******************************************************************************** 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/374/374.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11346 1.0000 500 11516 1.0000 500 1225 1.0000 500 16405 1.0000 500 21200 1.0000 500 22184 1.0000 500 22931 1.0000 500 2294 1.0000 500 262318 1.0000 500 34518 1.0000 500 3538 1.0000 500 3707 1.0000 500 4455 1.0000 500 6133 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/374/374.seqs.fa -oc motifs/374 -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= 14 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= 7000 N= 14 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.245 C 0.222 G 0.255 T 0.278 Background letter frequencies (from dataset with add-one prior applied): A 0.245 C 0.222 G 0.255 T 0.278 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 12 llr = 122 E-value = 1.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 2:99:79:44:4 pos.-specific C 1a1:a:18:573 probability G 2::1:3::6111 matrix T 6::::1:2::33 bits 2.2 * * 2.0 * * 1.7 ** * * 1.5 **** ** Relative 1.3 **** ** Entropy 1.1 **** *** (14.7 bits) 0.9 ********** 0.7 ********** 0.4 ********** 0.2 ************ 0.0 ------------ Multilevel TCAACAACGCCA consensus G AATC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 6133 489 3.37e-08 GAACACTTTG TCAACAACGCCA 34518 299 1.75e-06 AGCAGCAGCA TCAACAACGACG TGACGAGAAG 22931 462 3.70e-06 ACATGTTACT TCAACTACACCA TCATCACATA 21200 450 4.16e-06 TGGCTTTCAA ACAACAACGATA GACGTCGTAC 22184 101 7.58e-06 CGGAGCTCTG TCAACAACACGT GGACTAGCAG 262318 465 8.22e-06 AGCTGCCGAA GCAACAATACCA ACAACCTGTG 16405 119 1.13e-05 ACTCACTCCA TCAACGATGACC TCACAGACCT 11516 421 1.13e-05 TTTCTCCAAA TCAACAACGGTC GTCGCAAAGG 11346 39 1.13e-05 AGTATGCAGC ACAGCAACGCCA CGCCCATTCC 1225 478 1.84e-05 ACGTCAGGAC GCAACGACGCTT GATAAAAAAT 2294 101 2.84e-05 TAGAATTGTG TCAACGCCAACT CAACACGACA 4455 292 3.88e-05 AATCCCCCCG CCCACAACAACC GACGTCGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6133 3.4e-08 488_[+1] 34518 1.7e-06 298_[+1]_190 22931 3.7e-06 461_[+1]_27 21200 4.2e-06 449_[+1]_39 22184 7.6e-06 100_[+1]_388 262318 8.2e-06 464_[+1]_24 16405 1.1e-05 118_[+1]_370 11516 1.1e-05 420_[+1]_68 11346 1.1e-05 38_[+1]_450 1225 1.8e-05 477_[+1]_11 2294 2.8e-05 100_[+1]_388 4455 3.9e-05 291_[+1]_197 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=12 6133 ( 489) TCAACAACGCCA 1 34518 ( 299) TCAACAACGACG 1 22931 ( 462) TCAACTACACCA 1 21200 ( 450) ACAACAACGATA 1 22184 ( 101) TCAACAACACGT 1 262318 ( 465) GCAACAATACCA 1 16405 ( 119) TCAACGATGACC 1 11516 ( 421) TCAACAACGGTC 1 11346 ( 39) ACAGCAACGCCA 1 1225 ( 478) GCAACGACGCTT 1 2294 ( 101) TCAACGCCAACT 1 4455 ( 292) CCCACAACAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6846 bayes= 9.60169 E= 1.4e+000 -55 -141 -61 107 -1023 217 -1023 -1023 190 -141 -1023 -1023 190 -1023 -161 -1023 -1023 217 -1023 -1023 144 -1023 -3 -174 190 -141 -1023 -1023 -1023 191 -1023 -74 77 -1023 119 -1023 77 117 -161 -1023 -1023 158 -161 -15 77 17 -161 -15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 1.4e+000 0.166667 0.083333 0.166667 0.583333 0.000000 1.000000 0.000000 0.000000 0.916667 0.083333 0.000000 0.000000 0.916667 0.000000 0.083333 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.250000 0.083333 0.916667 0.083333 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.416667 0.000000 0.583333 0.000000 0.416667 0.500000 0.083333 0.000000 0.000000 0.666667 0.083333 0.250000 0.416667 0.250000 0.083333 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TCAAC[AG]AC[GA][CA][CT][ACT] -------------------------------------------------------------------------------- Time 2.00 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 10 llr = 117 E-value = 1.