******************************************************************************** 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/57/57.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 48246 1.0000 500 45739 1.0000 500 38589 1.0000 500 42594 1.0000 500 44317 1.0000 500 36611 1.0000 500 45740 1.0000 500 50431 1.0000 500 43603 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/57/57.seqs.fa -oc motifs/57 -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= 9 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= 4500 N= 9 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.270 C 0.230 G 0.220 T 0.280 Background letter frequencies (from dataset with add-one prior applied): A 0.270 C 0.230 G 0.220 T 0.280 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 18 sites = 7 llr = 109 E-value = 4.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::9637a1::aa641:9 pos.-specific C 11::46:::4:::1:91: probability G 973:::3:36a::11:91 matrix T :171:1::6::::14::: bits 2.2 * 2.0 * *** 1.7 * *** 1.5 * * *** ** Relative 1.3 * * * *** *** Entropy 1.1 * *** ** **** *** (22.4 bits) 0.9 ***** ** **** *** 0.7 ************* *** 0.4 ************* **** 0.2 ****************** 0.0 ------------------ Multilevel GGTAACAATGGAAAACGA consensus G CAG GC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 42594 254 1.52e-10 GAAGCCTCGG GGTACCAATCGAAATCGA GACGCCTGGT 48246 281 6.16e-09 GCGTCCGATT GGTACCGAACGAAAACGA GTTTGAGTAC 43603 323 3.55e-08 AAACCAGTGA CGTAAAAATGGAAGACGA GTGTAAGTTC 50431 122 6.71e-08 ACGCAAGAAC GCGAATGATGGAAATCGA TGAACTAATA 45739 223 6.71e-08 AGTGAAAGTT GGTTACAAGCGAAAAAGA AGTCTTCCCT 36611 32 1.10e-07 TGCTTTTACT GTTAACAATGGAATTCCA ACCATGAATG 44317 435 1.93e-07 TCGAAATTGC GGGACAAAGGGAACGCGG TATCCTTCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42594 1.5e-10 253_[+1]_229 48246 6.2e-09 280_[+1]_202 43603 3.6e-08 322_[+1]_160 50431 6.7e-08 121_[+1]_361 45739 6.7e-08 222_[+1]_260 36611 1.1e-07 31_[+1]_451 44317 1.9e-07 434_[+1]_48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=18 seqs=7 42594 ( 254) GGTACCAATCGAAATCGA 1 48246 ( 281) GGTACCGAACGAAAACGA 1 43603 ( 323) CGTAAAAATGGAAGACGA 1 50431 ( 122) GCGAATGATGGAAATCGA 1 45739 ( 223) GGTTACAAGCGAAAAAGA 1 36611 ( 32) GTTAACAATGGAATTCCA 1 44317 ( 435) GGGACAAAGGGAACGCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 4347 bayes= 9.11974 E= 4.5e-002 -945 -68 196 -945 -945 -68 170 -97 -945 -945 38 135 166 -945 -945 -97 108 90 -945 -945 8 131 -945 -97 140 -945 38 -945 189 -945 -945 -945 -92 -945 38 103 -945 90 138 -945 -945 -945 218 -945 189 -945 -945 -945 189 -945 -945 -945 108 -68 -62 -97 66 -945 -62 61 -92 190 -945 -945 -945 -68 196 -945 166 -945 -62 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 7 E= 4.5e-002 0.000000 0.142857 0.857143 0.000000 0.000000 0.142857 0.714286 0.142857 0.000000 0.000000 0.285714 0.714286 0.857143 0.000000 0.000000 0.142857 0.571429 0.428571 0.000000 0.000000 0.285714 0.571429 0.000000 0.142857 0.714286 0.000000 0.285714 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.285714 0.571429 0.000000 0.428571 0.571429 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.571429 0.142857 0.142857 0.142857 0.428571 0.000000 0.142857 0.428571 0.142857 0.857143 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.857143 0.000000 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GG[TG]A[AC][CA][AG]A[TG][GC]GAAA[AT]CGA -------------------------------------------------------------------------------- Time 1.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 6 llr = 100 E-value = 5.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 25::a::58::::28228a pos.-specific C :28::8a:223:58:722: probability G :3:::::5:22a::::5:: matrix T 8:2a:2:::75:5:222:: bits 2.2 * * 2.0 * * * * 1.7 ** * * * 1.5 ***** * * * Relative 1.3 ***** * * ** ** Entropy 1.1 * ******* * ** ** (24.0 bits) 0.9 * ******* ***** ** 0.7 ********** ***** ** 0.4 **************** ** 0.2 ******************* 0.0 ------------------- Multilevel TACTACCAATTGCCACGAA consensus G G C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 45739 67 8.75e-11 ATGTACGCCC TACTACCGATGGTCACGAA CGCTGATGTT 45740 482 3.63e-09 CAACAACTAC TACTACCAATTGCAACAAA 44317 411 7.36e-09 TAGCCTTGAT TGCTATCGATTGCCTCGAA ATTGCGGGAC 36611 424 8.54e-09 ACGACTATGG TGTTACCGCTCGTCACGAA ACTCGCTAGT 48246 442 4.45e-08 AGAGTGAACG AACTACCAACTGCCATCAA AGCATTCCTA 42594 477 1.18e-07 TGTAGTTTGT TCCTACCAAGCGTCAATCA ACTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45739 8.8e-11 66_[+2]_415 45740 3.6e-09 481_[+2] 44317 7.4e-09 