******************************************************************************** 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/336/336.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46730 1.0000 500 48518 1.0000 500 52547 1.0000 500 49624 1.0000 500 50218 1.0000 500 45463 1.0000 500 44286 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/336/336.seqs.fa -oc motifs/336 -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= 7 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= 3500 N= 7 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.301 C 0.223 G 0.207 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.301 C 0.223 G 0.207 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 7 llr = 117 E-value = 4.4e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :71::16a:::3994::1776 pos.-specific C :13::9:::97111161:13: probability G a:1:1:3:9136::::961:: matrix T :14a9:1:1:::::44:3::4 bits 2.3 * 2.0 * 1.8 * * * 1.6 * * * *** * Relative 1.4 * *** **** * Entropy 1.1 * *** **** ** ** (24.2 bits) 0.9 * *** **** ** ** ** 0.7 ** *** ******* ****** 0.5 ** ****************** 0.2 ********************* 0.0 --------------------- Multilevel GATTTCAAGCCGAAACGGAAA consensus C G GA TT T CT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 45463 378 4.15e-12 TTACATTAAG GATTTCAAGCCGAATTGGAAA AATCTGGATC 50218 378 4.15e-12 TTACATTAAG GATTTCAAGCCGAATTGGAAA AATCTGGATC 52547 228 1.27e-08 TGAGGATATT GTTTTCGAGCGAACTCGGAAT GGAGAATACG 44286 433 1.89e-08 GAAACTTCAT GACTTCTAGGGGAAACGAAAA TCAAACGCCT 49624 454 2.04e-08 TTCCGAGACG GCATTCAAGCCAAAACGTGAA GAAAAATTCT 48518 218 1.55e-07 CATACCATGC GACTTCGATCCGCAATCGCCT TCAAATCATT 46730 44 1.55e-07 GAAGAATGGA GAGTGAAAGCCCAACCGTACT CACAGAAGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45463 4.1e-12 377_[+1]_102 50218 4.1e-12 377_[+1]_102 52547 1.3e-08 227_[+1]_252 44286 1.9e-08 432_[+1]_47 49624 2e-08 453_[+1]_26 48518 1.5e-07 217_[+1]_262 46730 1.5e-07 43_[+1]_436 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=7 45463 ( 378) GATTTCAAGCCGAATTGGAAA 1 50218 ( 378) GATTTCAAGCCGAATTGGAAA 1 52547 ( 228) GTTTTCGAGCGAACTCGGAAT 1 44286 ( 433) GACTTCTAGGGGAAACGAAAA 1 49624 ( 454) GCATTCAAGCCAAAACGTGAA 1 48518 ( 218) GACTTCGATCCGCAATCGCCT 1 46730 ( 44) GAGTGAAAGCCCAACCGTACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 8.90388 E= 4.4e-003 -945 -945 227 -945 124 -64 -945 -91 -107 36 -54 67 -945 -945 -945 190 -945 -945 -54 167 -107 194 -945 -945 92 -945 46 -91 173 -945 -945 -945 -945 -945 205 -91 -945 194 -54 -945 -945 168 46 -945 -8 -64 146 -945 151 -64 -945 -945 151 -64 -945 -945 51 -64 -945 67 -945 136 -945 67 -945 -64 205 -945 -107 -945 146 9 124 -64 -54 -945 124 36 -945 -945 92 -945 -945 67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 4.4e-003 0.000000 0.000000 1.000000 0.000000 0.714286 0.142857 0.000000 0.142857 0.142857 0.285714 0.142857 0.428571 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.857143 0.142857 0.857143 0.000000 0.000000 0.571429 0.000000 0.285714 0.142857 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.857143 0.142857 0.000000 0.000000 0.714286 