******************************************************************************** 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/478/478.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 49857 1.0000 500 45143 1.0000 500 11563 1.0000 500 35395 1.0000 500 35733 1.0000 500 41350 1.0000 500 53967 1.0000 500 40538 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/478/478.seqs.fa -oc motifs/478 -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= 8 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= 4000 N= 8 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.239 G 0.237 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.239 G 0.238 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 5 llr = 63 E-value = 4.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::a::2:::::: pos.-specific C 8:::24:2:2a: probability G 28:a8:6:a::a matrix T :2:::448:8:: bits 2.1 * * ** 1.9 ** * ** 1.7 ** * ** 1.5 *** * ** Relative 1.2 ***** ***** Entropy 1.0 ***** ****** (18.2 bits) 0.8 ***** ****** 0.6 ***** ****** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CGAGGCGTGTCG consensus GT CTTC C sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 40538 440 1.97e-07 CCTGCACGAG CGAGGTTTGTCG GGGAAGCCTT 35395 243 3.81e-07 GGCGCGTGCT CGAGGCGTGCCG CCGCACCCAC 53967 325 7.07e-07 CAGGCTATTG CGAGCTGTGTCG GCAGGTGTCG 49857 354 1.75e-06 CGACTCAGAC GGAGGATTGTCG CACGCCGAAG 41350 283 2.33e-06 GGATAAATTT CTAGGCGCGTCG TACACGGGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40538 2e-07 439_[+1]_49 35395 3.8e-07 242_[+1]_246 53967 7.1e-07 324_[+1]_164 49857 1.8e-06 353_[+1]_135 41350 2.3e-06 282_[+1]_206 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=5 40538 ( 440) CGAGGTTTGTCG 1 35395 ( 243) CGAGGCGTGCCG 1 53967 ( 325) CGAGCTGTGTCG 1 49857 ( 354) GGAGGATTGTCG 1 41350 ( 283) CTAGGCGCGTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 3912 bayes= 9.86175 E= 4.0e+002 -897 174 -25 -897 -897 -897 175 -40 194 -897 -897 -897 -897 -897 207 -897 -897 -26 175 -897 -38 74 -897 60 -897 -897 134 60 -897 -26 -897 160 -897 -897 207 -897 -897 -26 -897 160 -897 206 -897 -897 -897 -897 207 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 5 E= 4.0e+002 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.800000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.200000 0.400000 0.000000 0.400000 0.000000 0.000000 0.600000 0.400000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][GT]AG[GC][CTA][GT][TC]G[TC]CG -------------------------------------------------------------------------------- Time 0.58 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 18 sites = 8 llr = 103 E-value = 5.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :1:53699341::53131 pos.-specific C a:::::1:114a3356:: probability G :3a:84:1111:1:338: matrix T :6:5::::544:63:::9 bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 * * ** * * Relative 1.2 * * * ** * ** Entropy 1.0 * ****** * ** (18.5 bits) 0.8 * ****** * *** 0.6 ******** ** **** 0.4 ******** ******* 0.2 ****************** 0.0 ------------------ Multilevel CTGAGAAATACCTACCGT consensus G TAG ATT CCAGA sequence TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 35733 159 8.38e-10 ATTCTGTTGA CTGTGAAAAATCTACCGT CGATTAGACC 11563 369 3.03e-07 AGGCCTGATT CGGAGAAAATCCTCCCGA GATGGTATGT 41350 155 4.03e-07 TGCCACGTCC CTGAGGAAGTTCGACGGT ATTTGTAGGA 35395 468 4.83e-07 TGTACAACGG CGGAGGAGTTTCTCGCGT TTATCCCAAT 53967 476 7.44e-07 AAAGCGAGCA CTGAAGAACACCTAGCAT TGTCACA 40538 29 8.74e-07 CATGAGTGCA CTGTGAAATGCCCTAAGT TGCGGTCATC 45143 122 2.34e-06 TTACATTTAA CAGTAAAATAGCTACGAT CATGACTACT 49857 306 2.81e-06 CGAGACACGG CTGTGACATCACCTACGT CCGCGCGACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35733 8.4e-10 158_[+2]_324 11563 3e-07 368_[+2]_114 41350 4e-07 154_[+2]_328 35395 4.8e-07 467_[+2]_15 53967 7.4e-07 475_[+2]_7 40538 8.7e-07 28_[+2]_454 45143 2.3e-06 121_[+2]_361 49857 2.8e-06 305_[+2]_177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=18 seqs=8 35733 ( 159) CTGTGAAAAATCTACCGT 1 11563 ( 369) CGGAGAAAATCCTCCCGA 1 41350 ( 155) CTGAGGAAGTTCGACGGT 1 35395 ( 468) CGGAGGAGTTTCTCGCGT 1 53967 ( 476) CTGAAGAACACCTAGCAT 1 40538 ( 29) CTGTGAAATGCCCTAAGT 1 45143 ( 122) CAGTAAAATAGCTACGAT 1 49857 ( 306) CTGTGACATCACCTACGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 3864 bayes= 8.91289 