******************************************************************************** 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/265/265.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21533 1.0000 500 25144 1.0000 500 25718 1.0000 500 262734 1.0000 500 263019 1.0000 500 263511 1.0000 500 264858 1.0000 500 269743 1.0000 500 31437 1.0000 500 4574 1.0000 500 5295 1.0000 500 6441 1.0000 500 9806 1.0000 500 bd1816 1.0000 500 bd935 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/265/265.seqs.fa -oc motifs/265 -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= 15 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= 7500 N= 15 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.241 G 0.237 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.241 G 0.237 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 15 llr = 145 E-value = 2.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::4::121:11: pos.-specific C :::::33:5::1 probability G :9::825:431: matrix T a16a24191699 bits 2.1 1.9 * * 1.7 ** * * 1.5 ** * * * Relative 1.2 ** ** * ** Entropy 1.0 ***** * ** (13.9 bits) 0.8 ***** ***** 0.6 ***** ***** 0.4 ***** ***** 0.2 ***** ****** 0.0 ------------ Multilevel TGTTGTGTCTTT consensus A TCC GG sequence GA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ bd935 386 3.61e-07 CATGTTGTTG TGTTGTGTCGTT GTGTTGCGCT 25718 386 6.47e-07 TTCTCGGTTT TGATGTGTGTTT GAACATTGTT 25144 89 7.81e-07 ACGATGGCGT TGATGCGTCTTT TGCAAATGAA 264858 113 4.06e-06 TGCATAGTTA TGTTTTGTGTTT AATCTATATG 263511 87 4.06e-06 GGTTGAAGAT TGATGCATCTTT TGGCGTATGC 21533 247 5.32e-06 ACAAGCTGTG TGTTGAATCTTT GGAGAGGGAG 269743 135 1.08e-05 AGGAGAGAAG TGTTGTGTGTGT GGGTGTGAAG 263019 56 1.22e-05 TCGCCTCCCT TGTTGCCTCTTC TATCTAACGA 9806 140 1.92e-05 GATGAAATGA TGATGGGTCATT GGTGTTACTG 262734 34 2.87e-05 TCATCTTTGT TTTTGCGTCGTT TGGCTGATAG bd1816 140 3.31e-05 GCGGTGACAC TGATGGCTTTTT CGATACTAGT 5295 177 3.31e-05 AACACTGTCC TGTTTGATGGTT TTGGTCAACT 4574 56 4.91e-05 AGCACGTGAA TGATGATTGGTT ACAACACTGC 6441 408 6.21e-05 TGTCGTCCCC TGTTTTCTGGTC CCCGTCGGTC 31437 397 1.20e-04 TGTTTGAGCA TGTTGTCACTAT GATGGTATTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd935 3.6e-07 385_[+1]_103 25718 6.5e-07 385_[+1]_103 25144 7.8e-07 88_[+1]_400 264858 4.1e-06 112_[+1]_376 263511 4.1e-06 86_[+1]_402 21533 5.3e-06 246_[+1]_242 269743 1.1e-05 134_[+1]_354 263019 1.2e-05 55_[+1]_433 9806 1.9e-05 139_[+1]_349 262734 2.9e-05 33_[+1]_455 bd1816 3.3e-05 139_[+1]_349 5295 3.3e-05 176_[+1]_312 4574 4.9e-05 55_[+1]_433 6441 6.2e-05 407_[+1]_81 31437 0.00012 396_[+1]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=15 bd935 ( 386) TGTTGTGTCGTT 1 25718 ( 386) TGATGTGTGTTT 1 25144 ( 89) TGATGCGTCTTT 1 264858 ( 113) TGTTTTGTGTTT 1 263511 ( 87) TGATGCATCTTT 1 21533 ( 247) TGTTGAATCTTT 1 269743 ( 135) TGTTGTGTGTGT 1 263019 ( 56) TGTTGCCTCTTC 1 9806 ( 140) TGATGGGTCATT 1 262734 ( 34) TTTTGCGTCGTT 1 bd1816 ( 140) TGATGGCTTTTT 1 5295 ( 177) TGTTTGATGGTT 