******************************************************************************** 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/296/296.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10063 1.0000 500 11004 1.0000 500 14482 1.0000 500 16912 1.0000 500 21847 1.0000 500 2671 1.0000 500 268408 1.0000 500 32678 1.0000 500 4646 1.0000 500 5108 1.0000 500 8904 1.0000 500 9835 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/296/296.seqs.fa -oc motifs/296 -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 0.251 C 0.230 G 0.255 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.251 C 0.230 G 0.255 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 128 E-value = 1.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :51::::1::811::: pos.-specific C 2:::61:12::1::31 probability G 8::815a44a219:19 matrix T :59234:44::7:a6: bits 2.1 1.9 * * * 1.7 * * * 1.5 * * * ** * Relative 1.3 * ** * ** ** * Entropy 1.1 **** * ** ** * (18.4 bits) 0.8 ***** * ** ** * 0.6 ******* ******* 0.4 ******* ******** 0.2 **************** 0.0 ---------------- Multilevel GATGCGGGGGATGTTG consensus CT TTT TT G C sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 5108 225 2.78e-09 TCCGATTCAT GTTGCGGTTGATGTTG AGAGCGTGCA 14482 317 1.25e-07 AGGCCGTCGT GTTGCCGTTGATGTCG TCGGTCGGTG 2671 160 2.07e-07 TGGAGTGAAG GATTCGGGGGGTGTTG ACGGCATTCG 32678 173 2.34e-07 AAGAGAATGT GATGCTGACGATGTCG TCGATAATGT 11004 85 7.48e-07 AGTGACGTTC GATGGGGGTGAGGTTG GTAGTTTCAC 10063 293 8.10e-07 TTCGTCTCCT CTTTTTGGTGATGTTG TTGGGTGGCG 16912 161 8.86e-07 GACGGTGTAT GTTGCGGTGGATGTGC GACGGTCGAA 8904 250 1.31e-06 ACAGTTACAG CTTGCTGGCGATATTG ATATTGACGG 4646 103 2.71e-06 CCCGGTTCCA GAAGTGGTGGACGTCG TCGTTAGGTA 21847 211 3.47e-06 GCGGTGGTGT GATGTTGCGGGAGTTG AAGCTGCCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5108 2.8e-09 224_[+1]_260 14482 1.2e-07 316_[+1]_168 2671 2.1e-07 159_[+1]_325 32678 2.3e-07 172_[+1]_312 11004 7.5e-07 84_[+1]_400 10063 8.1e-07 292_[+1]_192 16912 8.9e-07 160_[+1]_324 8904 1.3e-06 249_[+1]_235 4646 2.7e-06 102_[+1]_382 21847 3.5e-06 210_[+1]_274 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 5108 ( 225) GTTGCGGTTGATGTTG 1 14482 ( 317) GTTGCCGTTGATGTCG 1 2671 ( 160) GATTCGGGGGGTGTTG 1 32678 ( 173) GATGCTGACGATGTCG 1 11004 ( 85) GATGGGGGTGAGGTTG 1 10063 ( 293) CTTTTTGGTGATGTTG 1 16912 ( 161) GTTGCGGTGGATGTGC 1 8904 ( 250) CTTGCTGGCGATATTG 1 4646 ( 103) GAAGTGGTGGACGTCG 1 21847 ( 211) GATGTTGCGGGAGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5820 bayes= 9.43433 E= 1.7e-001 -997 -20 165 -997 99 -997 -997 92 -132 -997 -997 176 -997 -997 165 -40 -997 138 -135 18 -997 -120 97 59 -997 -997 197 -997 -132 -120 65 59 -997 -20 65 59 -997 -997 197 -997 167 -997 -35 -997 -132 -120 -135 140 -132 -997 182 -997 -997 -997 -997 192 -997 38 -135 118 -997 -120 182 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 1.7e-001 0.000000 0.200000 0.800000 0.000000 0.500000 0.000000 0.000000 0.500000 0.100000 0.000000 0.000000 0.900000 0.000000 0.000000 0.800000 0.200000 0.000000 0.600000 0.100000 0.300000 0.000000 0.100000 0.500000 0.400000 0.000000 0.000000 1.000000 0.000000 0.100000 0.100000 0.400000 0.400000 0.000000 0.200000 0.400000 0.400000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.100000 0.100000 0.100000 0.700000 0.100000 0.000000 0.900000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.300000 0.100000 0.600000 0.000000 0.100000 0.900000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC][AT]T[GT][CT][GT]G[GT][GTC]G[AG]TGT[TC]G -------------------------------------------------------------------------------- Time 1.35 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 9 llr = 102 E-value = 1.8e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :7::::4:6:4: pos.