******************************************************************************** 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/439/439.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 8754 1.0000 500 15666 1.0000 500 49971 1.0000 500 10409 1.0000 500 11116 1.0000 500 10674 1.0000 500 4563 1.0000 500 41530 1.0000 500 47827 1.0000 500 44993 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/439/439.seqs.fa -oc motifs/439 -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= 10 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= 5000 N= 10 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.265 G 0.233 T 0.241 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.265 G 0.233 T 0.241 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 10 llr = 100 E-value = 1.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::1:::17a::4 pos.-specific C 1a231:::::71 probability G 1:5::a82:214 matrix T 8:279:11:821 bits 2.1 * 1.9 * * * 1.7 * * * 1.5 * ** * Relative 1.3 * *** ** Entropy 1.0 ** **** ** (14.5 bits) 0.8 ** ******** 0.6 ** ******** 0.4 ** ******** 0.2 ************ 0.0 ------------ Multilevel TCGTTGGAATCA consensus CC G GTG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 49971 202 9.99e-08 CGACCATGAC TCGTTGGAATCA CGAAGACGTA 4563 468 1.52e-07 TGCAAAAGTT TCGCTGGAATCG AAGTATCAAG 10409 109 2.75e-06 GTTTTTCTTT TCTTTGGAAGCG CACACGCTCT 47827 4 1.22e-05 AAG TCGTTGGGATTC GGTACGGGGA 44993 446 1.28e-05 CAGCAGAATG GCATTGGAATCG GCATACATTC 15666 305 1.36e-05 TGCAGTCGAT TCCCTGGAATGA ACACAACGCT 8754 136 1.73e-05 CGGCACATGC TCCCTGAAATCG TTGATGACAA 10674 417 2.33e-05 CTCCGAGACG TCGTTGGTAGTA CAGGACTTGC 41530 59 2.75e-05 TACAATGGTA CCTTTGGAATCT AGGTAGCTAG 11116 413 5.44e-05 TACGCAAAAC TCGTCGTGATCA AGTCGAAGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49971 1e-07 201_[+1]_287 4563 1.5e-07 467_[+1]_21 10409 2.7e-06 108_[+1]_380 47827 1.2e-05 3_[+1]_485 44993 1.3e-05 445_[+1]_43 15666 1.4e-05 304_[+1]_184 8754 1.7e-05 135_[+1]_353 10674 2.3e-05 416_[+1]_72 41530 2.7e-05 58_[+1]_430 11116 5.4e-05 412_[+1]_76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=10 49971 ( 202) TCGTTGGAATCA 1 4563 ( 468) TCGCTGGAATCG 1 10409 ( 109) TCTTTGGAAGCG 1 47827 ( 4) TCGTTGGGATTC 1 44993 ( 446) GCATTGGAATCG 1 15666 ( 305) TCCCTGGAATGA 1 8754 ( 136) TCCCTGAAATCG 1 10674 ( 417) TCGTTGGTAGTA 1 41530 ( 59) CCTTTGGAATCT 1 11116 ( 413) TCGTCGTGATCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4890 bayes= 9.18275 E= 1.1e+002 -997 -141 -122 173 -997 191 -997 -997 -138 -41 110 -27 -997 18 -997 154 -997 -141 -997 190 -997 -997 210 -997 -138 -997 178 -127 143 -997 -22 -127 194 -997 -997 -997 -997 -997 -22 173 -997 140 -122 -27 62 -141 78 -127 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 1.1e+002 0.000000 0.100000 0.100000 0.800000 0.000000 1.000000 0.000000 0.000000 0.100000 0.200000 0.500000 0.200000 0.000000 0.300000 0.000000 0.700000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 1.000000 0.000000 0.100000 0.000000 0.800000 0.100000 0.700000 0.000000 0.200000 0.100000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.700000 0.100000 0.200000 0.400000 0.100000 0.400000 0.100000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TC[GCT][TC]TGG[AG]A[TG][CT][AG] -------------------------------------------------------------------------------- Time 1.09 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 9 llr = 94 E-value = 2.