1 4574 ( 56) TGATGATTGGTT 1 6441 ( 408) TGTTTTCTGGTC 1 31437 ( 397) TGTTGTCACTAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7335 bayes= 8.93074 E= 2.0e-002 -1055 -1055 -1055 192 -1055 -1055 198 -198 63 -1055 -1055 119 -1055 -1055 -1055 192 -1055 -1055 175 -40 -95 15 -25 60 -37 15 98 -198 -195 -1055 -1055 182 -1055 115 75 -198 -195 -1055 49 119 -195 -1055 -183 172 -1055 -85 -1055 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 2.0e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.933333 0.066667 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.133333 0.266667 0.200000 0.400000 0.200000 0.266667 0.466667 0.066667 0.066667 0.000000 0.000000 0.933333 0.000000 0.533333 0.400000 0.066667 0.066667 0.000000 0.333333 0.600000 0.066667 0.000000 0.066667 0.866667 0.000000 0.133333 0.000000 0.866667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TG[TA]T[GT][TCG][GCA]T[CG][TG]TT -------------------------------------------------------------------------------- Time 2.20 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 15 llr = 168 E-value = 5.1e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :12::1:12:13:4:: pos.-specific C :::1:1:351:2::1: probability G 69:99:5625:1a546 matrix T 4:8:17511394:154 bits 2.1 * 1.9 * 1.7 * * 1.5 * ** * * Relative 1.2 **** * * Entropy 1.0 ***** * * * * (16.2 bits) 0.8 ******* * * * 0.6 ******** ** **** 0.4 ******** ** **** 0.2 **************** 0.0 ---------------- Multilevel GGTGGTGGCGTTGGTG consensus T A TCAT A AGT sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- bd935 156 2.68e-07 AGATAAAGAG TGTGGAGGCGTTGAGG ACGAAGTTGG 9806 266 3.07e-07 GTATTGTTTT TGTGGTTGCTTTGTTG CAACAATCAT 21533 70 8.12e-07 ATGACGACGC TGTGTTGGCGTTGAGT TTGGAAATGT 31437 31 9.11e-07 TGAGGAAGGA TGTGGTTGCGTAGGCT AGCTGCCTTG 264858 70 9.11e-07 CAAGCGCATT GGTGGAGGAGTAGGGT ACTGACGAAA 262734 300 1.13e-06 GATAGGAGGT TGTGGTGGTGATGGTG GTTGGTGACG bd1816 187 1.26e-06 TTTCAATGTG GGAGGTGCAGTCGATG CTTTGTCAAG 25144 341 1.26e-06 TGGTGGGTGA GATGGTTGCTTTGATG AAGTTTGTAA 5295 366 1.72e-06 TCAAGCTAGC TGTCGTGGCGTGGGTG AACAGTGACT 6441 296 4.66e-06 GCGTCGTCGC GGAGGTGGGTTAGTGT ACATTATGTT 25718 88 5.94e-06 ATGTCGAAAA GGAGGTTCGCTAGGTT ACTTAATTAA 4574 262 7.50e-06 ACGTTCTACT GGTCGCTCGGTTGGGG GGACAAATAT 263019 113 7.50e-06 ACGAAACATT GGTGGCTTCTTCGATG GCTAATATTT 263511 267 1.33e-05 TGAGCTTGAA GGTGGTGAATAAGAGG TGAGGTGGAG 269743 453 2.06e-05 CATGTCGAAA GGTGTTTCTCTCGGTT GCAGACGTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd935 2.7e-07 155_[+2]_329 9806 3.1e-07 265_[+2]_219 21533 8.1e-07 69_[+2]_415 31437 9.1e-07 30_[+2]_454 264858 9.1e-07 69_[+2]_415 262734 1.1e-06 299_[+2]_185 bd1816 1.3e-06 186_[+2]_298 25144 1.3e-06 340_[+2]_144 5295 1.7e-06 365_[+2]_119 6441 4.7e-06 295_[+2]_189 25718 5.9e-06 87_[+2]_397 4574 7.5e-06 261_[+2]_223 263019 7.5e-06 112_[+2]_372 263511 1.3e-05 266_[+2]_218 269743 2.1e-05 452_[+2]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=15 bd935 ( 