******************************************************************************** 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/236/236.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1555 1.0000 500 21027 1.0000 500 22107 1.0000 500 23044 1.0000 500 24097 1.0000 500 24627 1.0000 500 24729 1.0000 500 25729 1.0000 500 261937 1.0000 500 264481 1.0000 500 34591 1.0000 500 3924 1.0000 500 7136 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/236/236.seqs.fa -oc motifs/236 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.232 G 0.237 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.232 G 0.237 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 12 llr = 163 E-value = 7.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :6:1::1734:3138:8:757 pos.-specific C 3:3::221:112::1::31:: probability G 423:28727293171a:8:42 matrix T 33498:1113:28:::3:312 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * * Relative 1.3 *** * * * Entropy 1.1 *** * ****** (19.5 bits) 0.8 *** * * ******* 0.6 * ****** * ********* 0.4 ********* * ********* 0.2 *********** ********* 0.0 --------------------- Multilevel GATTTGGAGAGATGAGAGAAA consensus TTG AT G A TCTG sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 261937 179 1.82e-10 TATACTGTGT CATTTGGAGTGGTGAGAGTAA CCTTGATGTC 264481 159 1.11e-09 GAGATCCTAA GATTTGGAATGCTAAGAGAAA GAATTCTTTA 34591 64 3.42e-09 AGTTCTATTG TATTTGGAGAGTTGAGTCAAA GAATGTCAGA 24627 87 1.09e-08 ATGAATCCGT CGGTTGGAGAGATGCGAGAGA GCGAGCAACG 1555 135 2.36e-07 GATGTAGAGC TAGTTCAAGACATGAGAGAGA TGGGATTGCA 3924 212 3.05e-07 GGAGTTGATG CTCTTGGAGGGAGAAGAGAGG AAGTAGGCGA 23044 176 5.39e-07 CCACAATTCA TATTTGCAAAGCAAAGACAGA GGAGAGGACA 21027 303 6.29e-07 TTATATTGTT GTGTTGGGATGGTAGGTGAGA GGGCGGTGGT 25729 5 8.50e-07 GTCT GACATGGAGAGGTGAGTGTTT GGTGAGCTGT 7136 272 1.14e-06 TTGGTTTTGA GACTTCGCGCGTTGAGACTAA ATAAGGTAGG 24729 308 4.07e-06 CTGCTGCTGC TGTTGGTGGTGGTGAGAGCAT CATCACTGCT 24097 126 4.83e-06 ATGTTCGCGC GTGTGGCTTGGATGAGAGAAG ACGACGCTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261937 1.8e-10 178_[+1]_301 264481 1.1e-09 158_[+1]_321 34591 3.4e-09 63_[+1]_416 24627 1.1e-08 86_[+1]_393 1555 2.4e-07 134_[+1]_345 3924 3.1e-07 211_[+1]_268 23044 5.4e-07 175_[+1]_304 21027 6.3e-07 302_[+1]_177 25729 8.5e-07 4_[+1]_475 7136 1.1e-06 271_[+1]_208 24729 4.1e-06 307_[+1]_172 24097 4.8e-06 125_[+1]_354 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=12 261937 ( 179) CATTTGGAGTGGTGAGAGTAA 1 264481 ( 159) GATTTGGAATGCTAAGAGAAA 1 34591 ( 64) TATTTGGAGAGTTGAGTCAAA 1 24627 ( 87) CGGTTGGAGAGATGCGAGAGA 1 1555 ( 135) TAGTTCAAGACATGAGAGAGA 1 3924 ( 212) CTCTTGGAGGGAGAAGAGAGG 1 23044 ( 176) TATTTGCAAAGCAAAGACAGA 1 21027 ( 303) GTGTTGGGATGGTAGGTGAGA 1 25729 ( 5) GACATGGAGAGGTGAGTGTTT 1 7136 ( 272) GACTTCGCGCGTTGAGACTAA 1 24729 ( 308) TGTTGGTGGTGGTGAGAGCAT 1 24097 ( 126) GTGTGGCTTGGATGAGAGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 9.46779 E= 7.8e-003 -1023 11 81 31 116 -1023 -51 -11 -1023 11 49 63 -165 -1023 -1023 176 -1023 -1023 -51 163 -1023 -48 181 -1023 -165 -48 149 -169 135 -147 -51 -169 -6 -1023 149 -169 67 -147 -51 31 -1023 -147 195 -1023 35 -48 49 -69 -165 -1023 -151 163 35 -1023 149 -1023 167 -147 -151 -1023 -1023 -1023 208 -1023 152 -1023 -1023 -11 -1023 11 166 -1023 135 -147 -1023 -11 94 -1023 81 -169 135 -1023 -51 -69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 12 E= 7.8e-003 0.000000 0.250000 0.416667 0.333333 0.583333 0.000000 0.166667 0.250000 0.000000 0.250000 0.333333 0.416667 0.083333 0.000000 0.000000 0.916667 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.833333 0.000000 0.083333 0.166667 0.666667 0.083333 0.666667 0.083333 0.166667 0.083333 0.250000 0.000000 0.666667 0.083333 0.416667 0.083333 0.166667 0.333333 0.000000 0.083333 0.916667 0.000000 0.333333 0.166667 0.333333 0.166667 0.083333 0.000000 0.083333 0.833333 0.333333 0.000000 0.666667 0.000000 0.833333 0.083333 0.083333 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.250000 0.750000 0.000000 0.666667 0.083333 0.000000 0.250000 0.500000 0.000000 0.416667 0.083333 0.666667 0.000000 0.166667 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GTC][AT][TGC]TTGGA[GA][AT]G[AG]T[GA]AG[AT][GC][AT][AG]A -------------------------------------------------------------------------------- Time 1.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 10 llr = 143 E-value = 3.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 14:572676:47:19572:33 pos.-specific C 7:a3181319623815:2677 probability G 1:::::::1:::::::132:: matrix T 16:22:3:21:171::232:: bits 2.1 * 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * * * ** Entropy 1.1 * * * ** **** ** (20.6 bits) 0.8 ** ** * ******** ** 0.6 *** **** ******** *** 0.4 ***************** *** 0.2 ***************** *** 0.0 --------------------- Multilevel CTCAACAAACCATCAAAGCCC consensus A CTATCT ACC CTTGAA sequence T AT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 7136 427 6.59e-11 AGATCTTCCT CTCAACAAACAACCACAACCC AGCAAACCAC 34591 474 9.57e-11 TTATCATAGA CACAACAAACAATCACAGCAC CTTCCA 264481 471 4.54e-08 TTCTCTCCTG CTCTCCACACCATCACTTCCA GTCACCCAT 1555 480 6.07e-08 TCATCAAATT CACCACCAATCATCAAAGGCC 22107 28 2.25e-07 GGATGCTTCG ATCCAATATCCATCAATTCCC GCCTAAGCGC 23044 471 2.64e-07 GCCCGCTCGC CACAAAAAGCAATCAAGCCAC CGACACACC 21027 85 3.59e-07 CCGCCCTTCC CTCCACTACCACTTACATTCC CCGAAAGACC 25729 261 4.16e-07 TGGTTCCACT TTCATCAAACCCTCCAAGTCC AAGGAAGAGG 24729 454 6.37e-07 CCACACAGCC GACAACACACCACAACAACAA CAACAACAAC 3924 451 1.93e-06 TGAACCGCCT CTCTTCTCTCCTCCAAACGCA GCCAGCAGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7136 6.6e-11 426_[+2]_53 34591 9.6e-11 473_[+2]_6 264481 4.5e-08 470_[+2]_9 1555 6.1e-08 