******************************************************************************** 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/90/90.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 262692 1.0000 500 9652 1.0000 500 bd1081 1.0000 500 bd1173 1.0000 500 bd1214 1.0000 500 bd529 1.0000 500 bd668 1.0000 500 bd765 1.0000 500 bd843 1.0000 500 bd890 1.0000 500 bd951 1.0000 500 ThpsCt016 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/90/90.seqs.fa -oc motifs/90 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.296 C 0.236 G 0.222 T 0.245 Background letter frequencies (from dataset with add-one prior applied): A 0.296 C 0.237 G 0.222 T 0.245 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 10 llr = 120 E-value = 2.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 21723:6112:a:1: pos.-specific C :3::1:1:5:6:::: probability G 82123a1:484:1:a matrix T :4263:29::::99: bits 2.2 * * 2.0 * * 1.7 * * * 1.5 * * **** Relative 1.3 * * * * **** Entropy 1.1 * * * ****** (17.3 bits) 0.9 * * * ****** 0.7 * ** * ******** 0.4 * ** * ******** 0.2 **** ********** 0.0 --------------- Multilevel GTATAGATCGCATTG consensus ACTAG T GAG sequence G GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- bd765 371 1.85e-08 GCAACGTGAT GGATTGATGGCATTG CCATCAATTT bd1173 212 4.32e-08 CCAACGCTTC GTTTGGATCGGATTG CATCAAGTCT bd890 123 9.20e-07 ACAACTCTCT ACAGAGATGGCATTG CGAGCTTACC 262692 354 1.21e-06 ATCATGAGAT GGATGGTTGAGATTG GTAGGATCGA bd1081 87 1.98e-06 GTTTCAGTTT GTGAAGTTCGCATTG AAGTTGAACT bd843 209 2.31e-06 TTCAATCTCC GCAACGCTCGCATTG CCCGTGGCAA bd1214 2 2.31e-06 C GAATGGAACGGATTG CCATCTCGTC 9652 461 3.35e-06 CCAACTACAA GCATTGATCAGATAG ACCCTCAATC bd668 102 3.61e-06 AACAACGAGG ATAGAGATAGCATTG CATCAAGTGA bd529 427 3.61e-06 GGGGCAATGA GTTTTGGTGGCAGTG TCAAGTCTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd765 1.9e-08 370_[+1]_115 bd1173 4.3e-08 211_[+1]_274 bd890 9.2e-07 122_[+1]_363 262692 1.2e-06 353_[+1]_132 bd1081 2e-06 86_[+1]_399 bd843 2.3e-06 208_[+1]_277 bd1214 2.3e-06 1_[+1]_484 9652 3.4e-06 460_[+1]_25 bd668 3.6e-06 101_[+1]_384 bd529 3.6e-06 426_[+1]_59 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=10 bd765 ( 371) GGATTGATGGCATTG 1 bd1173 ( 212) GTTTGGATCGGATTG 1 bd890 ( 123) ACAGAGATGGCATTG 1 262692 ( 354) GGATGGTTGAGATTG 1 bd1081 ( 87) GTGAAGTTCGCATTG 1 bd843 ( 209) GCAACGCTCGCATTG 1 bd1214 ( 2) GAATGGAACGGATTG 1 9652 ( 461) GCATTGATCAGATAG 1 bd668 ( 102) ATAGAGATAGCATTG 1 bd529 ( 427) GTTTTGGTGGCAGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 5832 bayes= 9.43731 E= 2.3e-001 -57 -997 185 -997 -156 34 -15 71 124 -997 -115 -29 -57 -997 -15 129 2 -124 43 29 -997 -997 217 -997 102 -124 -115 -29 -156 -997 -997 188 -156 108 85 -997 -57 -997 185 -997 -997 134 85 -997 175 -997 -997 -997 -997 -997 -115 188 -156 -997 -997 188 -997 -997 217 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 2.3e-001 0.200000 0.000000 0.800000 0.000000 0.100000 0.300000 0.200000 0.400000 0.700000 0.000000 0.100000 0.200000 0.200000 0.000000 0.200000 0.600000 0.300000 0.100000 0.300000 0.300000 0.000000 0.000000 1.000000 0.000000 0.600000 0.100000 0.100000 0.200000 0.100000 0.000000 0.000000 0.900000 0.100000 0.500000 0.400000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.600000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.900000 0.100000 0.000000 0.000000 0.900000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA][TCG][AT][TAG][AGT]G[AT]T[CG][GA][CG]ATTG -------------------------------------------------------------------------------- Time 1.29 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 7 llr = 112 E-value = 2.