-specific C a:98:a3a:a43 probability G :1::1:2:1::: matrix T :2129:::3:17 bits 2.1 * * * * 1.9 * * * * 1.7 * * * * * 1.5 * * ** * * Relative 1.3 * **** * * Entropy 1.1 * **** * * * (16.4 bits) 0.8 ****** * * * 0.6 ****** ***** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CACCTCACACAT consensus T T C T CC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 10063 484 1.14e-07 ATCACACCAC CACCTCCCACCT CCACG 11004 435 5.23e-07 CGTCGTGGAT CACCTCCCTCAT ATCTCCACTT 16912 476 1.46e-06 TCCCATCCCG CACCTCGCTCCC CATCAGGGTG 32678 408 1.93e-06 CTCCAATTCA CGCCTCACACAT CACCGACCAA 8904 482 3.16e-06 CGGGTTAGGA CATCTCACACAT CGTCATC 14482 6 3.16e-06 AAACA CTCCTCGCACCC TTGACCATCC 268408 135 4.06e-06 AGTTTGATCG CTCTTCACACCT ACGAGATGAT 9835 235 1.21e-05 CGGACTGGTG CACCGCCCGCAT AAAGAACTTC 4646 252 1.21e-05 TCCCCTCCAC CACTTCACTCTC AATACGTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10063 1.1e-07 483_[+2]_5 11004 5.2e-07 434_[+2]_54 16912 1.5e-06 475_[+2]_13 32678 1.9e-06 407_[+2]_81 8904 3.2e-06 481_[+2]_7 14482 3.2e-06 5_[+2]_483 268408 4.1e-06 134_[+2]_354 9835 1.2e-05 234_[+2]_254 4646 1.2e-05 251_[+2]_237 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=9 10063 ( 484) CACCTCCCACCT 1 11004 ( 435) CACCTCCCTCAT 1 16912 ( 476) CACCTCGCTCCC 1 32678 ( 408) CGCCTCACACAT 1 8904 ( 482) CATCTCACACAT 1 14482 ( 6) CTCCTCGCACCC 1 268408 ( 135) CTCTTCACACCT 1 9835 ( 235) CACCGCCCGCAT 1 4646 ( 252) CACTTCACTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5868 bayes= 9.48101 E= 1.8e+000 -982 212 -982 -982 141 -982 -119 -25 -982 195 -982 -125 -982 176 -982 -25 -982 -982 -119 175 -982 212 -982 -982 82 54 -20 -982 -982 212 -982 -982 115 -982 -119 33 -982 212 -982 -982 82 95 -982 -125 -982 54 -982 133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 1.8e+000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.111111 0.222222 0.000000 0.888889 0.000000 0.111111 0.000000 0.777778 0.000000 0.222222 0.000000 0.000000 0.111111 0.888889 0.000000 1.000000 0.000000 0.000000 0.444444 0.333333 0.222222 0.000000 0.000000 1.000000 0.000000 0.000000 0.555556 0.000000 0.111111 0.333333 0.000000 1.000000 0.000000 0.000000 0.444444 0.444444 0.000000 0.111111 0.000000 0.333333 0.000000 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[AT]C[CT]TC[ACG]C[AT]C[AC][TC] -------------------------------------------------------------------------------- Time 2.71 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 8 llr = 121 E-value = 8.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :6a6:13:541311:::1:8: pos.