******************************************************************************** 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/318/318.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 46384 1.0000 500 1196 1.0000 500 46628 1.0000 500 13439 1.0000 500 39432 1.0000 500 7959 1.0000 500 50038 1.0000 500 50039 1.0000 500 41302 1.0000 500 16861 1.0000 500 42671 1.0000 500 44170 1.0000 500 45315 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/318/318.seqs.fa -oc motifs/318 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.294 C 0.225 G 0.209 T 0.272 Background letter frequencies (from dataset with add-one prior applied): A 0.294 C 0.225 G 0.209 T 0.272 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 13 llr = 126 E-value = 4.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 39:4488822aa pos.-specific C 5::25:21:6:: probability G 21a1:2::82:: matrix T :::32::1:::: bits 2.3 * 2.0 * 1.8 * ** 1.6 * * ** Relative 1.4 ** * ** Entropy 1.1 ** **** ** (14.0 bits) 0.9 ** **** ** 0.7 *** ******* 0.5 *** ******** 0.2 *** ******** 0.0 ------------ Multilevel CAGACAAAGCAA consensus A TAGC A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 42671 276 1.82e-07 GAAGGTCAAA CAGTCAAAGCAA TTAAGCTGTA 50039 50 2.36e-06 CATAGTTGCA CAGACAAAGGAA AGTAGCGACG 13439 421 2.80e-06 GTACCACTTG CAGAAACAGCAA CAAACAAGTT 50038 412 3.44e-06 CGAAGCCCTG CAGCAGAAGCAA ACCGATTGTT 45315 307 3.79e-06 CCTCGCGAAG GAGTAAAAGCAA ATTGCGTCTT 41302 264 8.59e-06 AGTAAGGGTA AAGTAACAGCAA ACAACTCGCT 1196 216 1.57e-05 CTTTCGTTTG CAGCTAAAGAAA GTCTCACAAC 46628 306 1.68e-05 GACCAACAAC AGGACAAAGCAA AACAAATGGG 7959 154 1.85e-05 ACGCTTAGTG CAGACGACGCAA GGACCTGCGT 46384 324 1.97e-05 CTCTTGCACA AAGCCAAAACAA AATAGAATAG 16861 468 7.85e-05 AGCCTTTCAA CAGGTACAGGAA AACGAGTCAC 44170 404 9.46e-05 ACTGTTACAG AAGTCGAAAAAA TCTGTCCGCC 39432 305 9.83e-05 CCCAGCGGCA GAGAAAATGAAA GATTCAATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42671 1.8e-07 275_[+1]_213 50039 2.4e-06 49_[+1]_439 13439 2.8e-06 420_[+1]_68 50038 3.4e-06 411_[+1]_77 45315 3.8e-06 306_[+1]_182 41302 8.6e-06 263_[+1]_225 1196 1.6e-05 215_[+1]_273 46628 1.7e-05 305_[+1]_183 7959 1.8e-05 153_[+1]_335 46384 2e-05 323_[+1]_165 16861 7.8e-05 467_[+1]_21 44170 9.5e-05 403_[+1]_85 39432 9.8e-05 304_[+1]_184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=13 42671 ( 276) CAGTCAAAGCAA 1 50039 ( 50) CAGACAAAGGAA 1 13439 ( 421) CAGAAACAGCAA 1 50038 ( 412) CAGCAGAAGCAA 1 45315 ( 307) GAGTAAAAGCAA 1 41302 ( 264) AAGTAACAGCAA 1 1196 ( 216) CAGCTAAAGAAA 1 46628 ( 306) AGGACAAAGCAA 1 7959 ( 154) CAGACGACGCAA 1 46384 ( 324) AAGCCAAAACAA 1 16861 ( 468) CAGGTACAGGAA 1 44170 ( 404) AAGTCGAAAAAA 1 39432 ( 305) GAGAAAATGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 8.93074 E= 4.6e+000 7 126 -44 -1035 165 -1035 -144 -1035 -1035 -1035 226 -1035 39 4 -144 18 39 104 -1035 -82 139 -1035 15 -1035 139 4 -1035 -1035 152 -154 -1035 -182 -93 -1035 202 -1035 -35 145 -44 -1035 176 -1035 -1035 -1035 176 -1035 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 4.6e+000 0.307692 0.538462 0.153846 0.000000 0.923077 0.000000 0.076923 0.000000 0.000000 0.000000 1.000000 0.000000 0.384615 0.230769 0.076923 0.307692 0.384615 0.461538 0.000000 0.153846 0.769231 0.000000 0.230769 0.000000 0.769231 0.230769 0.000000 0.000000 0.846154 0.076923 0.000000 0.076923 0.153846 0.000000 0.846154 0.000000 0.230769 0.615385 0.153846 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]AG[ATC][CA][AG][AC]AG[CA]AA -------------------------------------------------------------------------------- Time 1.