******************************************************************************** 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/53/53.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 43104 1.0000 500 1785 1.0000 500 39090 1.0000 500 43559 1.0000 500 43759 1.0000 500 41042 1.0000 500 44086 1.0000 500 43056 1.0000 500 47628 1.0000 500 50286 1.0000 500 45920 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/53/53.seqs.fa -oc motifs/53 -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 0.301 C 0.215 G 0.224 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.301 C 0.215 G 0.224 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 10 llr = 108 E-value = 6.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::a:2:1:81 pos.-specific C 32:2:7:112:: probability G 62:8:::9:828 matrix T 16a::38:8::1 bits 2.2 2.0 * 1.8 * * * 1.6 *** * * Relative 1.3 **** * * Entropy 1.1 ********** (15.5 bits) 0.9 * ********** 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GTTGACTGTGAG consensus CC C TA CG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 41042 129 5.17e-07 AGGTTGTGAT CCTGACTGTGAG AATGTTCCGT 45920 265 8.13e-07 TTGCATCATG TTTGACTGTGAG ACATGAATAT 43056 277 1.23e-06 GATTACACTT CTTGACAGTGAG CGTACATTAA 43759 97 1.58e-06 GAAAGGAAGA GTTGACTGTGAA TGTGAGCACG 44086 359 2.06e-06 CACGGATCGC CGTGACTGTGGG TAGCCAAATA 43104 227 5.25e-06 ACGAGAAATG GGTGATAGTGAG CAGCTGTCCT 47628 304 5.47e-06 AATCACTCGA GTTCACTCTGAG GGAATATAGG 43559 21 8.26e-06 TAATGCGAGT GTTGATTGCGGG AGCTCCAAGC 1785 162 1.37e-05 GAAATTGGTG GCTGACTGACAG ACGATAAAAA 39090 479 3.88e-05 TGGTCCACGT GTTCATTGTCAT CATCATCATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41042 5.2e-07 128_[+1]_360 45920 8.1e-07 264_[+1]_224 43056 1.2e-06 276_[+1]_212 43759 1.6e-06 96_[+1]_392 44086 2.1e-06 358_[+1]_130 43104 5.3e-06 226_[+1]_262 47628 5.5e-06 303_[+1]_185 43559 8.3e-06 20_[+1]_468 1785 1.4e-05 161_[+1]_327 39090 3.9e-05 478_[+1]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=10 41042 ( 129) CCTGACTGTGAG 1 45920 ( 265) TTTGACTGTGAG 1 43056 ( 277) CTTGACAGTGAG 1 43759 ( 97) GTTGACTGTGAA 1 44086 ( 359) CGTGACTGTGGG 1 43104 ( 227) GGTGATAGTGAG 1 47628 ( 304) GTTCACTCTGAG 1 43559 ( 21) GTTGATTGCGGG 1 1785 ( 162) GCTGACTGACAG 1 39090 ( 479) GTTCATTGTCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 10.0132 E= 6.4e+000 -997 48 142 -138 -997 -10 -16 121 -997 -997 -997 194 -997 -10 184 -997 173 -997 -997 -997 -997 170 -997 21 -59 -997 -997 162 -997 -110 201 -997 -159 -110 -997 162 -997 -10 184 -997 141 -997 -16 -997 -159 -997 184 -138 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 6.4e+000 0.000000 0.300000 0.600000 0.100000 0.000000 0.200000 0.200000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.700000 0.000000 0.300000 0.200000 0.000000 0.000000 0.800000 0.000000 0.100000 0.900000 0.000000 0.100000 0.100000 0.000000 0.800000 0.000000 0.200000 0.800000 0.000000 0.800000 0.000000 0.200000 0.000000 0.100000 0.000000 0.800000 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC][TCG]T[GC]A[CT][TA]GT[GC][AG]G -------------------------------------------------------------------------------- Time 1.41 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 10 llr = 103 E-value = 2.