******************************************************************************** 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/181/181.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10499 1.0000 500 21482 1.0000 500 22722 1.0000 500 22822 1.0000 500 264096 1.0000 500 3051 1.0000 500 31564 1.0000 500 33574 1.0000 500 33941 1.0000 500 35116 1.0000 500 36330 1.0000 500 36481 1.0000 500 38270 1.0000 500 38460 1.0000 500 40817 1.0000 500 41694 1.0000 500 6383 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/181/181.seqs.fa -oc motifs/181 -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= 17 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= 8500 N= 17 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.234 G 0.248 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.234 G 0.248 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 147 E-value = 3.5e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 325496::8a:199:: pos.-specific C 76561397::99::89 probability G :::::::32:::1:21 matrix T :2:::11:::1::1:: bits 2.1 1.9 * 1.7 * *** * 1.5 * * ***** * Relative 1.3 * * ********** Entropy 1.0 * *** ********** (21.3 bits) 0.8 * *** ********** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CCACAACCAACCAACC consensus AACA C GG G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 33574 108 1.45e-10 CCCTACCTAA CCCCAACCAACCAACC AAATACCATG 22722 378 6.00e-09 AACCATTCTA CCCAAACCGACCAACC TCATCCGAGC 31564 251 8.42e-09 GGGACGTCAA CCAAACCGAACCAACC ACAACCACCA 35116 445 1.82e-08 CCTCTCCTTG CTCCAACCAACCAAGC CGAGCAAACG 6383 210 3.04e-08 ATACCAAAAC CTCCATCCAACCAACC TCGGTGTGTG 22822 462 1.07e-07 AGTCGCCAAC AAACACCCAACCAAGC TCGCTGTCCC 3051 401 1.89e-07 TTGTATCCGT CCAACACCAACCGACC TCCGAACGAC 10499 443 2.67e-07 CACTCTTCTC ACCAACTGAACCAACC GCCGCCGGCC 36330 81 7.88e-07 CTACACTTGA AAACAACCAACAATCC ATTATCCTGG 41694 453 8.35e-07 CTTATAAGAG CCACAACGGATCAACG ATCACCACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 33574 1.5e-10 107_[+1]_377 22722 6e-09 377_[+1]_107 31564 8.4e-09 250_[+1]_234 35116 1.8e-08 444_[+1]_40 6383 3e-08 209_[+1]_275 22822 1.1e-07 461_[+1]_23 3051 1.9e-07 400_[+1]_84 10499 2.7e-07 442_[+1]_42 36330 7.9e-07 80_[+1]_404 41694 8.3e-07 452_[+1]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 33574 ( 108) CCCCAACCAACCAACC 1 22722 ( 378) CCCAAACCGACCAACC 1 31564 ( 251) CCAAACCGAACCAACC 1 35116 ( 445) CTCCAACCAACCAAGC 1 6383 ( 210) CTCCATCCAACCAACC 1 22822 ( 462) AAACACCCAACCAAGC 1 3051 ( 401) CCAACACCAACCGACC 1 10499 ( 443) ACCAACTGAACCAACC 1 36330 ( 81) AAACAACCAACAATCC 1 41694 ( 453) CCACAACGGATCAACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 10.6299 E= 3.5e-008 21 158 -997 -997 -37 136 -997 -38 95 109 -997 -997 63 136 -997 -997 180 -123 -997 -997 121 36 -997 -137 -997 194 -997 -137 -997 158 28 -997 163 -997 -31 -997 195 -997 -997 -997 -997 194 -997 -137 -137 194 -997 -997 180 -997 -131 -997 180 -997 -997 -137 -997 177 -31 -997 -997 194 -131 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 3.5e-008 0.300000 0.700000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.500000 0.500000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.900000 0.100000 0.000000 0.000000 0.600000 0.300000 0.000000 0.100000 0.000000 0.900000 0.000000 0.100000 0.000000 0.700000 0.300000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.900000 0.000000 0.100000 0.100000 0.900000 0.000000 0.000000 0.900000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 0.100000 0.000000 0.800000 0.200000 0.000000 0.000000 0.900000 0.100000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][CAT][AC][CA]A[AC]C[CG][AG]ACCAA[CG]C -------------------------------------------------------------------------------- Time 2.47 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 113 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::7:::2:22:3::725:: pos.