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 13 llr = 123 E-value = 5.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 51:::41:4::: pos.-specific C :::::251:6:6 probability G 22::a345:2:3 matrix T 47aa:1:462a1 bits 2.3 * 2.0 * 1.8 *** * 1.6 *** * Relative 1.4 *** * Entropy 1.1 *** * (13.6 bits) 0.9 **** ****** 0.7 **** ****** 0.5 ***** ****** 0.2 ************ 0.0 ------------ Multilevel ATTTGACGTCTC consensus TG GGTAG G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 50039 398 9.38e-07 ACGTAACGGT GTTTGGCGTCTC AACGAAAGAC 50038 346 9.38e-07 GTGTGATTCC ATTTGCGGTCTC TCGCTGCTTT 45315 201 2.33e-06 AGAGAGAGAC TTTTGCCGACTC ACCAAAATGG 1196 193 2.33e-06 AGTGGCTGCT TTTTGAGGACTC GCTTTCGTTT 7959 179 8.74e-06 CCTGCGTTAC TTTTGACTTGTC CGCCTCGTCA 46628 340 1.51e-05 AAACCGAGGA AGTTGACTTCTG TCCCAAGCCT 44170 32 1.67e-05 GTTTTGGTAC ATTTGAAGTCTC TGTATCTATA 41302 309 2.89e-05 ATTGCCTGTA AATTGGCGTCTG ATTCTTGGGA 16861 322 3.40e-05 ATCGAAACAT TTTTGGGTATTC CATTTTTTGA 13439 105 4.34e-05 TATTGCACCA GGTTGACTTGTC CAGTCAATGC 39432 69 7.26e-05 GTCGCTGTCA AGTTGGGTTCTT GATGGACCTA 46384 459 9.97e-05 GTAGCCCGCT ATTTGCCCAGTG GGGTTTATCA 42671 116 1.10e-04 ACATTAGGTG TTTTGTGGATTG CTTGAACTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50039 9.4e-07 397_[+2]_91 50038 9.4e-07 345_[+2]_143 45315 2.3e-06 200_[+2]_288 1196 2.3e-06 192_[+2]_296 7959 8.7e-06 178_[+2]_310 46628 1.5e-05 339_[+2]_149 44170 1.7e-05 31_[+2]_457 41302 2.9e-05 308_[+2]_180 16861 3.4e-05 321_[+2]_167 13439 4.3e-05 104_[+2]_384 39432 7.3e-05 68_[+2]_420 46384 0.0001 458_[+2]_30 42671 0.00011 115_[+2]_373 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=13 50039 ( 398) GTTTGGCGTCTC 1 50038 ( 346) ATTTGCGGTCTC 1 45315 ( 201) TTTTGCCGACTC 1 1196 ( 193) TTTTGAGGACTC 1 7959 ( 179) TTTTGACTTGTC 1 46628 ( 340) AGTTGACTTCTG 1 44170 ( 32) ATTTGAAGTCTC 1 41302 ( 309) AATTGGCGTCTG 1 16861 ( 322) TTTTGGGTATTC 1 13439 ( 105) GGTTGACTTGTC 1 39432 ( 69) AGTTGGGTTCTT 1 46384 ( 459) ATTTGCCCAGTG 1 42671 ( 116) TTTTGTGGATTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 9.46216 E= 5.0e+001 65 -1035 -44 50 -193 -1035 15 134 -1035 -1035 -1035 188 -1035 -1035 -1035 188 -1035 -1035 226 -1035 39 4 56 -182 -193 126 88 -1035 -1035 -154 137 50 39 -1035 -1035 117 -1035 145 15 -82 -1035 -1035 -1035 188 -1035 145 56 -182 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 5.0e+001 0.461538 0.000000 0.153846 0.384615 0.076923 0.000000 0.230769 0.692308 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.384615 0.230769 0.307692 0.076923 0.076923 0.538462 0.384615 0.000000 0.000000 0.076923 0.538462 0.384615 0.384615 0.000000 0.000000 0.615385 0.000000 0.615385 0.230769 0.153846 0.000000 0.000000 0.000000 1.000000 0.000000 0.615385 0.307692 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AT][TG]TTG[AGC][CG][GT][TA][CG]T[CG] -------------------------------------------------------------------------------- Time 3.