156) TGTGGAGGCGTTGAGG 1 9806 ( 266) TGTGGTTGCTTTGTTG 1 21533 ( 70) TGTGTTGGCGTTGAGT 1 31437 ( 31) TGTGGTTGCGTAGGCT 1 264858 ( 70) GGTGGAGGAGTAGGGT 1 262734 ( 300) TGTGGTGGTGATGGTG 1 bd1816 ( 187) GGAGGTGCAGTCGATG 1 25144 ( 341) GATGGTTGCTTTGATG 1 5295 ( 366) TGTCGTGGCGTGGGTG 1 6441 ( 296) GGAGGTGGGTTAGTGT 1 25718 ( 88) GGAGGTTCGCTAGGTT 1 4574 ( 262) GGTCGCTCGGTTGGGG 1 263019 ( 113) GGTGGCTTCTTCGATG 1 263511 ( 267) GGTGGTGAATAAGAGG 1 269743 ( 453) GGTGTTTCTCTCGGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 7275 bayes= 8.91886 E= 5.1e-005 -1055 -1055 134 60 -195 -1055 198 -1055 -37 -1055 -1055 160 -1055 -85 187 -1055 -1055 -1055 187 -98 -95 -85 -1055 147 -1055 -1055 117 82 -195 15 134 -198 -37 95 -25 -98 -1055 -85 117 34 -95 -1055 -1055 172 37 -27 -183 60 -1055 -1055 208 -1055 63 -1055 98 -98 -1055 -185 75 102 -1055 -1055 134 60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 15 E= 5.1e-005 0.000000 0.000000 0.600000 0.400000 0.066667 0.000000 0.933333 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.133333 0.866667 0.000000 0.000000 0.000000 0.866667 0.133333 0.133333 0.133333 0.000000 0.733333 0.000000 0.000000 0.533333 0.466667 0.066667 0.266667 0.600000 0.066667 0.200000 0.466667 0.200000 0.133333 0.000000 0.133333 0.533333 0.333333 0.133333 0.000000 0.000000 0.866667 0.333333 0.200000 0.066667 0.400000 0.000000 0.000000 1.000000 0.000000 0.400000 0.000000 0.466667 0.133333 0.000000 0.066667 0.400000 0.533333 0.000000 0.000000 0.600000 0.400000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]G[TA]GGT[GT][GC][CAG][GT]T[TAC]G[GA][TG][GT] -------------------------------------------------------------------------------- Time 4.24 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 13 llr = 129 E-value = 2.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 4a11212:8822 pos.-specific C 2:68488a2:88 probability G 4:3221:::::: matrix T ::::2::::2:: bits 2.1 * 1.9 * * 1.7 * * 1.5 * ** * Relative 1.2 * ******* Entropy 1.0 * * ******* (14.3 bits) 0.8 *** ******* 0.6 *** ******* 0.4 **** ******* 0.2 **** ******* 0.0 ------------ Multilevel AACCCCCCAACC consensus G G A T A sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 5295 314 9.67e-08 CGAACCACTC AACCCCCCAACC TATCCTCACT 9806 423 1.15e-06 ACACCCAGCC CACCGCCCAACC CCAAACCAAG 264858 409 1.33e-06 CAGCAGCACA GACGCCCCAACC GATACACTTT bd1816 21 1.87e-06 GCACAAACGT GACCACCCATCC TGCTTTGACA 4574 456 2.30e-06 ATAACATAGT AACCCCCCAAAC TTCCTCCCCC 31437 259 1.06e-05 AAACGGAAGG AAGCCACCAACC GGTGGCGGTG 262734 436 1.26e-05 CATTTTTGAC GACGTCCCATCC TCTCTCGTCT bd935 473 1.72e-05 GCGCAATAGA AAGCAGCCAACC GACACATCGC 263511 399 1.72e-05 GGCACGGGGG GAGCCCCCAAAA GCCGAATTCC 21533 450 2.68e-05 GCTTTCATAA CACCTCACAACA GCCAGCCGTA 6441 69 3.70e-05 CAAGGCGTCA GAGCTCACCACC AAAATGAGCA 269743 385 4.35e-05 AGCCATTGCC CAACGCCCATCC GCCATCACAC 25718 434 9.49e-05 CTCAACTCTC AACAACCCCACA CAACGACCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5295 9.7e-08 