-specific C a38a:a282a:5:72a27285 probability G :22:2::2::::::::::2:5 matrix T :5::2:8:7:83a:8:2222: bits 2.1 * * * * * 1.9 * * * * * * 1.7 * * * * * * 1.5 * ** * * * * * * Relative 1.3 * ** *** ** * ** * Entropy 1.0 * ** *** ** **** ** (27.1 bits) 0.8 * ** *** ** **** * ** 0.6 ****************** ** 0.4 ****************** ** 0.2 ********************* 0.0 --------------------- Multilevel CTCCACTCTCTCTCTCACACC consensus C T A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 40817 287 4.25e-12 CCAATCCGCC CTCCGCTCTCTCTCTCACACC CATCCTACGC 38270 448 5.51e-10 CCGCTGGCTT CGCCACCGTCTCTCTCACACG ACAGCGTGCC 36481 103 1.16e-09 TCCTGTCGAT CTCCACTCTCATTCTCACGTG AGCCTACCAA 38460 67 2.21e-09 TGAGGTCATG CTCCTCTCTCTCTCTCTTTCG ATGGCATCGG 36330 463 6.71e-09 TCACCACATA CCCCACTCCCTTTATCCACCC ATAGTATTTG 3051 455 7.15e-09 ACCTCCTGCG CCGCACTCACTATACCACACC ACCACCTCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40817 4.2e-12 286_[+2]_193 38270 5.5e-10 447_[+2]_32 36481 1.2e-09 102_[+2]_377 38460 2.2e-09 66_[+2]_413 36330 6.7e-09 462_[+2]_17 3051 7.1e-09 454_[+2]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 40817 ( 287) CTCCGCTCTCTCTCTCACACC 1 38270 ( 448) CGCCACCGTCTCTCTCACACG 1 36481 ( 103) CTCCACTCTCATTCTCACGTG 1 38460 ( 67) CTCCTCTCTCTCTCTCTTTCG 1 36330 ( 463) CCCCACTCCCTTTATCCACCC 1 3051 ( 455) CCGCACTCACTATACCACACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8160 bayes= 10.8561 E= 1.4e-001 -923 209 -923 -923 -923 51 -57 94 -923 183 -57 -923 -923 209 -923 -923 137 -923 -57 -64 -923 209 -923 -923 -923 -49 -923 168 -923 183 -57 -923 -63 -49 -923 136 -923 209 -923 -923 -63 -923 -923 168 -63 109 -923 36 -923 -923 -923 194 37 151 -923 -923 -923 -49 -923 168 -923 209 -923 -923 137 -49 -923 -64 -63 151 -923 -64 95 -49 -57 -64 -923 183 -923 -64 -923 109 101 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 1.4e-001 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.166667 0.500000 0.000000 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.166667 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 0.833333 0.166667 0.000000 0.166667 0.166667 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.166667 0.500000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.666667 0.166667 0.000000 0.166667 0.166667 0.666667 0.000000 0.166667 0.500000 0.166667 0.166667 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TC]CCACTCTCT[CT]T[CA]TCACAC[CG] -------------------------------------------------------------------------------- Time 5.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 11 llr = 157 E-value = 8.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 368:9613:442625a5:45a pos.-specific C 741a:274655:454::951: probability G :::::1122112:1::2:14: matrix T ::1:11122::6:31:31::: bits 2.1 * 1.9 * * * 1.7 * * * * 1.5 ** * * * Relative 1.3 * ** * * * Entropy 1.0 ***** * * * * (20.6 bits) 0.8 ***** * * * * * * 0.6 ***** * ***** ******* 0.4 ******* ***** ******* 0.2 ******* ************* 0.0 --------------------- Multilevel CAACAACCCCCTACAAACCAA consensus AC A AA CTC T AG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 35116 471 1.60e-10 CGAGCAAACG CAACAACCCCGTACCAACCAA CACAGGAAG 33574 47 5.76e-09 CTGTGGCTTT CCACTACACCATACAAACAAA CGCCGACCGC 6383 449 2.53e-08 TCGACTCTGG ACACAACCGAATATCAACCGA ATATACACTC 3051 480 5.10e-08 CACACCACCA CCTCAACATCCTAAAAACAAA 33941 474 8.14e-08 ACAATCAAAC CAACACCGCACTCCAAATAGA TCTTCA 31564 472 1.92e-07 CTGCCACACT CAACAATACACAATTAACCGA ACAATATT 