479_[+2] 22107 2.3e-07 27_[+2]_452 23044 2.6e-07 470_[+2]_9 21027 3.6e-07 84_[+2]_395 25729 4.2e-07 260_[+2]_219 24729 6.4e-07 453_[+2]_26 3924 1.9e-06 450_[+2]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=10 7136 ( 427) CTCAACAAACAACCACAACCC 1 34591 ( 474) CACAACAAACAATCACAGCAC 1 264481 ( 471) CTCTCCACACCATCACTTCCA 1 1555 ( 480) CACCACCAATCATCAAAGGCC 1 22107 ( 28) ATCCAATATCCATCAATTCCC 1 23044 ( 471) CACAAAAAGCAATCAAGCCAC 1 21027 ( 85) CTCCACTACCACTTACATTCC 1 25729 ( 261) TTCATCAAACCCTCCAAGTCC 1 24729 ( 454) GACAACACACCACAACAACAA 1 3924 ( 451) CTCTTCTCTCCTCCAAACGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 10.2276 E= 3.3e+000 -138 159 -124 -143 61 -997 -997 115 -997 211 -997 -997 94 37 -997 -43 142 -121 -997 -43 -39 179 -997 -997 120 -121 -997 15 142 37 -997 -997 120 -121 -124 -43 -997 196 -997 -143 61 137 -997 -997 142 -21 -997 -143 -997 37 -997 138 -138 179 -997 -143 178 -121 -997 -997 94 111 -997 -997 142 -997 -124 -43 -39 -21 34 15 -997 137 -25 -43 20 159 -997 -997 20 159 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 10 E= 3.3e+000 0.100000 0.700000 0.100000 0.100000 0.400000 0.000000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.500000 0.300000 0.000000 0.200000 0.700000 0.100000 0.000000 0.200000 0.200000 0.800000 0.000000 0.000000 0.600000 0.100000 0.000000 0.300000 0.700000 0.300000 0.000000 0.000000 0.600000 0.100000 0.100000 0.200000 0.000000 0.900000 0.000000 0.100000 0.400000 0.600000 0.000000 0.000000 0.700000 0.200000 0.000000 0.100000 0.000000 0.300000 0.000000 0.700000 0.100000 0.800000 0.000000 0.100000 0.900000 0.100000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.700000 0.000000 0.100000 0.200000 0.200000 0.200000 0.300000 0.300000 0.000000 0.600000 0.200000 0.200000 0.300000 0.700000 0.000000 0.000000 0.300000 0.700000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TA]C[ACT][AT][CA][AT][AC][AT]C[CA][AC][TC]CA[AC][AT][GTAC][CGT][CA][CA] -------------------------------------------------------------------------------- Time 3.23 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 8 llr = 109 E-value = 1.1e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :a48::5:5:31:::: pos.-specific C 9:1118:9:a139:99 probability G 1:5:53:1::::11:1 matrix T :::14:5:5:66:91: bits 2.1 * 1.9 * * 1.7 * * 1.5 ** * * * ** Relative 1.3 ** * * * **** Entropy 1.1 ** * * * **** (19.7 bits) 0.8 ** * ***** **** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CAGAGCACACTTCTCC consensus A TGT T AC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 23044 374 2.49e-09 ATCAACAATG CAAAGCTCTCTTCTCC TTCCTCGTTT 21027 392 2.98e-08 TTGGAGGCGA CAGAGCACACTTGTCC TCAAATTCAA 34591 413 5.24e-08 CACCAACCAC CAAAGCAGTCTTCTCC TCCGCTGCAA 24729 174 1.79e-07 ACGACGATAG CAGAGCACACACCGCC GCAGGAAATC 264481 275 5.84e-07 CTTCGTTTGT CACTTGTCACTTCTCC