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 5 llr = 79 E-value = 1.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::6:a::8a::::8a pos.-specific C 228:8::::::::2:: probability G 8::42:::2::4842: matrix T :82:::aa::a624:: bits 2.3 2.0 1.8 *** ** * 1.6 * *** ** * Relative 1.4 * * **** ** * * Entropy 1.1 *** ********* ** (22.8 bits) 0.9 ************* ** 0.7 ************* ** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel GTCACATTAATTGGAA consensus CCTGG G GTTG sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 44170 238 6.48e-09 CTTACAGTTA GTCACATTGATGGGAA AATCGAGAAT 42671 305 9.68e-09 GTAAGCTACC GTCGCATTAATTGTGA TGAAATCAGG 46628 7 2.35e-08 CTTACA GTTACATTAATTGTAA CAAAAACATA 7959 326 4.20e-08 CCCCGTGAAA GCCGGATTAATTGGAA AAAGATCTCT 50039 223 1.50e-07 AAACTGCAGT CTCACATTAATGTCAA AACCAGGCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44170 6.5e-09 237_[+3]_247 42671 9.7e-09 304_[+3]_180 46628 2.4e-08 6_[+3]_478 7959 4.2e-08 325_[+3]_159 50039 1.5e-07 222_[+3]_262 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=5 44170 ( 238) GTCACATTGATGGGAA 1 42671 ( 305) GTCGCATTAATTGTGA 1 46628 ( 7) GTTACATTAATTGTAA 1 7959 ( 326) GCCGGATTAATTGGAA 1 50039 ( 223) CTCACATTAATGTCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 10.5509 E= 1.3e+003 -897 -17 194 -897 -897 -17 -897 155 -897 183 -897 -44 103 -897 94 -897 -897 183 -6 -897 176 -897 -897 -897 -897 -897 -897 187 -897 -897 -897 187 144 -897 -6 -897 176 -897 -897 -897 -897 -897 -897 187 -897 -897 94 114 -897 -897 194 -44 -897 -17 94 55 144 -897 -6 -897 176 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 5 E= 1.3e+003 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.800000 0.000000 0.200000 0.600000 0.000000 0.400000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.800000 0.200000 0.000000 0.200000 0.400000 0.400000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC][TC][CT][AG][CG]ATT[AG]AT[TG][GT][GTC][AG]A -------------------------------------------------------------------------------- Time 4.35 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46384 6.47e-03 323_[+1(1.97e-05)]_123_\ [+2(9.97e-05)]_30 1196 2.93e-04 192_[+2(2.33e-06)]_11_\ [+1(1.57e-05)]_273 46628 1.68e-07 6_[+3(2.35e-08)]_283_[+1(1.68e-05)]_\ 22_[+2(1.51e-05)]_149 13439 1.63e-03 104_[+2(4.34e-05)]_178_\ [+1(4.35e-05)]_114_[+1(2.80e-06)]_68 39432 2.75e-02 68_[+2(7.26e-05)]_224_\ [+1(9.83e-05)]_184 7959 1.89e-07 153_[+1(1.85e-05)]_13_\ [+2(8.74e-06)]_135_[+3(4.20e-08)]_159 50038 8.65e-05 345_[+2(9.38e-07)]_54_\ [+1(3.44e-06)]_77 50039 1.20e-08 49_[+1(2.36e-06)]_161_\ [+3(1.50e-07)]_159_[+2(9.38e-07)]_91 41302 4.32e-04 263_[+1(8.59e-06)]_33_\ [+2(2.89e-05)]_180 16861 1.95e-02 321_[+2(3.40e-05)]_134_\ [+1(7.85e-05)]_21 42671 7.14e-09 275_[+1(1.82e-07)]_17_\ [+3(9.68e-09)]_180 44170 2.70e-07 31_[+2(1.67e-05)]_194_\ [+3(6.48e-09)]_150_[+1(9.46e-05)]_85 45315 1.25e-04 200_[+2(2.33e-06)]_94_\ [+1(3.79e-06)]_182 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************