0.285714 0.000000 0.285714 0.142857 0.571429 0.000000 0.857143 0.142857 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.428571 0.142857 0.000000 0.428571 0.000000 0.571429 0.000000 0.428571 0.000000 0.142857 0.857143 0.000000 0.142857 0.000000 0.571429 0.285714 0.714286 0.142857 0.142857 0.000000 0.714286 0.285714 0.000000 0.000000 0.571429 0.000000 0.000000 0.428571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GA[TC]TTC[AG]AGC[CG][GA]AA[AT][CT]G[GT]A[AC][AT] -------------------------------------------------------------------------------- Time 0.42 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 5 llr = 95 E-value = 1.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::82a:::a62:8:::2:: pos.-specific C a:8:8:::a:2:4224:422 probability G :::2::a:::::2::62428 matrix T :a2::::a::284:8:8:6: bits 2.3 * * * 2.0 * * * 1.8 ** ***** 1.6 ** ***** * Relative 1.4 *** ****** ** * Entropy 1.1 ********** * **** * (27.5 bits) 0.9 ********** * **** * 0.7 ********** * ******* 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CTCACAGTCAATCATGTCTG consensus TGA CATCCCGGCC sequence T G AG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 45463 243 3.11e-12 TTAACTGTAA CTCACAGTCAATTATGTGTG TACATGCGGT 50218 243 3.11e-12 TTAACTGTAA CTCACAGTCAATTATGTGTG TACATGCGGT 46730 155 8.57e-10 GAAAACAAAG CTCACAGTCATTCACGTCCG GCGAGAAAAT 49624 291 1.20e-08 TGTATTGCTA CTTGCAGTCAATCATCGCGC GCCAAATATG 44286 56 1.52e-08 AAATTGCACA CTCAAAGTCACAGCTCTATG AAACTTATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45463 3.1e-12 242_[+2]_238 50218 3.1e-12 242_[+2]_238 46730 8.6e-10 154_[+2]_326 49624 1.2e-08 290_[+2]_190 44286 1.5e-08 55_[+2]_425 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=5 45463 ( 243) CTCACAGTCAATTATGTGTG 1 50218 ( 243) CTCACAGTCAATTATGTGTG 1 46730 ( 155) CTCACAGTCATTCACGTCCG 1 49624 ( 291) CTTGCAGTCAATCATCGCGC 1 44286 ( 56) CTCAAAGTCACAGCTCTATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 3367 bayes= 9.64506 E= 1.8e-001 -897 216 -897 -897 -897 -897 -897 189 -897 184 -897 -42 141 -897 -5 -897 -59 184 -897 -897 173 -897 -897 -897 -897 -897 227 -897 -897 -897 -897 189 -897 216 -897 -897 173 -897 -897 -897 99 -16 -897 -42 -59 -897 -897 157 -897 84 -5 57 141 -16 -897 -897 -897 -16 -897 157 -897 84 153 -897 -897 -897 -5 157 -59 84 95 -897 -897 -16 -5 116 -897 -16 195 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 5 E= 1.8e-001 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.200000 0.000000 0.200000 0.200000 0.000000 0.000000 0.800000 0.000000 0.400000 0.200000 0.400000 0.800000 0.200000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.200000 0.800000 0.200000 0.400000 0.400000 0.000000 0.000000 0.200000 0.200000 0.600000 0.000000 0.200000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CT[CT][AG][CA]AGTCA[ACT][TA][CTG][AC][TC][GC][TG][CGA][TCG][GC] -------------------------------------------------------------------------------- Time 0.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 6 llr = 106 E-value = 1.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3322:::3::2::38::::: pos.