Time 0.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 87 E-value = 7.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3::3:::::a:::5::85:5: pos.-specific C ::::3:::3::3a5:8::35: probability G :a5:8a:a8:a3::a335::a matrix T 8:58::a::::5::::::8:: bits 2.1 * * * * * * * 1.9 * *** ** * * * 1.7 * *** ** * * * 1.5 * *** ** * * * Relative 1.3 * ******* * ** * * Entropy 1.1 *********** ********* (31.5 bits) 0.8 *********** ********* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TGGTGGTGGAGTCAGCAATAG consensus A TAC C C C GGGCC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd828 302 1.52e-12 TATCACAAAA TGTTGGTGGAGTCCGCAATCG ATTACGCTTT 2047 434 1.52e-12 TATCACAAAA TGTTGGTGGAGTCCGCAATCG ATTACGCTTT 269547 193 1.37e-10 TGCTCCGTCT TGGTGGTGCAGCCAGCAGCAG CAGTTCATCC bd811 473 7.78e-10 ATGGGGGCCG AGGACGTGGAGGCAGGGGTAG AGGAAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd828 1.5e-12 301_[+2]_178 2047 1.5e-12 433_[+2]_46 269547 1.4e-10 192_[+2]_287 bd811 7.8e-10 472_[+2]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 bd828 ( 302) TGTTGGTGGAGTCCGCAATCG 1 2047 ( 434) TGTTGGTGGAGTCCGCAATCG 1 269547 ( 193) TGGTGGTGCAGCCAGCAGCAG 1 bd811 ( 473) AGGACGTGGAGGCAGGGGTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 10.3652 E= 7.0e+000 -15 -865 -865 156 -865 -865 211 -865 -865 -865 111 98 -15 -865 -865 156 -865 7 170 -865 -865 -865 211 -865 -865 -865 -865 198 -865 -865 211 -865 -865 7 170 -865 185 -865 -865 -865 -865 -865 211 -865 -865 7 11 98 -865 207 -865 -865 85 107 -865 -865 -865 -865 211 -865 -865 165 11 -865 143 -865 11 -865 85 -865 111 -865 -865 7 -865 156 85 107 -865 -865 -865 -865 211 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 7.0e+000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.250000 0.000000 0.000000 0.750000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.250000 0.000000 0.750000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TA]G[GT][TA][GC]GTG[GC]AG[TCG]C[AC]G[CG][AG][AG][TC][AC]G -------------------------------------------------------------------------------- Time 2.00 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 11 llr = 145 E-value = 2.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :432:123:::3115:9327: pos.-specific C 13225735a322:::1::5:: probability G ::2:21::::8:2855:5:3: matrix T 94464153:7:57115134:a bits 2.1 * 1.9 * * 1.7 * * 1.5 * * * * * Relative 1.3 * * * * * * Entropy 1.1 * *** * * ** (19.0 bits) 0.8 * * *** ** * ** 0.6 * **** *** ***** ** 0.4 ** ****************** 0.2 ** ****************** 0.0 --------------------- Multilevel TATTCCTCCTGTTGAGAGCAT consensus TA T CA C A GT ATG sequence C T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd828 174 6.29e-11 TTGAAATTGA TATTCCTCCTGTTGGGAATAT CAATCTCAGT 2047 306 6.29e-11 TTGAAATTGA TATTCCTCCTGTTGGGAATAT CAATCTCAGT 262000 91 3.19e-08 GTTTGTTGTC TTCTGCTTCTGATGATATTAT GCCGCAAGTA 21991 69 7.16e-08 TGGAGCGGCA TCAATCTCCCGATGATATCAT GTTCTTGACC 1586 189 4.92e-07 AGCTTGTTCT TATCGCTACTCCTGATAACAT ACAACATCTA 269547 10 1.45e-06 TCATCGGCT TTGTCATTCTGTTTGGAGAGT TTGAAACGTC 11727 43 1.45e-06 CTGCGGGGGT TCAACCCACTGAGGGCAGCGT ACACTCGGCA 19637 142 1.78e-06 GAGGACATAC TTTTTCACCTCTGAGGAGTGT GCTTAAGCAC 32015 384 1.91e-06 