TCCACGACGA 3924 70 7.19e-07 GAGCGAAATC GAGACCACTCACCTCC ATGAACGGCT 24627 458 1.01e-06 TTTGATACAT CAAATGTCTCCTCTCG CCTGCCACTG 25729 479 1.36e-06 AACTTCTACT CAGCTCTCACTACTTC ACAGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23044 2.5e-09 373_[+3]_111 21027 3e-08 391_[+3]_93 34591 5.2e-08 412_[+3]_72 24729 1.8e-07 173_[+3]_311 264481 5.8e-07 274_[+3]_210 3924 7.2e-07 69_[+3]_415 24627 1e-06 457_[+3]_27 25729 1.4e-06 478_[+3]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=8 23044 ( 374) CAAAGCTCTCTTCTCC 1 21027 ( 392) CAGAGCACACTTGTCC 1 34591 ( 413) CAAAGCAGTCTTCTCC 1 24729 ( 174) CAGAGCACACACCGCC 1 264481 ( 275) CACTTGTCACTTCTCC 1 3924 ( 70) GAGACCACTCACCTCC 1 24627 ( 458) CAAATGTCTCCTCTCG 1 25729 ( 479) CAGCTCTCACTACTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 10.3581 E= 1.1e+000 -965 191 -92 -965 193 -965 -965 -965 52 -89 108 -965 152 -89 -965 -111 -965 -89 108 48 -965 169 8 -965 93 -965 -965 89 -965 191 -92 -965 93 -965 -965 89 -965 211 -965 -965 -6 -89 -965 121 -106 11 -965 121 -965 191 -92 -965 -965 -965 -92 170 -965 191 -965 -111 -965 191 -92 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 1.1e+000 0.000000 0.875000 0.125000 0.000000 1.000000 0.000000 0.000000 0.000000 0.375000 0.125000 0.500000 0.000000 0.750000 0.125000 0.000000 0.125000 0.000000 0.125000 0.500000 0.375000 0.000000 0.750000 0.250000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.875000 0.125000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.250000 0.125000 0.000000 0.625000 0.125000 0.250000 0.000000 0.625000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.875000 0.000000 0.125000 0.000000 0.875000 0.125000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CA[GA]A[GT][CG][AT]C[AT]C[TA][TC]CTCC -------------------------------------------------------------------------------- Time 4.73 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1555 6.18e-07 134_[+1(2.36e-07)]_324_\ [+2(6.07e-08)] 21027 3.15e-10 18_[+3(3.42e-05)]_50_[+2(3.59e-07)]_\ 197_[+1(6.29e-07)]_68_[+3(2.98e-08)]_93 22107 2.73e-03 27_[+2(2.25e-07)]_452 23044 2.01e-11 175_[+1(5.39e-07)]_177_\ [+3(2.49e-09)]_81_[+2(2.64e-07)]_9 24097 1.11e-02 125_[+1(4.83e-06)]_354 24627 3.23e-07 42_[+1(7.43e-05)]_23_[+1(1.09e-08)]_\ 350_[+3(1.01e-06)]_27 24729 1.58e-08 173_[+3(1.79e-07)]_118_\ [+1(4.07e-06)]_125_[+2(6.37e-07)]_26 25729 1.64e-08 4_[+1(8.50e-07)]_235_[+2(4.16e-07)]_\ 197_[+3(1.36e-06)]_6 261937 6.25e-06 178_[+1(1.82e-10)]_301 264481 1.95e-12 158_[+1(1.11e-09)]_95_\ [+3(5.84e-07)]_180_[+2(4.54e-08)]_9 34591 1.67e-15 63_[+1(3.42e-09)]_25_[+2(4.71e-05)]_\ 282_[+3(5.24e-08)]_9_[+2(3.74e-05)]_15_[+2(9.57e-11)]_6 3924 1.46e-08 69_[+3(7.19e-07)]_126_\ [+1(3.05e-07)]_218_[+2(1.93e-06)]_29 7136 2.44e-09 271_[+1(1.14e-06)]_134_\ [+2(6.59e-11)]_53 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************