-specific C 83738:8:3:77::222:2a: probability G 22:::::::3323a::228:2 matrix T :2:5:a2a37::7:5:78::8 bits 2.3 * * 2.0 * * 1.8 * * * * 1.6 * * * * ** Relative 1.4 * **** * * **** Entropy 1.1 * * **** ** ** * **** (25.6 bits) 0.9 * * **** ***** * **** 0.7 * * **** ***** ****** 0.5 * ******************* 0.2 * ******************* 0.0 --------------------- Multilevel CACTCTCTATCCTGTATTGCT consensus CAC CGG G A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 45463 102 4.35e-12 GAGCTAGAAG CCCTCTCTAGCCTGTATTGCT GAACAATATG 50218 102 4.35e-12 GAGCTAGAAG CCCTCTCTAGCCTGTATTGCT GAACAATATG 49624 269 1.69e-09 GACTCACTGT CAACCTTTCTGCTGTATTGCT ACTTGCAGTC 48518 346 2.21e-08 AAGGCCTGAA CTCCCTCTCTCGTGACGTGCG CTGCGCTCCC 46730 77 2.77e-08 CAGAAGTAAA GACTATCTTTCAGGCATTGCT TATCCTGTAA 52547 75 7.57e-08 TCAAGGATTG CGAACTCTTTGCGGAACGCCT GGTTACTTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45463 4.3e-12 101_[+3]_378 50218 4.3e-12 101_[+3]_378 49624 1.7e-09 268_[+3]_211 48518 2.2e-08 345_[+3]_134 46730 2.8e-08 76_[+3]_403 52547 7.6e-08 74_[+3]_405 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=6 45463 ( 102) CCCTCTCTAGCCTGTATTGCT 1 50218 ( 102) CCCTCTCTAGCCTGTATTGCT 1 49624 ( 269) CAACCTTTCTGCTGTATTGCT 1 48518 ( 346) CTCCCTCTCTCGTGACGTGCG 1 46730 ( 77) GACTATCTTTCAGGCATTGCT 1 52547 ( 75) CGAACTCTTTGCGGAACGCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 9.57485 E= 1.3e-001 -923 190 -31 -923 15 58 -31 -69 15 158 -923 -923 -85 58 -923 90 -85 190 -923 -923 -923 -923 -923 189 -923 190 -923 -69 -923 -923 -923 189 15 58 -923 31 -923 -923 69 131 -923 158 69 -923 -85 158 -31 -923 -923 -923 69 131 -923 -923 227 -923 15 -42 -923 90 147 -42 -923 -923 -923 -42 -31 131 -923 -923 -31 163 -923 -42 201 -923 -923 216 -923 -923 -923 -923 -31 163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 1.3e-001 0.000000 0.833333 0.166667 0.000000 0.333333 0.333333 0.166667 0.166667 0.333333 0.666667 0.000000 0.000000 0.166667 0.333333 0.000000 0.500000 0.166667 0.833333 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.333333 0.333333 0.000000 0.333333 0.000000 0.000000 0.333333 0.666667 0.000000 0.666667 0.333333 0.000000 0.166667 0.666667 0.166667 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.333333 0.166667 0.000000 0.500000 0.833333 0.166667 0.000000 0.000000 0.000000 0.166667 0.166667 0.666667 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AC][CA][TC]CTCT[ACT][TG][CG]C[TG]G[TA]ATTGCT -------------------------------------------------------------------------------- Time 1.22 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46730 2.71e-13 43_[+1(1.55e-07)]_12_[+3(2.77e-08)]_\ 57_[+2(8.57e-10)]_326 48518 3.79e-08 217_[+1(1.55e-07)]_107_\ [+3(2.21e-08)]_134 52547 5.85e-08 74_[+3(7.57e-08)]_132_\ [+1(1.27e-08)]_252 49624 3.42e-14 268_[+3(1.69e-09)]_1_[+2(1.20e-08)]_\ 143_[+1(2.04e-08)]_26 50218 1.17e-23 101_[+3(4.35e-12)]_120_\ [+2(3.11e-12)]_115_[+1(4.15e-12)]_102 45463 1.17e-23 101_[+3(4.35e-12)]_120_\ [+2(3.11e-12)]_115_[+1(4.15e-12)]_102 44286 1.83e-08 55_[+2(1.52e-08)]_357_\ [+1(1.89e-08)]_47 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************