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::1:3:14 pos.-specific C ::4:::1:4:32 probability G 322:a:89:a1: matrix T 783a:a:12:43 bits 2.1 *** * 1.9 *** * 1.7 *** * * 1.5 *** * * Relative 1.3 * *** * * Entropy 1.0 ** ***** * (15.0 bits) 0.8 ** ***** * 0.6 ** ***** * 0.4 ********** * 0.2 ************ 0.0 ------------ Multilevel TTCTGTGGCGTA consensus GGT A CT sequence G T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 11116 50 1.14e-06 CGCTGTTTGC GTCTGTGGAGTA ACGAACCACA 47827 232 2.78e-06 GATTGTGGAA TGCTGTGGAGTA GTAGGTTTTC 41530 348 5.19e-06 CGTTGCACCA TTGTGTGGCGAA TACACCACTC 49971 161 6.06e-06 ATGGTAACTA GTTTGTGGTGCT CATAACCTTA 44993 203 7.48e-06 CTCTTTCTTT TTCTGTAGAGTA GACGCTACCA 10674 208 7.48e-06 CATGGAGATA TTCTGTGTCGTT CCCCGTGAAA 15666 29 1.13e-05 ATAAAGAGTC TGTTGTGGTGCT TGCACGCTTA 8754 206 1.88e-05 TAACGTCAGG GTGTGTGGCGGC TGATCTTCGC 10409 445 1.99e-05 CCGTTGTTCT TTTTGTCGCGCC GCGATTATCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11116 1.1e-06 49_[+2]_439 47827 2.8e-06 231_[+2]_257 41530 5.2e-06 347_[+2]_141 49971 6.1e-06 160_[+2]_328 44993 7.5e-06 202_[+2]_286 10674 7.5e-06 207_[+2]_281 15666 1.1e-05 28_[+2]_460 8754 1.9e-05 205_[+2]_283 10409 2e-05 444_[+2]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=9 11116 ( 50) GTCTGTGGAGTA 1 47827 ( 232) TGCTGTGGAGTA 1 41530 ( 348) TTGTGTGGCGAA 1 49971 ( 161) GTTTGTGGTGCT 1 44993 ( 203) TTCTGTAGAGTA 1 10674 ( 208) TTCTGTGTCGTT 1 15666 ( 29) TGTTGTGGTGCT 1 8754 ( 206) GTGTGTGGCGGC 1 10409 ( 445) TTTTGTCGCGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 4890 bayes= 9.93221 E= 2.1e+002 -982 -982 51 147 -982 -982 -7 169 -982 74 -7 47 -982 -982 -982 205 -982 -982 210 -982 -982 -982 -982 205 -123 -125 174 -982 -982 -982 193 -112 36 74 -982 -12 -982 -982 210 -982 -123 33 -107 88 77 -26 -982 47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 2.1e+002 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.222222 0.777778 0.000000 0.444444 0.222222 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.111111 0.111111 0.777778 0.000000 0.000000 0.000000 0.888889 0.111111 0.333333 0.444444 0.000000 0.222222 0.000000 0.000000 1.000000 0.000000 0.111111 0.333333 0.111111 0.444444 0.444444 0.222222 0.000000 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][TG][CTG]TGTGG[CAT]G[TC][ATC] -------------------------------------------------------------------------------- Time 1.97 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 10 llr = 128 E-value = 3.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 811174213234:4494:49 pos.-specific C ::6:::7:671:94:16231 probability G 1:2923:8114:115::83: matrix T 191:1311::26:11::::: bits 2.1 1.9 1.7 * 1.5 * * * * * Relative 1.3 * * * * * * * Entropy 1.0 ** * * ** *** * (18.5 bits) 0.8 ** ** ** * ** *** * 0.6 ** ** **** ** **** * 0.4 ********** ** ****** 0.2 ******************** 0.0 -------------------- Multilevel ATCGAACGCCGTCAGACGAA consensus G GGA AAAA CA ACC sequence T T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 10674 139 5.65e-11 GGGTTACGGG ATCGAGCGCCGACAGACGAA CTTCAATTTT 41530 167 3.09e-09 GTGCCGGTAG AACGAACGCCGTCCGACGGA TGAGTTTCGG 11116 295 1.20e-08 CAGCCGCCGA ATCGAACGACGTCCGACGCC GGAAGCAGTA 49971 112 4.59e-07 GAAAAGCCAG ATGGAACGAATACGAAAGAA