******************************************************************************** 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/490/490.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10035 1.0000 500 10442 1.0000 500 10541 1.0000 500 12075 1.0000 500 21666 1.0000 500 2412 1.0000 500 25026 1.0000 500 3238 1.0000 500 3800 1.0000 500 3848 1.0000 500 6714 1.0000 500 6886 1.0000 500 8075 1.0000 500 8111 1.0000 500 9297 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/490/490.seqs.fa -oc motifs/490 -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 0.286 C 0.238 G 0.213 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.286 C 0.238 G 0.213 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 17 sites = 7 llr = 106 E-value = 6.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1:33::::14:11::3: pos.-specific C :::3:::1:::3:::1: probability G 91739:4914a::a:19 matrix T :9:11a6:71:69:a41 bits 2.2 * * 2.0 * * ** 1.8 * * ** 1.6 * ** * * ** * Relative 1.3 *** ** * * *** * Entropy 1.1 *** **** * *** * (21.8 bits) 0.9 *** ***** * *** * 0.7 *** ***** ***** * 0.4 *** *********** * 0.2 *** ************* 0.0 ----------------- Multilevel GTGAGTTGTAGTTGTTG consensus AC G G C A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------- 8111 85 4.61e-10 TTGTTTGTCG GTGCGTGGTGGCTGTTG CAAGAACTGA 2412 131 8.18e-09 ACCAACTTGT GTGCGTTGGAGTTGTAG GCAAGCAAGC 6886 278 1.15e-08 CTATTGAGCA GTGGGTGGAGGTTGTGG GGCACCGTAA 8075 39 4.82e-08 ACCGTCGCAG GTAAGTTGTAGATGTAG GCACACGTTA 3848 212 2.42e-07 CAACTCTTGC GTAGTTTGTAGTTGTTT CGACTCAGGC 10541 320 2.42e-07 GTCACCGGCA GTGAGTGCTGGCAGTCG TTAGGCAGTG 9297 309 3.28e-07 TTGTGTTTCT AGGTGTTGTTGTTGTTG TTGGATGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8111 4.6e-10 84_[+1]_399 2412 8.2e-09 130_[+1]_353 6886 1.1e-08 277_[+1]_206 8075 4.8e-08 38_[+1]_445 3848 2.4e-07 211_[+1]_272 10541 2.4e-07 319_[+1]_164 9297 3.3e-07 308_[+1]_175 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=17 seqs=7 8111 ( 85) GTGCGTGGTGGCTGTTG 1 2412 ( 131) GTGCGTTGGAGTTGTAG 1 6886 ( 278) GTGGGTGGAGGTTGTGG 1 8075 ( 39) GTAAGTTGTAGATGTAG 1 3848 ( 212) GTAGTTTGTAGTTGTTT 1 10541 ( 320) GTGAGTGCTGGCAGTCG 1 9297 ( 309) AGGTGTTGTTGTTGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 17 n= 7260 bayes= 9.86073 E= 6.0e-001 -100 -945 201 -945 -945 -945 -58 170 0 -945 174 -945 0 26 42 -88 -945 -945 201 -88 -945 -945 -945 193 -945 -945 101 112 -945 -73 201 -945 -100 -945 -58 144 58 -945 101 -88 -945 -945 223 -945 -100 26 -945 112 -100 -945 -945 170 -945 -945 223 -945 -945 -945 -945 193 0 -73 -58 71 -945 -945 201 -88 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 17 nsites= 7 E= 6.0e-001 0.142857 0.000000 0.857143 0.000000 0.000000 0.000000 0.142857 0.857143 0.285714 0.000000 0.714286 0.000000 0.285714 0.285714 0.285714 0.142857 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.571429 0.000000 0.142857 0.857143 0.000000 0.142857 0.000000 0.142857 0.714286 0.428571 0.000000 0.428571 0.142857 0.000000 0.000000 1.000000 0.000000 0.142857 0.285714 0.000000 0.571429 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.285714 0.142857 0.142857 0.428571 0.000000 0.000000 0.857143 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GT[GA][ACG]GT[TG]GT[AG]G[TC]TGT[TA]G -------------------------------------------------------------------------------- Time 1.