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2::::::2:2:: pos.-specific C 81:544::7417 probability G :::5:::2:2:3 matrix T :9a:66a6329: bits 2.2 2.0 * * 1.8 * * 1.6 ** * * Relative 1.3 *** * * ** Entropy 1.1 ******* * ** (14.9 bits) 0.9 ******* * ** 0.7 ********* ** 0.4 ********* ** 0.2 ************ 0.0 ------------ Multilevel CTTCTTTTCCTC consensus A GCC ATA G sequence G G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 50286 318 2.25e-07 CATCAACCAC CTTCCCTTCCTC GCTTTACCCT 43104 264 1.11e-06 GGATCAGTGA CTTGTCTTCTTC AAACATTCCA 39090 435 2.43e-06 TCTGTCTATA CTTCTTTGCGTC TGTGTGCGTC 43559 43 8.11e-06 AGCTCCAAGC ATTGTTTTCGTC TTATTCTTTT 47628 458 8.99e-06 TTTTTGGAAC CTTGCCTACCTG GGAAATTTTG 1785 248 8.99e-06 AGTGGCTTCA CTTCTTTGCTTG AGACTTTCTG 41042 429 1.04e-05 AGTGTTGTTG CTTGCCTATCTC CAGACGTTTA 45920 465 1.28e-05 TAGCCTATAA ATTCCTTTTCTC CTTCTGTACA 44086 341 2.84e-05 AAAGCCGCAG CTTGTTTTCACG GATCGCCGTG 43056 189 3.05e-05 TCAGCAACCA CCTCTTTTTATC TTAGGTGATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50286 2.3e-07 317_[+2]_171 43104 1.1e-06 263_[+2]_225 39090 2.4e-06 434_[+2]_54 43559 8.1e-06 42_[+2]_446 47628 9e-06 457_[+2]_31 1785 9e-06 247_[+2]_241 41042 1e-05 428_[+2]_60 45920 1.3e-05 464_[+2]_24 44086 2.8e-05 340_[+2]_148 43056 3e-05 188_[+2]_300 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=10 50286 ( 318) CTTCCCTTCCTC 1 43104 ( 264) CTTGTCTTCTTC 1 39090 ( 435) CTTCTTTGCGTC 1 43559 ( 43) ATTGTTTTCGTC 1 47628 ( 458) CTTGCCTACCTG 1 1785 ( 248) CTTCTTTGCTTG 1 41042 ( 429) CTTGCCTATCTC 1 45920 ( 465) ATTCCTTTTCTC 1 44086 ( 341) CTTGTTTTCACG 1 43056 ( 189) CCTCTTTTTATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 10.0132 E= 2.5e+001 -59 190 -997 -997 -997 -110 -997 179 -997 -997 -997 194 -997 122 116 -997 -997 90 -997 121 -997 90 -997 121 -997 -997 -997 194 -59 -997 -16 121 -997 170 -997 21 -59 90 -16 -38 -997 -110 -997 179 -997 170 42 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 2.5e+001 0.200000 0.800000 0.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.200000 0.600000 0.000000 0.700000 0.000000 0.300000 0.200000 0.400000 0.200000 0.200000 0.000000 0.100000 0.000000 0.900000 0.000000 0.700000 0.300000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA]TT[CG][TC][TC]T[TAG][CT][CAGT]T[CG] -------------------------------------------------------------------------------- Time 2.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 7 llr = 111 E-value = 6.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 7:14::::9a:4191:7aa6 pos.