E= 5.8e+002 -965 206 -965 -965 -106 -965 7 125 -965 -965 207 -965 94 -965 -965 92 -6 -965 166 -965 126 -965 66 -965 175 -93 -965 -965 175 -965 -92 -965 -6 -93 -92 92 53 -93 -92 51 -106 65 -92 51 -965 206 -965 -965 -965 6 -92 125 94 6 -965 -7 -6 106 7 -965 -106 139 7 -965 -6 -965 166 -965 -106 -965 -965 173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 8 E= 5.8e+002 0.000000 1.000000 0.000000 0.000000 0.125000 0.000000 0.250000 0.625000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.250000 0.000000 0.750000 0.000000 0.625000 0.000000 0.375000 0.000000 0.875000 0.125000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.250000 0.125000 0.125000 0.500000 0.375000 0.125000 0.125000 0.375000 0.125000 0.375000 0.125000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.125000 0.625000 0.500000 0.250000 0.000000 0.250000 0.250000 0.500000 0.250000 0.000000 0.125000 0.625000 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.125000 0.000000 0.000000 0.875000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TG]G[AT][GA][AG]AA[TA][AT][CT]C[TC][ACT][CAG][CG][GA]T -------------------------------------------------------------------------------- Time 1.09 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 5 llr = 86 E-value = 2.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :aa8:4::2::6:4a46a4: pos.-specific C 2::24264:a62:4::2:48 probability G 8:::6:2:8::2a2:6::22 matrix T :::::426::4:::::2::: bits 2.1 * * 1.9 ** * * * * 1.7 ** * * * * 1.5 *** * * * * Relative 1.2 **** ** * * * * Entropy 1.0 ***** **** * ** * * (24.7 bits) 0.8 ***** **** * ** * * 0.6 ***** ******* **** * 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GAAAGACTGCCAGAAGAAAC consensus C CCTGCA TC C AC CG sequence CT G G T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 53967 287 9.56e-11 GAGAACAAAT GAAAGCCCGCCAGCAGAAAC GATGCCAGCA 40538 72 6.67e-09 TCATTTCATA GAAAGTCTGCTGGGAAAAGC ATCTTATTTT 35733 391 1.33e-08 AATCTTGGGA GAACGAGTGCTAGCAGCAAC GCCACCTGTT 11563 279 2.24e-08 AGAAGAAATT GAAACTTCACCAGAAGTACC GGAGCAAGCA 35395 320 2.73e-08 AACGAACGCA CAAACACTGCCCGAAAAACG TGTGTTACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 53967 9.6e-11 286_[+3]_194 40538 6.7e-09 71_[+3]_409 35733 1.3e-08 390_[+3]_90 11563 2.2e-08 278_[+3]_202 35395 2.7e-08 319_[+3]_161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=5 53967 ( 287) GAAAGCCCGCCAGCAGAAAC 1 40538 ( 72) GAAAGTCTGCTGGGAAAAGC 1 35733 ( 391) GAACGAGTGCTAGCAGCAAC 1 11563 ( 279) GAAACTTCACCAGAAGTACC 1 35395 ( 320) CAAACACTGCCCGAAAAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 3848 bayes= 9.83793 E= 2.9e+003 -897 -26 175 -897 194 -897 -897 -897 194 -897 -897 -897 162 -26 -897 -897 -897 74 134 -897 62 -26 -897 60 -897 133 -25 -40 -897 74 -897 119 -38 -897 175 -897 -897 206 -897 -897 -897 133 -897 60 120 -26 -25 -897 -897 -897 207 -897 62 74 -25 -897 194 -897 -897 -897 62 -897 134 -897 120 -26 -897 -40 194 -897 -897 -897 62 74 -25 -897 -897 174 -25 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 5 E= 2.9e+003 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.400000 0.200000 0.000000 0.400000 0.000000 0.600000 0.200000 0.200000 0.000000 0.400000 0.000000 0.600000 0.200000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.600000 0.200000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.400000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.600000 0.200000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.400000 0.400000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC]AA[AC][GC][ATC][CGT][TC][GA]C[CT][ACG]G[ACG]A[GA][ACT]A[ACG][CG] -------------------------------------------------------------------------------- Time 1.57 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49857 6.11e-05 305_[+2(2.81e-06)]_30_\ [+1(1.75e-06)]_135 45143 2.16e-02 121_[+2(2.34e-06)]_361 11563 2.07e-07 278_[+3(2.24e-08)]_70_\ [+2(3.03e-07)]_79_[+3(3.53e-05)]_15 35395 2.43e-10 242_[+1(3.81e-07)]_65_\ [+3(2.73e-08)]_128_[+2(4.83e-07)]_15 35733 6.05e-10 158_[+2(8.38e-10)]_214_\ [+3(1.33e-08)]_90 41350 2.72e-05 154_[+2(4.03e-07)]_110_\ [+1(2.33e-06)]_206 53967 3.26e-12 286_[+3(9.56e-11)]_18_\ [+1(7.07e-07)]_139_[+2(7.44e-07)]_7 40538 6.15e-11 28_[+2(8.74e-07)]_25_[+3(6.67e-09)]_\ 348_[+1(1.97e-07)]_49 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************