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 9 llr = 115 E-value = 9.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :7:28:3412a112: pos.-specific C ::8::a:16::6:11 probability G a:18::7128:397: matrix T :31:2::31:::::9 bits 2.2 * 2.0 * * 1.8 * * * * 1.6 * * * * Relative 1.3 * * * ** * * Entropy 1.1 * ***** ** * * (18.4 bits) 0.9 ******* ** *** 0.7 ******* ****** 0.4 ******* ******* 0.2 *************** 0.0 --------------- Multilevel GACGACGACGACGGT consensus T AT ATGA G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 9297 464 5.27e-10 GAGATGAGGC GACGACGACGACGGT GACAACTCAA 3848 353 1.31e-07 TTTGCGCAAT GACGACGTGAAGGGT AGAAAGATAC 6886 7 3.60e-07 AAGGTG GACGACGGGGACGGC AGGACGGCGG 8111 333 5.98e-07 GGCGTTCTTT GTTGACGTCGACGAT AAAGGCGATT 10442 49 5.98e-07 ACACTCCAAT GACGACATTGACGAT TTGGTCCGTG 2412 436 8.48e-07 AAGGAATAGA GACGACGCCAACGCT AATTGACACT 3800 82 1.67e-06 ATTGACGGAA GACATCGACGAGAGT TGGGTATCGC 21666 23 1.67e-06 CGTAGAGAAC GTGAACAACGAGGGT TTGCTTTGTC 10541 104 3.39e-06 AGATTCTGCT GTCGTCAAAGAAGGT GCGTGGTCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9297 5.3e-10 463_[+2]_22 3848 1.3e-07 352_[+2]_133 6886 3.6e-07 6_[+2]_479 8111 6e-07 332_[+2]_153 10442 6e-07 48_[+2]_437 2412 8.5e-07 435_[+2]_50 3800 1.7e-06 81_[+2]_404 21666 1.7e-06 22_[+2]_463 10541 3.4e-06 103_[+2]_382 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=9 9297 ( 464) GACGACGACGACGGT 1 3848 ( 353) GACGACGTGAAGGGT 1 6886 ( 7) GACGACGGGGACGGC 1 8111 ( 333) GTTGACGTCGACGAT 1 10442 ( 49) GACGACATTGACGAT 1 2412 ( 436) GACGACGCCAACGCT 1 3800 ( 82) GACATCGACGAGAGT 1 21666 ( 23) GTGAACAACGAGGGT 1 10541 ( 104) GTCGTCAAAGAAGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 7290 bayes= 9.79446 E= 9.5e+000 -982 -982 223 -982 122 -982 -982 34 -982 171 -94 -124 -37 -982 187 -982 144 -982 -982 -24 -982 207 -982 -982 22 -982 164 -982 63 -110 -94 34 -136 122 6 -124 -37 -982 187 -982 180 -982 -982 -982 -136 122 64 -982 -136 -982 206 -982 -37 -110 164 -982 -982 -110 -982 176 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 9.5e+000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.777778 0.111111 0.111111 0.222222 0.000000 0.777778 0.000000 0.777778 0.000000 0.000000 0.222222 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.444444 0.111111 0.111111 0.333333 0.111111 0.555556 0.222222 0.111111 0.222222 0.000000 0.777778 0.000000 1.000000 0.000000 0.000000 0.000000 0.111111 0.555556 0.333333 0.000000 0.111111 0.000000 0.888889 0.000000 0.222222 0.111111 0.666667 0.000000 0.000000 0.111111 0.000000 0.888889 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[AT]C[GA][AT]C[GA][AT][CG][GA]A[CG]G[GA]T -------------------------------------------------------------------------------- Time 3.73 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 8 llr = 104 E-value = 7.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::1::43:4:::11 pos.