******************************************************************************** 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/253/253.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10266 1.0000 500 1042 1.0000 500 11589 1.0000 500 21832 1.0000 500 24752 1.0000 500 260754 1.0000 500 260886 1.0000 500 263205 1.0000 500 34203 1.0000 500 41780 1.0000 500 4903 1.0000 500 8384 1.0000 500 8928 1.0000 500 bd683 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/253/253.seqs.fa -oc motifs/253 -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= 14 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= 7000 N= 14 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.272 C 0.223 G 0.249 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.272 C 0.223 G 0.249 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 7 llr = 102 E-value = 1.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 64:a:a4:91::a13 pos.-specific C 44::::3::3:::1: probability G :1a:a::a::aa:67 matrix T ::::::3:16:::1: bits 2.2 1.9 **** * *** 1.7 **** * *** 1.5 **** * *** Relative 1.3 **** ** *** Entropy 1.1 * **** ** *** * (21.1 bits) 0.9 * **** ** *** * 0.6 ****** ****** * 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel AAGAGAAGATGGAGG consensus CC C C A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 11589 91 1.52e-08 CCTGACGTCC ACGAGAAGACGGAGG AAACGTAGAC 4903 13 5.98e-08 TTGTGTTGGA AGGAGATGATGGAGG CAAATACACG 41780 135 9.28e-08 AGAGACTCGT CCGAGACGAAGGAGG GAGAAAAACC 8384 168 1.59e-07 CAGCTAACGG CCGAGATGTTGGAGG CGAAAGCCGC 1042 77 1.79e-07 GAGTCCGAGG AAGAGAAGACGGAAG AGGAAGGAAG 24752 155 2.30e-07 CGAACGTGAG CAGAGAAGATGGACA GTACGGATAC 10266 2 2.88e-07 T AAGAGACGATGGATA GTGTAGATGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11589 1.5e-08 90_[+1]_395 4903 6e-08 12_[+1]_473 41780 9.3e-08 134_[+1]_351 8384 1.6e-07 167_[+1]_318 1042 1.8e-07 76_[+1]_409 24752 2.3e-07 154_[+1]_331 10266 2.9e-07 1_[+1]_484 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=7 11589 ( 91) ACGAGAAGACGGAGG 1 4903 ( 13) AGGAGATGATGGAGG 1 41780 ( 135) CCGAGACGAAGGAGG 1 8384 ( 168) CCGAGATGTTGGAGG 1 1042 ( 77) AAGAGAAGACGGAAG 1 24752 ( 155) CAGAGAAGATGGACA 1 10266 ( 2) AAGAGACGATGGATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 6804 bayes= 9.76704 E= 1.5e+000 107 94 -945 -945 66 94 -80 -945 -945 -945 200 -945 188 -945 -945 -945 -945 -945 200 -945 188 -945 -945 -945 66 36 -945 16 -945 -945 200 -945 166 -945 -945 -84 -92 36 -945 116 -945 -945 200 -945 -945 -945 200 -945 188 -945 -945 -945 -92 -64 119 -84 7 -945 152 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 1.5e+000 0.571429 0.428571 0.000000 0.000000 0.428571 0.428571 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.285714 0.000000 0.285714 0.000000 0.000000 1.000000 0.000000 0.857143 0.000000 0.000000 0.142857 0.142857 0.285714 0.000000 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.142857 0.571429 0.142857 0.285714 0.000000 0.714286 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC][AC]GAGA[ACT]GA[TC]GGAG[GA] -------------------------------------------------------------------------------- Time 1.