ATCGGAGATC TCATTGATCCGTTGTTATCAT TGTTGTACAG 9299 137 2.17e-06 TTGTCCAATA TAGTTTCCCCGTTGAGTGAAT TGTAGTAGCT bd811 204 3.36e-06 CGACCCTACC CTCCCCCACTGCAGATAGCAT ACCGACGGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd828 6.3e-11 173_[+3]_306 2047 6.3e-11 305_[+3]_174 262000 3.2e-08 90_[+3]_389 21991 7.2e-08 68_[+3]_411 1586 4.9e-07 188_[+3]_291 269547 1.4e-06 9_[+3]_470 11727 1.4e-06 42_[+3]_437 19637 1.8e-06 141_[+3]_338 32015 1.9e-06 383_[+3]_96 9299 2.2e-06 136_[+3]_343 bd811 3.4e-06 203_[+3]_276 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=11 bd828 ( 174) TATTCCTCCTGTTGGGAATAT 1 2047 ( 306) TATTCCTCCTGTTGGGAATAT 1 262000 ( 91) TTCTGCTTCTGATGATATTAT 1 21991 ( 69) TCAATCTCCCGATGATATCAT 1 1586 ( 189) TATCGCTACTCCTGATAACAT 1 269547 ( 10) TTGTCATTCTGTTTGGAGAGT 1 11727 ( 43) TCAACCCACTGAGGGCAGCGT 1 19637 ( 142) TTTTTCACCTCTGAGGAGTGT 1 32015 ( 384) TCATTGATCCGTTGTTATCAT 1 9299 ( 137) TAGTTTCCCCGTTGAGTGAAT 1 bd811 ( 204) CTCCCCCACTGCAGATAGCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 8.90388 E= 2.7e+000 -1010 -139 -1010 184 39 20 -1010 52 -3 -39 -34 52 -61 -39 -1010 133 -1010 93 -34 52 -161 161 -134 -148 -61 20 -1010 111 -3 93 -1010 11 -1010 207 -1010 -1010 -1010 20 -1010 152 -1010 -39 182 -1010 -3 -39 -1010 111 -161 -1010 -34 152 -161 -1010 182 -148 71 -1010 98 -148 -1010 -139 98 84 171 -1010 -1010 -148 -3 -1010 98 11 -61 93 -1010 52 139 -1010 24 -1010 -1010 -1010 -1010 198 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 2.7e+000 0.000000 0.090909 0.000000 0.909091 0.363636 0.272727 0.000000 0.363636 0.272727 0.181818 0.181818 0.363636 0.181818 0.181818 0.000000 0.636364 0.000000 0.454545 0.181818 0.363636 0.090909 0.727273 0.090909 0.090909 0.181818 0.272727 0.000000 0.545455 0.272727 0.454545 0.000000 0.272727 0.000000 1.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.727273 0.000000 0.181818 0.818182 0.000000 0.272727 0.181818 0.000000 0.545455 0.090909 0.000000 0.181818 0.727273 0.090909 0.000000 0.818182 0.090909 0.454545 0.000000 0.454545 0.090909 0.000000 0.090909 0.454545 0.454545 0.909091 0.000000 0.000000 0.090909 0.272727 0.000000 0.454545 0.272727 0.181818 0.454545 0.000000 0.363636 0.727273 0.000000 0.272727 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[ATC][TA]T[CT]C[TC][CAT]C[TC]G[TA]TG[AG][GT]A[GAT][CT][AG]T -------------------------------------------------------------------------------- Time 2.94 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11727 1.71e-05 42_[+3(1.45e-06)]_79_[+1(1.02e-06)]_\ 342 1586 1.24e-05 188_[+3(4.92e-07)]_31_\ [+1(2.41e-06)]_244 19637 3.84e-05 141_[+3(1.78e-06)]_222_\ [+1(9.35e-07)]_100 2047 5.59e-19 267_[+1(4.15e-08)]_22_\ [+3(6.29e-11)]_107_[+2(1.52e-12)]_46 21991 4.04e-07 68_[+3(7.16e-08)]_320_\ [+1(1.13e-07)]_75 262000 1.95e-06 90_[+3(3.19e-08)]_27_[+1(1.43e-06)]_\ 346 269547 1.63e-11 9_[+3(1.45e-06)]_162_[+2(1.37e-10)]_\ 42_[+1(1.43e-06)]_229 32015 1.63e-04 59_[+1(7.53e-06)]_308_\ [+3(1.91e-06)]_96 9299 5.87e-03 136_[+3(2.17e-06)]_343 bd811 1.04e-10 182_[+1(7.85e-07)]_5_[+3(3.36e-06)]_\ 248_[+2(7.78e-10)]_7 bd828 5.59e-19 135_[+1(4.15e-08)]_22_\ [+3(6.29e-11)]_107_[+2(1.52e-12)]_178 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************