-specific C 1a:14::1::1:3::1:::4 probability G ::1:1469:::641:73::: matrix T 1:74464:1:9:1:91:::: bits 2.2 * 2.0 * 1.8 * * ** 1.6 * * * ** Relative 1.3 * * ** * ** Entropy 1.1 * ****** ** ** (22.9 bits) 0.9 ** ******* ******* 0.7 *** ******** ******* 0.4 ************ ******* 0.2 ******************** 0.0 -------------------- Multilevel ACTACTGGAATGGATGAAAA consensus TTGT AC G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 47628 207 1.01e-09 GCAAGCCCCG ACGACTGGAATGCATGAAAC CGCCCATCAC 41042 390 8.12e-09 AAAGATATCC ACTACTGGTATGGGTGAAAA TTGATGCACA 43104 346 9.00e-09 AGACCTTAAC CCTATTGCAATGGATGAAAC ATATTGATGT 43559 438 2.36e-08 ACAAACTGAT ACTCGGGGAATGCATCAAAA GACGAACTCG 44086 266 3.05e-08 TATATGAAAA ACATTGTGAATATATGAAAA ACATTTTGGA 45920 96 6.55e-08 CCTTGCAGCT TCTTTGTGAATAGATTGAAC GAAAGAAAAA 39090 276 1.99e-07 AGATGTCTGT ACTTCTTGAACAAAAGGAAA CCCGGAGTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47628 1e-09 206_[+3]_274 41042 8.1e-09 389_[+3]_91 43104 9e-09 345_[+3]_135 43559 2.4e-08 437_[+3]_43 44086 3.1e-08 265_[+3]_215 45920 6.6e-08 95_[+3]_385 39090 2e-07 275_[+3]_205 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=7 47628 ( 207) ACGACTGGAATGCATGAAAC 1 41042 ( 390) ACTACTGGTATGGGTGAAAA 1 43104 ( 346) CCTATTGCAATGGATGAAAC 1 43559 ( 438) ACTCGGGGAATGCATCAAAA 1 44086 ( 266) ACATTGTGAATATATGAAAA 1 45920 ( 96) TCTTTGTGAATAGATTGAAC 1 39090 ( 276) ACTTCTTGAACAAAAGGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 5291 bayes= 9.40372 E= 6.8e+001 124 -59 -945 -86 -945 222 -945 -945 -107 -945 -65 146 51 -59 -945 72 -945 100 -65 72 -945 -945 93 113 -945 -945 135 72 -945 -59 193 -945 151 -945 -945 -86 173 -945 -945 -945 -945 -59 -945 172 51 -945 135 -945 -107 41 93 -86 151 -945 -65 -945 -107 -945 -945 172 -945 -59 167 -86 124 -945 35 -945 173 -945 -945 -945 173 -945 -945 -945 92 100 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 7 E= 6.8e+001 0.714286 0.142857 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.142857 0.000000 0.142857 0.714286 0.428571 0.142857 0.000000 0.428571 0.000000 0.428571 0.142857 0.428571 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.571429 0.428571 0.000000 0.142857 0.857143 0.000000 0.857143 0.000000 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.857143 0.428571 0.000000 0.571429 0.000000 0.142857 0.285714 0.428571 0.142857 0.857143 0.000000 0.142857 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.142857 0.714286 0.142857 0.714286 0.000000 0.285714 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- ACT[AT][CT][TG][GT]GAAT[GA][GC]ATG[AG]AA[AC] -------------------------------------------------------------------------------- Time 3.54 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43104 2.17e-09 226_[+1(5.25e-06)]_25_\ [+2(1.11e-06)]_70_[+3(9.00e-09)]_135 1785 1.59e-03 161_[+1(1.37e-05)]_74_\ [+2(8.99e-06)]_241 39090 4.70e-07 197_[+2(3.62e-05)]_66_\ [+3(1.99e-07)]_139_[+2(2.43e-06)]_32_[+1(3.88e-05)]_10 43559 4.99e-08 20_[+1(8.26e-06)]_10_[+2(8.11e-06)]_\ 383_[+3(2.36e-08)]_43 43759 6.70e-03 96_[+1(1.58e-06)]_392 41042 1.84e-09 128_[+1(5.17e-07)]_249_\ [+3(8.12e-09)]_19_[+2(1.04e-05)]_60 44086 5.57e-08 245_[+3(8.35e-05)]_[+3(3.05e-08)]_\ 55_[+2(2.84e-05)]_6_[+1(2.06e-06)]_130 43056 6.66e-04 188_[+2(3.05e-05)]_76_\ [+1(1.23e-06)]_212 47628 2.05e-09 206_[+3(1.01e-09)]_77_\ [+1(5.47e-06)]_142_[+2(8.99e-06)]_31 50286 2.36e-03 317_[+2(2.25e-07)]_171 45920 2.31e-08 95_[+3(6.55e-08)]_149_\ [+1(8.13e-07)]_188_[+2(1.28e-05)]_24 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************