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 9 llr = 131 E-value = 6.1e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 936:3:1:8:2:3::2::1: pos.-specific C 17:a1763:a2264184666 probability G ::::21:71:::::1:1:3: matrix T ::4:323:1:68168:44:4 bits 2.2 * * 1.9 * * 1.7 * * 1.5 * * * Relative 1.3 * * * * * Entropy 1.1 ** * * * * *** * * (21.0 bits) 0.9 **** * *** * *** * * 0.6 **** *************** 0.4 **** *************** 0.2 **** *************** 0.0 -------------------- Multilevel ACACACCGACTTCTTCCCCC consensus AT TTTC ACAC ATTGT sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 1042 469 2.41e-10 TTCCGCTCTC ACACACCCACCTCTTCCCCC ATACTCTCCA 8384 385 1.16e-08 TTGGAACTGG ACACTTCGACCTACTCCTCT CCATAATCAT 11589 173 5.34e-08 GATCGGCACC ACACCCCCACTCCTTACCGC GGCAGCCTGC 10266 421 7.80e-08 TTCACACATC AAACGCTGACATCTTCGTCT CCTCACACAC 260754 150 8.54e-08 GCCCACCCAA ACTCACAGTCTTATTCCTCC CTTCGCCCAA bd683 284 2.66e-07 AGGTTGAGCA AATCTCTGACTTTCGCTTCT TTCTACATAC 8928 432 2.86e-07 CGTACATCAA AATCATCGGCTTCCTCTCAC AATACTACAC 34203 27 2.86e-07 GCTCAAACCT CCACTGCCACATCTTCTCGT TCAATGGCAC 263205 20 4.92e-07 CATTCTTTCC ACTCGCTGACTCACCATCGC GTTTGAGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1042 2.4e-10 468_[+2]_12 8384 1.2e-08 384_[+2]_96 11589 5.3e-08 172_[+2]_308 10266 7.8e-08 420_[+2]_60 260754 8.5e-08 149_[+2]_331 bd683 2.7e-07 283_[+2]_197 8928 2.9e-07 431_[+2]_49 34203 2.9e-07 26_[+2]_454 263205 4.9e-07 19_[+2]_461 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=9 1042 ( 469) ACACACCCACCTCTTCCCCC 1 8384 ( 385) ACACTTCGACCTACTCCTCT 1 11589 ( 173) ACACCCCCACTCCTTACCGC 1 10266 ( 421) AAACGCTGACATCTTCGTCT 1 260754 ( 150) ACTCACAGTCTTATTCCTCC 1 bd683 ( 284) AATCTCTGACTTTCGCTTCT 1 8928 ( 432) AATCATCGGCTTCCTCTCAC 1 34203 ( 27) CCACTGCCACATCTTCTCGT 1 263205 ( 20) ACTCGCTGACTCACCATCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 6734 bayes= 10.951 E= 6.1e+001 171 -100 -982 -982 30 158 -982 -982 103 -982 -982 80 -982 216 -982 -982 30 -100 -17 38 -982 158 -116 -20 -129 132 -982 38 -982 58 142 -982 152 -982 -116 -120 -982 216 -982 -982 -29 -1 -982 112 -982 -1 -982 160 30 132 -982 -120 -982 99 -982 112 -982 -100 -116 160 -29 180 -982 -982 -982 99 -116 80 -982 132 -982 80 -129 132 42 -982 -982 132 -982 80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.1e+001 0.888889 0.111111 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.555556 0.000000 0.000000 0.444444 0.000000 1.000000 0.000000 0.000000 0.333333 0.111111 0.222222 0.333333 0.000000 0.666667 0.111111 0.222222 0.111111 0.555556 0.000000 0.333333 0.000000 0.333333 0.666667 0.000000 0.777778 0.000000 0.111111 0.111111 0.000000 1.000000 0.000000 0.000000 0.222222 0.222222 0.000000 0.555556 0.000000 0.222222 0.000000 0.777778 0.333333 0.555556 0.000000 0.111111 0.000000 0.444444 0.000000 0.555556 0.000000 0.111111 0.111111 0.777778 0.222222 0.777778 0.000000 0.000000 0.000000 0.444444 0.111111 0.444444 0.000000 0.555556 0.000000 0.444444 0.111111 0.555556 0.333333 0.000000 0.000000 0.555556 0.000000 0.444444 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[CA][AT]C[ATG][CT][CT][GC]AC[TAC][TC][CA][TC]T[CA][CT][CT][CG][CT] -------------------------------------------------------------------------------- Time 3.33 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 6 llr = 76 E-value = 3.