-specific C 91:391663391965993919 probability G 1::::8::31:1::11:31:: matrix T :3:11:14:3:5:34:14:11 bits 2.1 1.9 * 1.7 * 1.5 * * * * * ** * * Relative 1.3 * * * * * ** * * Entropy 1.1 * * * * * * ** * * (21.9 bits) 0.8 * * **** * ** ** *** 0.6 ******** * ***** *** 0.4 ********* * ***** *** 0.2 ********* ******* *** 0.0 --------------------- Multilevel CAAACGCCAACTCCCCCTCAC consensus T C ATCC A TT C sequence GT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 14482 423 4.92e-10 AATTACCAAA CAAACGCCATCACCCCCCCAT CAACCCTCCT 32678 441 5.65e-10 CCACTCTCGG CAAACGCTGCCTCCGCCGCAC AAACTTCATC 10063 449 4.15e-08 ATTAATCAAA CAAACATCAGCTCATCCTCAC TACCATCACA 4646 231 8.60e-08 TGACTGCCTC CTATCCACAACTCCCCTCCAC CACTTCACTC 8904 369 1.17e-07 GCCGCTGCCG CTACCGCTCCCGCTCCCGCTC CACGATCAAC 5108 449 1.25e-07 TACACAACCT CAAACGACGAATCTTCCACCC ACAAGCACAC 21847 69 1.35e-07 GAGGTAGTAT GAACCGCCATCAACCCCTGAC AACGAAATGC 268408 463 2.22e-07 AACACGTGCA CCAATGCTCACCCCTGCTCAC AACGAGCTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14482 4.9e-10 422_[+3]_57 32678 5.6e-10 440_[+3]_39 10063 4.2e-08 448_[+3]_31 4646 8.6e-08 230_[+3]_249 8904 1.2e-07 368_[+3]_111 5108 1.3e-07 448_[+3]_31 21847 1.4e-07 68_[+3]_411 268408 2.2e-07 462_[+3]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=8 14482 ( 423) CAAACGCCATCACCCCCCCAT 1 32678 ( 441) CAAACGCTGCCTCCGCCGCAC 1 10063 ( 449) CAAACATCAGCTCATCCTCAC 1 4646 ( 231) CTATCCACAACTCCCCTCCAC 1 8904 ( 369) CTACCGCTCCCGCTCCCGCTC 1 5108 ( 449) CAAACGACGAATCTTCCACCC 1 21847 ( 69) GAACCGCCATCAACCCCTGAC 1 268408 ( 463) CCAATGCTCACCCCTGCTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 10.2276 E= 8.3e-001 -965 193 -102 -965 132 -88 -965 -8 199 -965 -965 -965 132 12 -965 -108 -965 193 -965 -108 -100 -88 156 -965 0 144 -965 -108 -965 144 -965 50 99 12 -3 -965 58 12 -102 -8 -100 193 -965 -965 0 -88 -102 92 -100 193 -965 -965 -100 144 -965 -8 -965 112 -102 50 -965 193 -102 -965 -965 193 -965 -108 -100 12 -3 50 -965 193 -102 -965 158 -88 -965 -108 -965 193 -965 -108 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 8.3e-001 0.000000 0.875000 0.125000 0.000000 0.625000 0.125000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.625000 0.250000 0.000000 0.125000 0.000000 0.875000 0.000000 0.125000 0.125000 0.125000 0.750000 0.000000 0.250000 0.625000 0.000000 0.125000 0.000000 0.625000 0.000000 0.375000 0.500000 0.250000 0.250000 0.000000 0.375000 0.250000 0.125000 0.250000 0.125000 0.875000 0.000000 0.000000 0.250000 0.125000 0.125000 0.500000 0.125000 0.875000 0.000000 0.000000 0.125000 0.625000 0.000000 0.250000 0.000000 0.500000 0.125000 0.375000 0.000000 0.875000 0.125000 0.000000 0.000000 0.875000 0.000000 0.125000 0.125000 0.250000 0.250000 0.375000 0.000000 0.875000 0.125000 0.000000 0.750000 0.125000 0.000000 0.125000 0.000000 0.875000 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AT]A[AC]CG[CA][CT][ACG][ACT]C[TA]C[CT][CT]CC[TCG]CAC -------------------------------------------------------------------------------- Time 3.91 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10063 1.89e-10 292_[+1(8.10e-07)]_140_\ [+3(4.15e-08)]_14_[+2(1.14e-07)]_5 11004 4.66e-06 84_[+1(7.48e-07)]_334_\ [+2(5.23e-07)]_54 14482 1.16e-11 5_[+2(3.16e-06)]_299_[+1(1.25e-07)]_\ 90_[+3(4.92e-10)]_57 16912 4.68e-06 160_[+1(8.86e-07)]_299_\ [+2(1.46e-06)]_13 21847 1.18e-05 68_[+3(1.35e-07)]_121_\ [+1(3.47e-06)]_274 2671 4.86e-03 159_[+1(2.07e-07)]_325 268408 1.67e-05 134_[+2(4.06e-06)]_316_\ [+3(2.22e-07)]_17 32678 1.50e-11 172_[+1(2.34e-07)]_219_\ [+2(1.93e-06)]_21_[+3(5.65e-10)]_39 4646 8.41e-08 102_[+1(2.71e-06)]_112_\ [+3(8.60e-08)]_[+2(1.21e-05)]_237 5108 1.77e-08 224_[+1(2.78e-09)]_208_\ [+3(1.25e-07)]_31 8904 1.67e-08 249_[+1(1.31e-06)]_103_\ [+3(1.17e-07)]_92_[+2(3.16e-06)]_7 9835 4.71e-02 234_[+2(1.21e-05)]_254 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************