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 6:1:633::a6:a3:a9:a pos.-specific C 4:93443:9:37::a::9: probability G :6:1::171:1::7::1:: matrix T :4:6:333:::3:::::1: bits 2.2 * 2.0 * 1.7 * * ** * 1.5 * ** * ** ** Relative 1.3 * *** ** ***** Entropy 1.1 ** *** ******** (23.0 bits) 0.9 *** * *** ******** 0.7 ***** *** ******** 0.4 ****** ************ 0.2 ****** ************ 0.0 ------------------- Multilevel AGCTACAGCAACAGCAACA consensus CT CCACT CT A sequence TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- bd890 448 6.02e-10 CCGACAACAA CGCCACAGCAACAGCAACA CAACAGCAAC bd765 100 4.71e-09 GGGCCGATCA ATCTCCTTCACCAGCAACA TTGCGCCCCC bd668 178 5.31e-09 TTGTTACGAC AGCCATTGCAATAGCAACA CATGGAACAC bd1081 446 7.69e-09 CAGCATTCAT CTCTCACGCAACAACAACA TTCAATCTAC bd1173 444 8.87e-08 GAAGTCCGTT ATCGAAAGCAATAACAACA ATGATGTTGA bd529 71 1.12e-07 ATGAAGCTGT AGCTCTCGCAGCAGCAGTA AAGGAAAGCC bd951 479 2.11e-07 TTTCAACCAA CGATACGTGACCAGCAACA ACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd890 6e-10 447_[+2]_34 bd765 4.7e-09 99_[+2]_382 bd668 5.3e-09 177_[+2]_304 bd1081 7.7e-09 445_[+2]_36 bd1173 8.9e-08 443_[+2]_38 bd529 1.1e-07 70_[+2]_411 bd951 2.1e-07 478_[+2]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=7 bd890 ( 448) CGCCACAGCAACAGCAACA 1 bd765 ( 100) ATCTCCTTCACCAGCAACA 1 bd668 ( 178) AGCCATTGCAATAGCAACA 1 bd1081 ( 446) CTCTCACGCAACAACAACA 1 bd1173 ( 444) ATCGAAAGCAATAACAACA 1 bd529 ( 71) AGCTCTCGCAGCAGCAGTA 1 bd951 ( 479) CGATACGTGACCAGCAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 5784 bayes= 9.53243 E= 2.7e+000 95 86 -945 -945 -945 -945 136 81 -105 186 -945 -945 -945 27 -64 122 95 86 -945 -945 -5 86 -945 22 -5 27 -64 22 -945 -945 168 22 -945 186 -64 -945 175 -945 -945 -945 95 27 -64 -945 -945 159 -945 22 175 -945 -945 -945 -5 -945 168 -945 -945 208 -945 -945 175 -945 -945 -945 153 -945 -64 -945 -945 186 -945 -78 175 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 7 E= 2.7e+000 0.571429 0.428571 0.000000 0.000000 0.000000 0.000000 0.571429 0.428571 0.142857 0.857143 0.000000 0.000000 0.000000 0.285714 0.142857 0.571429 0.571429 0.428571 0.000000 0.000000 0.285714 0.428571 0.000000 0.285714 0.285714 0.285714 0.142857 0.285714 0.000000 0.000000 0.714286 0.285714 0.000000 0.857143 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.571429 0.285714 0.142857 0.000000 0.000000 0.714286 0.000000 0.285714 1.000000 0.000000 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC][GT]C[TC][AC][CAT][ACT][GT]CA[AC][CT]A[GA]CAACA -------------------------------------------------------------------------------- Time 2.57 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 8 llr = 124 E-value = 1.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :a83:33:5439:41:4:5:: pos.