******************************************************************************** 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/299/299.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21066 1.0000 500 23466 1.0000 500 25788 1.0000 500 263203 1.0000 500 35711 1.0000 500 38609 1.0000 500 6401 1.0000 500 7453 1.0000 500 8446 1.0000 500 9287 1.0000 500 9291 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/299/299.seqs.fa -oc motifs/299 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.251 G 0.241 T 0.251 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.251 G 0.241 T 0.251 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 11 llr = 134 E-value = 5.6e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :9::44:41143:::: pos.-specific C 816a12953764a5:a probability G ::1:4::1:::1:4:: matrix T 2:3:251162:3:1a: bits 2.1 * * ** 1.8 * * ** 1.6 * * * ** 1.4 * * * * ** Relative 1.2 ** * * * ** Entropy 1.0 ** * * * * ** (17.6 bits) 0.8 **** * *** * ** 0.6 **** * *** **** 0.4 **** ****** **** 0.2 **************** 0.0 ---------------- Multilevel CACCATCCTCCCCCTC consensus T GA AC AA G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 8446 306 1.54e-08 CATTCACCTC CACCTTCCTCCTCCTC TCTCTACACA 25788 40 1.71e-08 CTTGCTGACC CACCGTCCTCACCGTC AGTCGTCAAG 9291 7 1.91e-07 TCATCA CATCACCATCCACCTC ATGGCCGGCG 9287 485 1.91e-07 GCGCTCATCA CATCACCATCCACCTC 7453 476 4.75e-07 CTCCTCCACC CACCCACACCCTCCTC CTCGCCACG 23466 169 7.01e-07 TCCGCAACGC CACCTACACCAACGTC AGAGGAGAGG 6401 245 1.01e-06 GTTTGGGCGA CACCATCGCCATCGTC GATCTTGGAT 21066 395 1.31e-06 TCGTTGTATG TATCGACCTTCCCCTC CACGCAGTGG 263203 71 5.01e-06 TCCACGCGAA TAGCGTCTTCCCCGTC TCCACTGGAG 38609 335 1.10e-05 GGTCAGTATT CCCCGTTCTACCCCTC TTTTCAGCGC 35711 284 1.48e-05 AGGTAACCAC CACCAACCATAGCTTC ATTGTACGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8446 1.5e-08 305_[+1]_179 25788 1.7e-08 39_[+1]_445 9291 1.9e-07 6_[+1]_478 9287 1.9e-07 484_[+1] 7453 4.7e-07 475_[+1]_9 23466 7e-07 168_[+1]_316 6401 1e-06 244_[+1]_240 21066 1.3e-06 394_[+1]_90 263203 5e-06 70_[+1]_414 38609 1.1e-05 334_[+1]_150 35711 1.5e-05 283_[+1]_201 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=11 8446 ( 306) CACCTTCCTCCTCCTC 1 25788 ( 40) CACCGTCCTCACCGTC 1 9291 ( 7) CATCACCATCCACCTC 1 9287 ( 485) CATCACCATCCACCTC 1 7453 ( 476) CACCCACACCCTCCTC 1 23466 ( 169) CACCTACACCAACGTC 1 6401 ( 245) CACCATCGCCATCGTC 1 21066 ( 395) TATCGACCTTCCCCTC 1 263203 ( 71) TAGCGTCTTCCCCGTC 1 38609 ( 335) CCCCGTTCTACCCCTC 1 35711 ( 284) CACCAACCATAGCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5335 bayes= 9.27461 E= 5.6e-003 -1010 171 -1010 -47 182 -146 -1010 -1010 -1010 134 -140 12 -1010 199 -1010 -1010 50 -146 59 -47 50 -46 -1010 85 -1010 186 -1010 -146 50 86 -140 -146 -150 12 -1010 134 -150 154 -1010 -47 50 134 -1010 -1010 9 54 -140 12 -1010 199 -1010 -1010 -1010 112 59 -146 -1010 -1010 -1010 199 -1010 199 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 11 E= 5.6e-003 0.000000 0.818182 0.000000 0.181818 0.909091 0.090909 0.000000 0.000000 0.000000 0.636364 0.090909 0.272727 0.000000 1.000000 0.000000 0.000000 0.363636 0.090909 0.363636 0.181818 0.363636 0.181818 0.000000 0.454545 0.000000 0.909091 0.000000 0.090909 0.363636 0.454545 0.090909 0.090909 0.090909 0.272727 0.000000 0.636364 0.090909 0.727273 0.000000 0.181818 0.363636 0.636364 0.000000 0.000000 0.272727 0.363636 0.090909 0.272727 0.000000 1.000000 0.000000 0.000000 0.000000 0.545455 0.363636 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[CT]C[AG][TA]C[CA][TC]C[CA][CAT]C[CG]TC -------------------------------------------------------------------------------- Time 1.11 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 103 E-value = 1.