TGCAAAAGAC 8754 60 1.27e-06 GCTGACCAAG ATTGGTCGCCTAGAAAAGGA AGTCAACATG 47827 473 1.81e-06 ATCCATCCAC TTCGATTGCGGTCAAACCAA CAAAAAGC 10409 463 2.22e-06 CGCCGCGATT ATCAAAAACCATCTAACGGA ATTTCCTCGA 15666 352 2.54e-06 GTGTCACACA ATCGTGCTGCCTCCGAAGCA ACCACTGAGA 4563 132 2.90e-06 GTGCAAGGGC ATGGGTAGACATCCTACCCA GCACCGACTG 44993 424 3.98e-06 GCGACACAAT GTAGAGCGCAAACAGCAGAA TGGCATTGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10674 5.7e-11 138_[+3]_342 41530 3.1e-09 166_[+3]_314 11116 1.2e-08 294_[+3]_186 49971 4.6e-07 111_[+3]_369 8754 1.3e-06 59_[+3]_421 47827 1.8e-06 472_[+3]_8 10409 2.2e-06 462_[+3]_18 15666 2.5e-06 351_[+3]_129 4563 2.9e-06 131_[+3]_349 44993 4e-06 423_[+3]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=10 10674 ( 139) ATCGAGCGCCGACAGACGAA 1 41530 ( 167) AACGAACGCCGTCCGACGGA 1 11116 ( 295) ATCGAACGACGTCCGACGCC 1 49971 ( 112) ATGGAACGAATACGAAAGAA 1 8754 ( 60) ATTGGTCGCCTAGAAAAGGA 1 47827 ( 473) TTCGATTGCGGTCAAACCAA 1 10409 ( 463) ATCAAAAACCATCTAACGGA 1 15666 ( 352) ATCGTGCTGCCTCCGAAGCA 1 4563 ( 132) ATGGGTAGACATCCTACCCA 1 44993 ( 424) GTAGAGCGCAAACAGCAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 4810 bayes= 9.15891 E= 3.2e+002 162 -997 -122 -127 -138 -997 -997 190 -138 118 -22 -127 -138 -997 195 -997 143 -997 -22 -127 62 -997 36 32 -38 140 -997 -127 -138 -997 178 -127 21 118 -122 -997 -38 140 -122 -997 21 -141 78 -27 62 -997 -997 132 -997 176 -122 -997 62 59 -122 -127 62 -997 110 -127 179 -141 -997 -997 62 118 -997 -997 -997 -41 178 -997 62 18 36 -997 179 -141 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.2e+002 0.800000 0.000000 0.100000 0.100000 0.100000 0.000000 0.000000 0.900000 0.100000 0.600000 0.200000 0.100000 0.100000 0.000000 0.900000 0.000000 0.700000 0.000000 0.200000 0.100000 0.400000 0.000000 0.300000 0.300000 0.200000 0.700000 0.000000 0.100000 0.100000 0.000000 0.800000 0.100000 0.300000 0.600000 0.100000 0.000000 0.200000 0.700000 0.100000 0.000000 0.300000 0.100000 0.400000 0.200000 0.400000 0.000000 0.000000 0.600000 0.000000 0.900000 0.100000 0.000000 0.400000 0.400000 0.100000 0.100000 0.400000 0.000000 0.500000 0.100000 0.900000 0.100000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.400000 0.300000 0.300000 0.000000 0.900000 0.100000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AT[CG]G[AG][AGT][CA]G[CA][CA][GAT][TA]C[AC][GA]A[CA][GC][ACG]A -------------------------------------------------------------------------------- Time 2.83 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8754 7.54e-06 59_[+3(1.27e-06)]_56_[+1(1.73e-05)]_\ 58_[+2(1.88e-05)]_283 15666 7.21e-06 28_[+2(1.13e-05)]_264_\ [+1(1.36e-05)]_35_[+3(2.54e-06)]_129 49971 1.01e-08 111_[+3(4.59e-07)]_29_\ [+2(6.06e-06)]_29_[+1(9.99e-08)]_287 10409 2.54e-06 108_[+1(2.75e-06)]_324_\ [+2(1.99e-05)]_6_[+3(2.22e-06)]_18 11116 2.48e-08 49_[+2(1.14e-06)]_233_\ [+3(1.20e-08)]_98_[+1(5.44e-05)]_76 10674 4.58e-10 138_[+3(5.65e-11)]_49_\ [+2(7.48e-06)]_197_[+1(2.33e-05)]_72 4563 1.43e-05 131_[+3(2.90e-06)]_316_\ [+1(1.52e-07)]_21 41530 1.54e-08 58_[+1(2.75e-05)]_96_[+3(3.09e-09)]_\ 161_[+2(5.19e-06)]_141 47827 1.37e-06 3_[+1(1.22e-05)]_216_[+2(2.78e-06)]_\ 229_[+3(1.81e-06)]_8 44993 7.03e-06 16_[+1(4.32e-05)]_174_\ [+2(7.48e-06)]_209_[+3(3.98e-06)]_2_[+1(1.28e-05)]_43 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************