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a4:a:2a9196617 pos.-specific C ::4:83:111::1: probability G :65:24::7:3481 matrix T ::1::1::1:1::2 bits 2.2 2.0 * * * 1.7 * * * 1.5 * * ** * Relative 1.3 * ** ** * Entropy 1.1 ** ** ** * ** (16.8 bits) 0.9 ** ** ** * *** 0.7 ***** ******** 0.4 ***** ******** 0.2 ************** 0.0 -------------- Multilevel AGGACGAAGAAAGA consensus AC GC GG T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 11516 479 1.09e-08 CCTTTTCAGA AGCACCAAGAAAGA TTTCCAGG 22931 361 1.25e-07 ACAACAAGAC AGGAGGAAGAAAGA TGGTTTCCAG 6133 160 1.52e-07 TGTGACCGCT AAGACAAAGAGAGA TATCCAAATG 16405 65 4.48e-07 CCAGATCTTC AACACGAAGAAGGT GCACCCACCA 11346 164 9.79e-07 TAATGAAATT AGTACGAAGAGGGA AGTGTACAAC 2294 158 1.15e-06 TGTGTTGTCG AAGACGAAGAGAGG TACATGTTCA 22184 118 6.54e-06 CACGTGGACT AGCAGTAAAAAAGA GCTGAAACGC 34518 28 9.16e-06 TGAAGACCCT AACACAAATATGGA ACGGACACAA 3707 75 1.45e-05 GATCGATTGA AGGACCACCAAACA TAGAAATGTC 4455 125 1.63e-05 TGCGGATACC AGGACCAAGCAGAT TGCCTTTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11516 1.1e-08 478_[+2]_8 22931 1.3e-07 360_[+2]_126 6133 1.5e-07 159_[+2]_327 16405 4.5e-07 64_[+2]_422 11346 9.8e-07 163_[+2]_323 2294 1.2e-06 157_[+2]_329 22184 6.5e-06 117_[+2]_369 34518 9.2e-06 27_[+2]_459 3707 1.5e-05 74_[+2]_412 4455 1.6e-05 124_[+2]_362 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=10 11516 ( 479) AGCACCAAGAAAGA 1 22931 ( 361) AGGAGGAAGAAAGA 1 6133 ( 160) AAGACAAAGAGAGA 1 16405 ( 65) AACACGAAGAAGGT 1 11346 ( 164) AGTACGAAGAGGGA 1 2294 ( 158) AAGACGAAGAGAGG 1 22184 ( 118) AGCAGTAAAAAAGA 1 34518 ( 28) AACACAAATATGGA 1 3707 ( 75) AGGACCACCAAACA 1 4455 ( 125) AGGACCAAGCAGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 6818 bayes= 9.66297 E= 1.9e+001 203 -997 -997 -997 71 -997 124 -997 -997 85 97 -147 203 -997 -997 -997 -997 185 -35 -997 -29 43 65 -147 203 -997 -997 -997 188 -115 -997 -997 -129 -115 146 -147 188 -115 -997 -997 129 -997 24 -147 129 -997 65 -997 -129 -115 165 -997 151 -997 -135 -48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 10 E= 1.9e+001 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.400000 0.500000 0.100000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.200000 0.300000 0.400000 0.100000 1.000000 0.000000 0.000000 0.000000 0.900000 0.100000 0.000000 0.000000 0.100000 0.100000 0.700000 0.100000 0.900000 0.100000 0.000000 0.000000 0.600000 0.000000 0.300000 0.100000 0.600000 0.000000 0.400000 0.000000 0.100000 0.100000 0.800000 0.000000 0.700000 0.000000 0.100000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[GA][GC]A[CG][GCA]AAGA[AG][AG]G[AT] -------------------------------------------------------------------------------- Time 3.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 95 E-value = 5.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::6:4::2a::2:2:::::: pos.