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::2::4::::24::a:::2:: pos.-specific C 22:a4:::::::2::8aa6:: probability G :8::42244:8::a:2::::: matrix T 8:8:24866a:68:::::2aa bits 2.1 * * ** ** ** 1.8 * * ** ** ** 1.6 * * ** ** ** 1.4 * * ** ** ** Relative 1.2 **** * ** ****** ** Entropy 1.0 **** ************ ** (29.7 bits) 0.8 **** ************ ** 0.6 **** *************** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TGTCCATTTTGTTGACCCCTT consensus CCA GTGGG AAC G A sequence TG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 23466 393 3.04e-12 CCAATCTAAA TGTCCATGTTGTTGACCCCTT AAGAAGCAAA 9287 361 5.90e-11 TGTCGGATCG TGTCTAGTTTGTTGACCCCTT GTTGTGAAAC 7453 371 9.70e-11 GTCCACAAAT TGTCCGTTGTATTGACCCCTT AAAGTGAAAA 21066 245 1.03e-09 GACGACATAG TGACGTTTGTGATGAGCCATT GCCATCAGCG 38609 416 2.50e-09 CTTTCTCTCT CCTCGTTGTTGACGACCCTTT CATTCTTCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23466 3e-12 392_[+2]_87 9287 5.9e-11 360_[+2]_119 7453 9.7e-11 370_[+2]_109 21066 1e-09 244_[+2]_235 38609 2.5e-09 415_[+2]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 23466 ( 393) TGTCCATGTTGTTGACCCCTT 1 9287 ( 361) TGTCTAGTTTGTTGACCCCTT 1 7453 ( 371) TGTCCGTTGTATTGACCCCTT 1 21066 ( 245) TGACGTTTGTGATGAGCCATT 1 38609 ( 416) CCTCGTTGTTGACGACCCTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 10.2948 E= 1.7e+000 -897 -33 -897 167 -897 -33 173 -897 -36 -897 -897 167 -897 199 -897 -897 -897 67 73 -33 64 -897 -27 67 -897 -897 -27 167 -897 -897 73 125 -897 -897 73 125 -897 -897 -897 199 -36 -897 173 -897 64 -897 -897 125 -897 -33 -897 167 -897 -897 205 -897 196 -897 -897 -897 -897 167 -27 -897 -897 199 -897 -897 -897 199 -897 -897 -36 126 -897 -33 -897 -897 -897 199 -897 -897 -897 199 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.7e+000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.400000 0.200000 0.400000 0.000000 0.200000 0.400000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.800000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC][GC][TA]C[CGT][ATG][TG][TG][TG]T[GA][TA][TC]GA[CG]CC[CAT]TT -------------------------------------------------------------------------------- Time 2.16 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 135 E-value = 6.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 11::1218111:::2:3::4: pos.-specific C :62978622884438a:6a2a probability G :11:::::::::11::31:3: matrix T 92712:3:711646::33::: bits 2.1 * * * 1.8 * * * 1.6 * * * 1.4 * * * * * Relative 1.2 * * * * ** * * Entropy 1.0 * * * * *** ** * * (21.7 bits) 0.8 * **** ***** ** * * 0.6 * ************** ** * 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TCTCCCCATCCTCTCCACCAC consensus TC TATCC CTCA GT G sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 263203 382 1.88e-10 AACACAATCA TCTCCCCAACCTTTCCTCCAC AAAACTCATT 6401 464 5.68e-09 AACAGACTCC TCCCTCTCTCCTCTCCTCCAC CCTCTCTCCC 9291 60 