410_[+2]_71 36611 8.5e-09 423_[+2]_58 48246 4.5e-08 441_[+2]_40 42594 1.2e-07 476_[+2]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=6 45739 ( 67) TACTACCGATGGTCACGAA 1 45740 ( 482) TACTACCAATTGCAACAAA 1 44317 ( 411) TGCTATCGATTGCCTCGAA 1 36611 ( 424) TGTTACCGCTCGTCACGAA 1 48246 ( 442) AACTACCAACTGCCATCAA 1 42594 ( 477) TCCTACCAAGCGTCAATCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 4338 bayes= 9.15429 E= 5.2e+000 -70 -923 -923 157 89 -46 60 -923 -923 186 -923 -75 -923 -923 -923 183 189 -923 -923 -923 -923 186 -923 -75 -923 212 -923 -923 89 -923 118 -923 162 -46 -923 -923 -923 -46 -40 125 -923 54 -40 84 -923 -923 218 -923 -923 112 -923 84 -70 186 -923 -923 162 -923 -923 -75 -70 154 -923 -75 -70 -46 118 -75 162 -46 -923 -923 189 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 6 E= 5.2e+000 0.166667 0.000000 0.000000 0.833333 0.500000 0.166667 0.333333 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.166667 0.166667 0.666667 0.000000 0.333333 0.166667 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.166667 0.833333 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.166667 0.666667 0.000000 0.166667 0.166667 0.166667 0.500000 0.166667 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[AG]CTACC[AG]AT[TC]G[CT]CACGAA -------------------------------------------------------------------------------- Time 1.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 89 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::4a284:8::4:2::2:::: pos.-specific C 224:622::::4626:28:82 probability G 882:::4a2:a:2:2a2::28 matrix T ::::2::::a:2262:42a:: bits 2.2 * * * 2.0 * * * * 1.7 * * ** * * 1.5 ** * * ** * * * Relative 1.3 ** * * **** * **** Entropy 1.1 ** * * **** * **** (25.8 bits) 0.9 ** * * **** * **** 0.7 ** *** **** * ** **** 0.4 **************** **** 0.2 **************** **** 0.0 --------------------- Multilevel GGAACAAGATGACTCGTCTCG consensus CCC ACG G CGAG AT GC sequence G T C TTCT C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 45740 208 1.12e-10 ACCGCAGAAA GGAACAAGGTGTCTCGTCTCG TAAATCACTT 44317 351 3.32e-10 GCGACGGCAA GGCACAGGATGCCACGACTCC CTTTATCCAT 50431 367 4.53e-09 GTAACTGATA GGGATAGGATGATTGGGCTCG ATCTTCATAT 38589 215 7.22e-09 GGAATACAGT GGCACCAGATGAGTTGTTTCG GCAGTTTCGT 36611 148 3.54e-08 AAGGGCCGAA CCAAAACGATGCCCCGCCTGG CTTCCGATTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45740 1.1e-10 207_[+3]_272 44317 3.3e-10 350_[+3]_129 50431 4.5e-09 366_[+3]_113 38589 7.2e-09 214_[+3]_265 36611 3.5e-08 147_[+3]_332 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 45740 ( 208) GGAACAAGGTGTCTCGTCTCG 1 44317 ( 351) GGCACAGGATGCCACGACTCC 1 50431 ( 367) GGGATAGGATGATTGGGCTCG 1 38589 ( 215) GGCACCAGATGAGTTGTTTCG 1 36611 ( 148) CCAAAACGATGCCCCGCCTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4320 bayes= 10.005 E= 1.1e+002 -897 -20 186 -897 -897 -20 186 -897 57 80 -14 -897 189 -897 -897 -897 -43 138 -897 -48 156 -20 -897 -897 57 -20 86 -897 -897 -897 218 -897 156 -897 -14 -897 -897 -897 -897 183 -897 -897 218 -897 57 80 -897 -48 -897 138 -14 -48 -43 -20 -897 110 -897 138 -14 -48 -897 -897 218 -897 -43 -20 -14 51 -897 180 -897 -48 -897 -897 -897 183 -897 180 -14 -897 -897 -20 186 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.1e+002 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.400000 0.400000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.800000 0.200000 0.000000 0.000000 0.400000 0.200000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.400000 0.000000 0.200000 0.000000 0.600000 0.200000 0.200000 0.200000 0.200000 0.000000 0.600000 0.000000 0.600000 0.200000 0.200000 0.000000 0.000000 1.000000 0.000000 0.200000 0.200000 0.200000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC][GC][ACG]A[CAT][AC][AGC]G[AG]TG[ACT][CGT][TAC][CGT]G[TACG][CT]T[CG][GC] -------------------------------------------------------------------------------- Time 2.55 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48246 1.35e-08 75_[+2(1.81e-05)]_186_\ [+1(6.16e-09)]_143_[+2(4.45e-08)]_40 45739 3.71e-11 66_[+2(8.75e-11)]_137_\ [+1(6.71e-08)]_260 38589 1.78e-04 214_[+3(7.22e-09)]_265 42594 1.07e-09 253_[+1(1.52e-10)]_205_\ [+2(1.18e-07)]_5 44317 3.92e-14 350_[+3(3.32e-10)]_39_\ [+2(7.36e-09)]_5_[+1(1.93e-07)]_48 36611 2.17e-12 31_[+1(1.10e-07)]_98_[+3(3.54e-08)]_\ 255_[+2(8.54e-09)]_58 45740 9.40e-12 207_[+3(1.12e-10)]_253_\ [+2(3.63e-09)] 50431 1.76e-08 121_[+1(6.71e-08)]_227_\ [+3(4.53e-09)]_113 43603 5.42e-05 322_[+1(3.55e-08)]_160 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************