313_[+3]_175 9806 1.1e-06 422_[+3]_66 264858 1.3e-06 408_[+3]_80 bd1816 1.9e-06 20_[+3]_468 4574 2.3e-06 455_[+3]_33 31437 1.1e-05 258_[+3]_230 262734 1.3e-05 435_[+3]_53 bd935 1.7e-05 472_[+3]_16 263511 1.7e-05 398_[+3]_90 21533 2.7e-05 449_[+3]_39 6441 3.7e-05 68_[+3]_420 269743 4.4e-05 384_[+3]_104 25718 9.5e-05 433_[+3]_55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=13 5295 ( 314) AACCCCCCAACC 1 9806 ( 423) CACCGCCCAACC 1 264858 ( 409) GACGCCCCAACC 1 bd1816 ( 21) GACCACCCATCC 1 4574 ( 456) AACCCCCCAAAC 1 31437 ( 259) AAGCCACCAACC 1 262734 ( 436) GACGTCCCATCC 1 bd935 ( 473) AAGCAGCCAACC 1 263511 ( 399) GAGCCCCCAAAA 1 21533 ( 450) CACCTCACAACA 1 6441 ( 69) GAGCTCACCACC 1 269743 ( 385) CAACGCCCATCC 1 25718 ( 434) AACAACCCCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7335 bayes= 9.66888 E= 2.7e+001 57 -6 70 -1035 195 -1035 -1035 -1035 -175 135 38 -1035 -175 167 -62 -1035 -16 68 -62 -19 -175 181 -162 -1035 -75 181 -1035 -1035 -1035 205 -1035 -1035 171 -65 -1035 -1035 157 -1035 -1035 -19 -75 181 -1035 -1035 -16 167 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 2.7e+001 0.384615 0.230769 0.384615 0.000000 1.000000 0.000000 0.000000 0.000000 0.076923 0.615385 0.307692 0.000000 0.076923 0.769231 0.153846 0.000000 0.230769 0.384615 0.153846 0.230769 0.076923 0.846154 0.076923 0.000000 0.153846 0.846154 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.846154 0.153846 0.000000 0.000000 0.769231 0.000000 0.000000 0.230769 0.153846 0.846154 0.000000 0.000000 0.230769 0.769231 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AGC]A[CG]C[CAT]CCCA[AT]C[CA] -------------------------------------------------------------------------------- Time 5.91 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21533 2.44e-06 69_[+2(8.12e-07)]_161_\ [+1(5.32e-06)]_127_[+3(7.56e-05)]_52_[+3(2.68e-05)]_39 25144 2.72e-05 88_[+1(7.81e-07)]_75_[+1(1.33e-05)]_\ 153_[+2(1.26e-06)]_144 25718 6.71e-06 87_[+2(5.94e-06)]_282_\ [+1(6.47e-07)]_36_[+3(9.49e-05)]_55 262734 7.52e-06 33_[+1(2.87e-05)]_254_\ [+2(1.13e-06)]_120_[+3(1.26e-05)]_53 263019 1.45e-03 55_[+1(1.22e-05)]_45_[+2(7.50e-06)]_\ 372 263511 1.55e-05 86_[+1(4.06e-06)]_168_\ [+2(1.33e-05)]_116_[+3(1.72e-05)]_90 264858 1.42e-07 69_[+2(9.11e-07)]_27_[+1(4.06e-06)]_\ 284_[+3(1.33e-06)]_80 269743 1.20e-04 134_[+1(1.08e-05)]_238_\ [+3(4.35e-05)]_56_[+2(2.06e-05)]_32 31437 1.86e-05 30_[+2(9.11e-07)]_212_\ [+3(1.06e-05)]_230 4574 1.43e-05 55_[+1(4.91e-05)]_194_\ [+2(7.50e-06)]_178_[+3(2.30e-06)]_33 5295 1.56e-07 176_[+1(3.31e-05)]_125_\ [+3(9.67e-08)]_40_[+2(1.72e-06)]_119 6441 1.30e-04 68_[+3(3.70e-05)]_215_\ [+2(4.66e-06)]_96_[+1(6.21e-05)]_81 9806 1.89e-07 139_[+1(1.92e-05)]_114_\ [+2(3.07e-07)]_141_[+3(1.15e-06)]_66 bd1816 1.72e-06 20_[+3(1.87e-06)]_107_\ [+1(3.31e-05)]_35_[+2(1.26e-06)]_298 bd935 5.26e-08 155_[+2(2.68e-07)]_214_\ [+1(3.61e-07)]_75_[+3(1.72e-05)]_16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************