-specific C 1::4::1:::::1:3:11::4 probability G 9:3:a819:58:565a18545 matrix T :::4::5151:14:1:41:61 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 GAACGGTGAGGAGGGGAGATG consensus GT AA TAA TAC T GGC sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd529 369 3.76e-11 GATTGTAGGA GAGTGGTGTGGAGGGGAGGGG CAGGCGAAGG bd951 37 7.00e-09 TTACGAGAGC GAAAGGAGAGGATGAGAGATG AAAAGTAATC 262692 133 2.17e-08 TCACATTCAC CAATGGTGAGAAGGCGTGGGC GATGAGTCCA bd1214 163 3.44e-08 GGAGGAGCTT GAAAGGTGTAGAGAGGCCATC ACCAGTCTGG bd1173 119 3.75e-08 CTCGAGTAGT GAACGGATTGAATGGGGGGTG CTGTACTACT bd765 330 1.13e-07 TCGCATTGGC GAGTGGTGAAGTCACGTGATG GCGAGTGATG bd843 77 2.05e-07 AGAGGACTGC GAACGAGGAAGAGAGGTTGTT GGGGGTTTTC bd1081 27 2.05e-07 CAACCACAAC GAACGACGTTGATGTGAGAGC CGCACGTTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd529 3.8e-11 368_[+3]_111 bd951 7e-09 36_[+3]_443 262692 2.2e-08 132_[+3]_347 bd1214 3.4e-08 162_[+3]_317 bd1173 3.8e-08 118_[+3]_361 bd765 1.1e-07 329_[+3]_150 bd843 2e-07 76_[+3]_403 bd1081 2e-07 26_[+3]_453 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=8 bd529 ( 369) GAGTGGTGTGGAGGGGAGGGG 1 bd951 ( 37) GAAAGGAGAGGATGAGAGATG 1 262692 ( 133) CAATGGTGAGAAGGCGTGGGC 1 bd1214 ( 163) GAAAGGTGTAGAGAGGCCATC 1 bd1173 ( 119) GAACGGATTGAATGGGGGGTG 1 bd765 ( 330) GAGTGGTGAAGTCACGTGATG 1 bd843 ( 77) GAACGAGGAAGAGAGGTTGTT 1 bd1081 ( 27) GAACGACGTTGATGTGAGAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 10.2276 E= 1.1e+001 -965 -92 198 -965 175 -965 -965 -965 134 -965 17 -965 -24 66 -965 61 -965 -965 217 -965 -24 -965 175 -965 -24 -92 -83 103 -965 -965 198 -97 75 -965 -965 103 34 -965 117 -97 -24 -965 175 -965 156 -965 -965 -97 -965 -92 117 61 34 -965 149 -965 -124 8 117 -97 -965 -965 217 -965 34 -92 -83 61 -965 -92 175 -97 75 -965 117 -965 -965 -965 75 135 -965 66 117 -97 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 1.1e+001 0.000000 0.125000 0.875000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.375000 0.000000 0.375000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.125000 0.125000 0.500000 0.000000 0.000000 0.875000 0.125000 0.500000 0.000000 0.000000 0.500000 0.375000 0.000000 0.500000 0.125000 0.250000 0.000000 0.750000 0.000000 0.875000 0.000000 0.000000 0.125000 0.000000 0.125000 0.500000 0.375000 0.375000 0.000000 0.625000 0.000000 0.125000 0.250000 0.500000 0.125000 0.000000 0.000000 1.000000 0.000000 0.375000 0.125000 0.125000 0.375000 0.000000 0.125000 0.750000 0.125000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.375000 0.625000 0.000000 0.375000 0.500000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GA[AG][CTA]G[GA][TA]G[AT][GA][GA]A[GT][GA][GC]G[AT]G[AG][TG][GC] -------------------------------------------------------------------------------- Time 3.81 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262692 1.09e-06 132_[+3(2.17e-08)]_200_\ [+1(1.21e-06)]_132 9652 3.04e-02 460_[+1(3.35e-06)]_25 bd1081 1.55e-10 26_[+3(2.05e-07)]_39_[+1(1.98e-06)]_\ 275_[+2(6.84e-05)]_50_[+2(7.69e-09)]_36 bd1173 8.68e-12 118_[+3(3.75e-08)]_72_\ [+1(4.32e-08)]_217_[+2(8.87e-08)]_38 bd1214 2.42e-06 1_[+1(2.31e-06)]_146_[+3(3.44e-08)]_\ 67_[+1(5.19e-05)]_235 bd529 1.05e-12 70_[+2(1.12e-07)]_259_\ [+1(4.75e-05)]_5_[+3(3.76e-11)]_37_[+1(3.61e-06)]_59 bd668 6.60e-07 101_[+1(3.61e-06)]_61_\ [+2(5.31e-09)]_233_[+2(6.61e-05)]_52 bd765 6.95e-13 99_[+2(4.71e-09)]_211_\ [+3(1.13e-07)]_20_[+1(1.85e-08)]_115 bd843 8.35e-06 76_[+3(2.05e-07)]_111_\ [+1(2.31e-06)]_277 bd890 2.46e-08 122_[+1(9.20e-07)]_310_\ [+2(6.02e-10)]_34 bd951 1.05e-08 36_[+3(7.00e-09)]_421_\ [+2(2.11e-07)]_3 ThpsCt016 9.22e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************