7.91e-09 CCCATCTCCG TCTCCCTATCACTTACACCAC CACGAAGTCC 38609 206 4.99e-08 GGTAGCCCTT TCCCTCTATCCCTGCCATCCC TGCTATAAGG 7453 454 8.92e-08 CGTGGTCCCC TGTTCCCCCCCCCTCCTCCAC CCACCCACAC 8446 100 1.31e-07 GACGACGAAG ATTCCACATCCCGTCCGTCGC TGGCAGAGAA 21066 479 1.63e-07 GGGGGCTTGA TCTCCACACACTTCACACCCC T 9287 458 2.02e-07 ATGTTCTTCG TTTCCCCATTTTCCCCGGCGC TCATCACATC 25788 85 4.13e-07 CAAACAACAG TAGCACAATCCTCCCCGTCGC CATCGCGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263203 1.9e-10 381_[+3]_98 6401 5.7e-09 463_[+3]_16 9291 7.9e-09 59_[+3]_420 38609 5e-08 205_[+3]_274 7453 8.9e-08 453_[+3]_26 8446 1.3e-07 99_[+3]_380 21066 1.6e-07 478_[+3]_1 9287 2e-07 457_[+3]_22 25788 4.1e-07 84_[+3]_395 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 263203 ( 382) TCTCCCCAACCTTTCCTCCAC 1 6401 ( 464) TCCCTCTCTCCTCTCCTCCAC 1 9291 ( 60) TCTCCCTATCACTTACACCAC 1 38609 ( 206) TCCCTCTATCCCTGCCATCCC 1 7453 ( 454) TGTTCCCCCCCCCTCCTCCAC 1 8446 ( 100) ATTCCACATCCCGTCCGTCGC 1 21066 ( 479) TCTCCACACACTTCACACCCC 1 9287 ( 458) TTTCCCCATTTTCCCCGGCGC 1 25788 ( 85) TAGCACAATCCTCCCCGTCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 9.32846 E= 6.7e+000 -121 -982 -982 182 -121 115 -111 -18 -982 -17 -111 141 -982 182 -982 -118 -121 141 -982 -18 -21 163 -982 -982 -121 115 -982 41 160 -17 -982 -982 -121 -17 -982 141 -121 163 -982 -118 -121 163 -982 -118 -982 83 -982 114 -982 83 -111 82 -982 41 -111 114 -21 163 -982 -982 -982 199 -982 -982 37 -982 47 41 -982 115 -111 41 -982 199 -982 -982 79 -17 47 -982 -982 199 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 6.7e+000 0.111111 0.000000 0.000000 0.888889 0.111111 0.555556 0.111111 0.222222 0.000000 0.222222 0.111111 0.666667 0.000000 0.888889 0.000000 0.111111 0.111111 0.666667 0.000000 0.222222 0.222222 0.777778 0.000000 0.000000 0.111111 0.555556 0.000000 0.333333 0.777778 0.222222 0.000000 0.000000 0.111111 0.222222 0.000000 0.666667 0.111111 0.777778 0.000000 0.111111 0.111111 0.777778 0.000000 0.111111 0.000000 0.444444 0.000000 0.555556 0.000000 0.444444 0.111111 0.444444 0.000000 0.333333 0.111111 0.555556 0.222222 0.777778 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.333333 0.333333 0.000000 0.555556 0.111111 0.333333 0.000000 1.000000 0.000000 0.000000 0.444444 0.222222 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CT][TC]C[CT][CA][CT][AC][TC]CC[TC][CT][TC][CA]C[AGT][CT]C[AGC]C -------------------------------------------------------------------------------- Time 3.33 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21066 1.29e-11 244_[+2(1.03e-09)]_129_\ [+1(1.31e-06)]_68_[+3(1.63e-07)]_1 23466 1.81e-10 168_[+1(7.01e-07)]_208_\ [+2(3.04e-12)]_87 25788 1.52e-07 39_[+1(1.71e-08)]_29_[+3(4.13e-07)]_\ 395 263203 5.06e-08 70_[+1(5.01e-06)]_295_\ [+3(1.88e-10)]_98 35711 1.20e-01 283_[+1(1.48e-05)]_201 38609 7.11e-11 205_[+3(4.99e-08)]_108_\ [+1(1.10e-05)]_65_[+2(2.50e-09)]_64 6401 6.64e-08 244_[+1(1.01e-06)]_203_\ [+3(5.68e-09)]_16 7453 3.03e-13 370_[+2(9.70e-11)]_62_\ [+3(8.92e-08)]_1_[+1(4.75e-07)]_9 8446 8.55e-08 99_[+3(1.31e-07)]_169_\ [+1(1.85e-05)]_[+1(1.54e-08)]_179 9287 1.73e-13 360_[+2(5.90e-11)]_76_\ [+3(2.02e-07)]_6_[+1(1.91e-07)] 9291 8.17e-08 6_[+1(1.91e-07)]_37_[+3(7.91e-09)]_\ 142_[+1(3.67e-06)]_262 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************