-specific C 4:a:8:4a4:8a2a:a2284: probability G :::::4::2:::::2:22::: matrix T 6a:4226:2:2:6:6:6626a bits 2.2 * * * * * 2.0 ** * * * * * * 1.7 ** * * * * * * 1.5 ** * * * * * * Relative 1.3 ** * * *** * * * * Entropy 1.1 ***** ** *** * * *** (27.5 bits) 0.9 ***** ** *** * * *** 0.7 ***** ** ***** ****** 0.4 ******** ************ 0.2 ********************* 0.0 --------------------- Multilevel TTCACATCCACCTCTCTTCTT consensus C TTGC A T A A CCTC sequence T G C G GG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 2294 447 5.24e-11 ATGGCATACC TTCACATCGACCTCTCTCCTT CCATCCACAC 3538 258 9.89e-11 TCCTACTCCT CTCTCGCCCACCTCGCTTCTT CTCCCAGCGG 1225 408 1.49e-09 CTGCGTTCCT TTCACGTCCATCTCACGTCCT TCGTTCGCCA 11346 334 4.06e-09 TGGCGGTGGC CTCTTATCAACCCCTCCTCCT CGTCATGCAA 6133 418 6.20e-09 TGTCCTTAAT TTCACTCCTACCACTCTGTTT AATAATCATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2294 5.2e-11 446_[+3]_33 3538 9.9e-11 257_[+3]_222 1225 1.5e-09 407_[+3]_72 11346 4.1e-09 333_[+3]_146 6133 6.2e-09 417_[+3]_62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 2294 ( 447) TTCACATCGACCTCTCTCCTT 1 3538 ( 258) CTCTCGCCCACCTCGCTTCTT 1 1225 ( 408) TTCACGTCCATCTCACGTCCT 1 11346 ( 334) CTCTTATCAACCCCTCCTCCT 1 6133 ( 418) TTCACTCCTACCACTCTGTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6720 bayes= 9.82513 E= 5.0e+001 -897 85 -897 111 -897 -897 -897 184 -897 217 -897 -897 129 -897 -897 52 -897 185 -897 -48 71 -897 65 -48 -897 85 -897 111 -897 217 -897 -897 -29 85 -35 -48 203 -897 -897 -897 -897 185 -897 -48 -897 217 -897 -897 -29 -15 -897 111 -897 217 -897 -897 -29 -897 -35 111 -897 217 -897 -897 -897 -15 -35 111 -897 -15 -35 111 -897 185 -897 -48 -897 85 -897 111 -897 -897 -897 184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 5.0e+001 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.800000 0.000000 0.200000 0.400000 0.000000 0.400000 0.200000 0.000000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.200000 0.400000 0.200000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.200000 0.200000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.200000 0.000000 0.200000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.600000 0.000000 0.200000 0.200000 0.600000 0.000000 0.800000 0.000000 0.200000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC]TC[AT][CT][AGT][TC]C[CAGT]A[CT]C[TAC]C[TAG]C[TCG][TCG][CT][TC]T -------------------------------------------------------------------------------- Time 5.52 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11346 1.87e-09 38_[+1(1.13e-05)]_113_\ [+2(9.79e-07)]_156_[+3(4.06e-09)]_146 11516 2.21e-07 392_[+3(6.74e-05)]_7_[+1(1.13e-05)]_\ 46_[+2(1.09e-08)]_8 1225 4.40e-07 407_[+3(1.49e-09)]_49_\ [+1(1.84e-05)]_11 16405 5.03e-05 64_[+2(4.48e-07)]_40_[+1(1.13e-05)]_\ 370 21200 2.18e-02 449_[+1(4.16e-06)]_39 22184 7.40e-04 100_[+1(7.58e-06)]_5_[+2(6.54e-06)]_\ 369 22931 1.15e-05 360_[+2(1.25e-07)]_87_\ [+1(3.70e-06)]_27 2294 8.90e-11 100_[+1(2.84e-05)]_45_\ [+2(1.15e-06)]_275_[+3(5.24e-11)]_33 262318 1.87e-02 464_[+1(8.22e-06)]_24 34518 1.45e-04 27_[+2(9.16e-06)]_257_\ [+1(1.75e-06)]_190 3538 5.48e-06 257_[+3(9.89e-11)]_222 3707 7.26e-02 74_[+2(1.45e-05)]_412 4455 1.64e-03 124_[+2(1.63e-05)]_153_\ [+1(3.88e-05)]_197 6133 2.13e-12 159_[+2(1.52e-07)]_244_\ [+3(6.20e-09)]_50_[+1(3.37e-08)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************