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2:::22:::3 pos.-specific C a58a:8:3:2a: probability G ::::a225:::7 matrix T :5::::7:a8:: bits 2.2 * * * 1.9 * ** * * 1.7 * ** * * 1.5 * **** * * Relative 1.3 * **** *** Entropy 1.1 ****** **** (18.2 bits) 0.9 ****** **** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCCCGCTGTTCG consensus T C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 41780 253 2.70e-07 ACAAGAGTAG CCCCGCTATTCG ATACCCCGAC bd683 427 4.74e-07 CGCGTTGTGT CTCCGCGGTTCG ACGAACACCA 10266 80 6.39e-07 CCTGTGCGCC CCCCGGTGTTCG TTTGAGAAGC 1042 445 7.34e-07 CATCCCCCCC CCCCGCTCTCCG CTTTCCGCTC 34203 166 1.29e-06 TTTTGAGCTT CTCCGCAGTTCA GCTTCTCGGT 24752 489 2.35e-06 TCTAAATCTA CTACGCTCTTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41780 2.7e-07 252_[+3]_236 bd683 4.7e-07 426_[+3]_62 10266 6.4e-07 79_[+3]_409 1042 7.3e-07 444_[+3]_44 34203 1.3e-06 165_[+3]_323 24752 2.3e-06 488_[+3] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=6 41780 ( 253) CCCCGCTATTCG 1 bd683 ( 427) CTCCGCGGTTCG 1 10266 ( 80) CCCCGGTGTTCG 1 1042 ( 445) CCCCGCTCTCCG 1 34203 ( 166) CTCCGCAGTTCA 1 24752 ( 489) CTACGCTCTTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6846 bayes= 10.6026 E= 3.7e+002 -923 216 -923 -923 -923 116 -923 96 -70 190 -923 -923 -923 216 -923 -923 -923 -923 200 -923 -923 190 -58 -923 -70 -923 -58 138 -70 58 100 -923 -923 -923 -923 196 -923 -42 -923 170 -923 216 -923 -923 30 -923 142 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 6 E= 3.7e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.166667 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.166667 0.000000 0.166667 0.666667 0.166667 0.333333 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[CT]CCGCT[GC]TTC[GA] -------------------------------------------------------------------------------- Time 4.90 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10266 6.50e-10 1_[+1(2.88e-07)]_63_[+3(6.39e-07)]_\ 329_[+2(7.80e-08)]_60 1042 2.13e-12 76_[+1(1.79e-07)]_353_\ [+3(7.34e-07)]_12_[+2(2.41e-10)]_12 11589 2.32e-08 90_[+1(1.52e-08)]_67_[+2(5.34e-08)]_\ 147_[+1(5.60e-05)]_146 21832 6.98e-01 500 24752 1.28e-05 154_[+1(2.30e-07)]_319_\ [+3(2.35e-06)] 260754 1.71e-03 149_[+2(8.54e-08)]_331 260886 2.27e-01 500 263205 2.36e-03 19_[+2(4.92e-07)]_461 34203 9.75e-06 26_[+2(2.86e-07)]_119_\ [+3(1.29e-06)]_323 41780 5.76e-07 134_[+1(9.28e-08)]_103_\ [+3(2.70e-07)]_236 4903 4.32e-04 12_[+1(5.98e-08)]_473 8384 1.97e-08 167_[+1(1.59e-07)]_202_\ [+2(1.16e-08)]_96 8928 2.07e-03 431_[+2(2.86e-07)]_49 bd683 2.17e-06 283_[+2(2.66e-07)]_123_\ [+3(4.74e-07)]_62 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************