-specific C :91441:3a::96:9 probability G 31:5:94::3a::9: matrix T 8:9:6:35:4:14:: bits 2.2 * 2.0 * * 1.8 * * 1.6 * * * ** ** Relative 1.3 ** * * ** ** Entropy 1.1 *** ** * ***** (18.8 bits) 0.9 *** ** * ***** 0.7 ****** * ***** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel TCTGTGATCAGCCGC consensus G CC GA T T sequence TC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 8075 356 1.75e-07 CTCCCTGGAT TCCGCGGTCAGCCGC AATCATCGGC 25026 376 1.90e-07 TCTCTCCGGC TCTCCGAACAGCTGC TGTTCGTGAA 21666 246 2.29e-07 AACTGCTCTG TGTGTGTTCGGCCGC TCGCATTCCT 10541 237 2.56e-07 TCCTCTTCTG TCTCTCGTCGGCCGC CGAGTTGTGA 6714 459 4.18e-07 CAACGTCTTG TCTGCGGCCAGTCGC AACGCACCCG 12075 412 6.06e-07 TCCTCTCTGC TCTCTGACCTGCCAC TCTCATACCT 2412 411 9.04e-07 TCGATCTCAA GCTGTGATCTGCTGA AAGGAATAGA 3848 133 1.49e-06 GACTCTGACT GCTATGTACTGCTGC TAAATACTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8075 1.8e-07 355_[+3]_130 25026 1.9e-07 375_[+3]_110 21666 2.3e-07 245_[+3]_240 10541 2.6e-07 236_[+3]_249 6714 4.2e-07 458_[+3]_27 12075 6.1e-07 411_[+3]_74 2412 9e-07 410_[+3]_75 3848 1.5e-06 132_[+3]_353 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=8 8075 ( 356) TCCGCGGTCAGCCGC 1 25026 ( 376) TCTCCGAACAGCTGC 1 21666 ( 246) TGTGTGTTCGGCCGC 1 10541 ( 237) TCTCTCGTCGGCCGC 1 6714 ( 459) TCTGCGGCCAGTCGC 1 12075 ( 412) TCTCTGACCTGCCAC 1 2412 ( 411) GCTGTGATCTGCTGA 1 3848 ( 133) GCTATGTACTGCTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 7290 bayes= 10.5677 E= 7.4e+001 -965 -965 23 151 -965 188 -77 -965 -965 -93 -965 173 -119 66 123 -965 -965 66 -965 125 -965 -93 204 -965 39 -965 81 -7 -20 7 -965 93 -965 207 -965 -965 39 -965 23 51 -965 -965 223 -965 -965 188 -965 -107 -965 139 -965 51 -119 -965 204 -965 -119 188 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 7.4e+001 0.000000 0.000000 0.250000 0.750000 0.000000 0.875000 0.125000 0.000000 0.000000 0.125000 0.000000 0.875000 0.125000 0.375000 0.500000 0.000000 0.000000 0.375000 0.000000 0.625000 0.000000 0.125000 0.875000 0.000000 0.375000 0.000000 0.375000 0.250000 0.250000 0.250000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.375000 0.000000 0.250000 0.375000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.625000 0.000000 0.375000 0.125000 0.000000 0.875000 0.000000 0.125000 0.875000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TG]CT[GC][TC]G[AGT][TAC]C[ATG]GC[CT]GC -------------------------------------------------------------------------------- Time 5.39 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10035 2.91e-01 500 10442 1.98e-03 48_[+2(5.98e-07)]_437 10541 7.76e-09 103_[+2(3.39e-06)]_118_\ [+3(2.56e-07)]_68_[+1(2.42e-07)]_164 12075 3.97e-03 411_[+3(6.06e-07)]_74 21666 5.68e-06 22_[+2(1.67e-06)]_208_\ [+3(2.29e-07)]_240 2412 3.01e-10 130_[+1(8.18e-09)]_263_\ [+3(9.04e-07)]_10_[+2(8.48e-07)]_50 25026 1.99e-03 375_[+3(1.90e-07)]_110 3238 9.78e-01 500 3800 1.20e-02 81_[+2(1.67e-06)]_404 3848 1.96e-09 132_[+3(1.49e-06)]_64_\ [+1(2.42e-07)]_124_[+2(1.31e-07)]_133 6714 3.54e-04 320_[+1(6.47e-05)]_121_\ [+3(4.18e-07)]_27 6886 1.41e-07 6_[+2(3.60e-07)]_256_[+1(1.15e-08)]_\ 206 8075 1.60e-07 38_[+1(4.82e-08)]_300_\ [+3(1.75e-07)]_130 8111 1.79e-08 84_[+1(4.61e-10)]_231_\ [+2(5.98e-07)]_153 9297 5.19e-09 308_[+1(3.28e-07)]_6_[+1(7.82e-05)]_\ 115_[+2(5.27e-10)]_22 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************