10499 468 2.84e-07 CGCCGCCGGC CAACACCTCGCACACATCCAA AGCGACGTCA 40817 331 3.31e-07 CAGCTCCCAA CAACAGCCCCATCGCAGCCCA CAACGCCTCA 41694 474 3.56e-07 CAACGATCAC CACCAAGTCACGACAATCAAA ACAACC 38460 443 4.43e-07 CTTTGCAATC ACACATCGTCATCTAATCCAA TCTATCTTTT 38270 138 9.84e-07 GCCGAGCCAC AAACAAACGCCGACAAGCGGA AAGTCAACGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35116 1.6e-10 470_[+3]_9 33574 5.8e-09 46_[+3]_433 6383 2.5e-08 448_[+3]_31 3051 5.1e-08 479_[+3] 33941 8.1e-08 473_[+3]_6 31564 1.9e-07 471_[+3]_8 10499 2.8e-07 467_[+3]_12 40817 3.3e-07 330_[+3]_149 41694 3.6e-07 473_[+3]_6 38460 4.4e-07 442_[+3]_37 38270 9.8e-07 137_[+3]_342 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=11 35116 ( 471) CAACAACCCCGTACCAACCAA 1 33574 ( 47) CCACTACACCATACAAACAAA 1 6383 ( 449) ACACAACCGAATATCAACCGA 1 3051 ( 480) CCTCAACATCCTAAAAACAAA 1 33941 ( 474) CAACACCGCACTCCAAATAGA 1 31564 ( 472) CAACAATACACAATTAACCGA 1 10499 ( 468) CAACACCTCGCACACATCCAA 1 40817 ( 331) CAACAGCCCCATCGCAGCCCA 1 41694 ( 474) CACCAAGTCACGACAATCAAA 1 38460 ( 443) ACACATCGTCATCTAATCCAA 1 38270 ( 138) AAACAAACGCCGACAAGCGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8160 bayes= 9.8885 E= 8.4e-001 8 163 -1010 -1010 130 63 -1010 -1010 166 -136 -1010 -151 -1010 209 -1010 -1010 181 -1010 -1010 -151 130 -37 -144 -151 -151 163 -144 -151 8 63 -44 -51 -1010 144 -44 -51 49 122 -144 -1010 49 122 -144 -1010 -51 -1010 -44 129 130 63 -1010 -1010 -51 96 -144 7 108 63 -1010 -151 195 -1010 -1010 -1010 108 -1010 -44 7 -1010 195 -1010 -151 49 122 -144 -1010 108 -136 55 -1010 195 -1010 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 8.4e-001 0.272727 0.727273 0.000000 0.000000 0.636364 0.363636 0.000000 0.000000 0.818182 0.090909 0.000000 0.090909 0.000000 1.000000 0.000000 0.000000 0.909091 0.000000 0.000000 0.090909 0.636364 0.181818 0.090909 0.090909 0.090909 0.727273 0.090909 0.090909 0.272727 0.363636 0.181818 0.181818 0.000000 0.636364 0.181818 0.181818 0.363636 0.545455 0.090909 0.000000 0.363636 0.545455 0.090909 0.000000 0.181818 0.000000 0.181818 0.636364 0.636364 0.363636 0.000000 0.000000 0.181818 0.454545 0.090909 0.272727 0.545455 0.363636 0.000000 0.090909 1.000000 0.000000 0.000000 0.000000 0.545455 0.000000 0.181818 0.272727 0.000000 0.909091 0.000000 0.090909 0.363636 0.545455 0.090909 0.000000 0.545455 0.090909 0.363636 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CA][AC]ACAAC[CA]C[CA][CA]T[AC][CT][AC]A[AT]C[CA][AG]A -------------------------------------------------------------------------------- Time 7.61 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10499 1.63e-06 442_[+1(2.67e-07)]_9_[+3(2.84e-07)]_\ 12 21482 3.89e-02 450_[+3(2.70e-05)]_29 22722 3.43e-06 377_[+1(6.00e-09)]_35_\ [+2(8.82e-05)]_51 22822 3.12e-04 461_[+1(1.07e-07)]_23 264096 5.83e-01 500 3051 4.32e-12 400_[+1(1.89e-07)]_38_\ [+2(7.15e-09)]_4_[+3(5.10e-08)] 31564 4.15e-08 165_[+1(7.76e-05)]_69_\ [+1(8.42e-09)]_205_[+3(1.92e-07)]_8 33574 7.18e-12 46_[+3(5.76e-09)]_40_[+1(1.45e-10)]_\ 377 33941 9.06e-05 451_[+3(3.61e-05)]_1_[+3(8.14e-08)]_\ 6 35116 4.77e-11 444_[+1(1.82e-08)]_10_\ [+3(1.60e-10)]_9 36330 1.46e-07 80_[+1(7.88e-07)]_323_\ [+2(3.31e-05)]_22_[+2(6.71e-09)]_17 36481 1.73e-05 102_[+2(1.16e-09)]_377 38270 1.42e-08 137_[+3(9.84e-07)]_289_\ [+2(5.51e-10)]_32 38460 4.78e-08 66_[+2(2.21e-09)]_355_\ [+3(4.43e-07)]_37 40817 4.19e-11 8_[+3(8.86e-05)]_257_[+2(4.25e-12)]_\ 23_[+3(3.31e-07)]_86_[+2(2.85e-05)]_42 41694 7.64e-06 452_[+1(8.35e-07)]_5_[+3(3.56e-07)]_\ 6 6383 5.48e-09 209_[+1(3.04e-08)]_34_\ [+3(9.78e-05)]_168_[+3(2.53e-08)]_6_[+3(8.57e-05)]_4 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************