******************************************************************************** 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/316/316.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10339 1.0000 500 12810 1.0000 500 25522 1.0000 500 28544 1.0000 500 2938 1.0000 500 36339 1.0000 500 40958 1.0000 500 5405 1.0000 500 8777 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/316/316.seqs.fa -oc motifs/316 -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= 9 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= 4500 N= 9 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.245 C 0.231 G 0.263 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.245 C 0.231 G 0.263 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 9 llr = 113 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3191:1::a13:412 pos.-specific C 64911942a:269627 probability G ::::8:17:::11::1 matrix T 42:::131::7:::7: bits 2.1 ** 1.9 ** 1.7 * * ** * 1.5 ** * ** * Relative 1.3 ** * ** * Entropy 1.1 * **** ** ** (18.2 bits) 0.8 * **** **** **** 0.6 * **** ********* 0.4 ****** ********* 0.2 **************** 0.0 ---------------- Multilevel CCCAGCCGCATCCCTC consensus TA TC CA ACA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 8777 49 4.05e-08 TTCATCCGGA TCCAACCGCATCCATC TCAGCCTACA 5405 20 1.33e-07 CTTCTGCTTT CTCAGCCTCATACCTC ATACACTGAG 36339 424 2.75e-07 CGTGGAACGG TACACCTCCATCCCTC CACCTACAGC 28544 371 3.65e-07 CAGATCCTTT CACAGCCGCACACCCA CACCAAACTT 2938 440 4.42e-07 TGTGCGGCTG TCCAGCAGCATCGATC CCCCCGTAGT 40958 463 5.29e-07 GTCTCGCCAT TCCAGCTGCATGCCTG CTCACCCTGC 10339 155 5.29e-07 AGACAGAGGC CCCAGTTGCATCCCAC AAGGCGCAAT 12810 477 2.33e-06 CCAATTGAAG CTCAGCCCCAACCACA CATCAACC 25522 22 8.50e-06 GCGATCCGAA CAACGCGGCACACATC AAGATTGGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8777 4.1e-08 48_[+1]_436 5405 1.3e-07 19_[+1]_465 36339 2.7e-07 423_[+1]_61 28544 3.7e-07 370_[+1]_114 2938 4.4e-07 439_[+1]_45 40958 5.3e-07 462_[+1]_22 10339 5.3e-07 154_[+1]_330 12810 2.3e-06 476_[+1]_8 25522 8.5e-06 21_[+1]_463 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=9 8777 ( 49) TCCAACCGCATCCATC 1 5405 ( 20) CTCAGCCTCATACCTC 1 36339 ( 424) TACACCTCCATCCCTC 1 28544 ( 371) CACAGCCGCACACCCA 1 2938 ( 440) TCCAGCAGCATCGATC 1 40958 ( 463) TCCAGCTGCATGCCTG 1 10339 ( 155) CCCAGTTGCATCCCAC 1 12810 ( 477) CTCAGCCCCAACCACA 1 25522 ( 22) CAACGCGGCACACATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 4365 bayes= 9.05343 E= 1.4e-001 -982 127 -982 77 44 94 -982 -23 -114 194 -982 -982 186 -105 -982 -982 -114 -105 156 -982 -982 194 -982 -123 -114 94 -124 35 -982 -6 134 -123 -982 211 -982 -982 203 -982 -982 -982 -114 -6 -982 135 44 127 -124 -982 -982 194 -124 -982 86 127 -982 -982 -114 -6 -982 135 -14 153 -124 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 9 E= 1.4e-001 0.000000 0.555556 0.000000 0.444444 0.333333 0.444444 0.000000 0.222222 0.111111 0.888889 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.111111 0.111111 0.777778 0.000000 0.000000 0.888889 0.000000 0.111111 0.111111 0.444444 0.111111 0.333333 0.000000 0.222222 0.666667 0.111111 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.111111 0.222222 0.000000 0.666667 0.333333 0.555556 0.111111 0.000000 0.000000 0.888889 0.111111 0.000000 0.444444 0.555556 0.000000 0.000000 0.111111 0.222222 0.000000 0.666667 0.222222 0.666667 0.111111 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CAT]CAGC[CT][GC]CA[TC][CA]C[CA][TC][CA] -------------------------------------------------------------------------------- Time 0.76 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 7 llr = 92 E-value = 2.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::::::31414: pos.-specific C a:93939a:39:941 probability G :3:1:::::1::::1 matrix T :716171:a3:6:17 bits 2.1 * * 1.9 * ** 1.7 * ** 1.5 * * * *** * * Relative 1.3 * * * *** * * Entropy 1.1 *** ***** *** (19.0 bits) 0.8 *** ***** *** * 0.6 ********* ***** 0.4 ********* ***** 0.2 ********* ***** 0.0 --------------- Multilevel CTCTCTCCTACTCAT consensus G C C C A C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 5405 291 2.04e-08 TGTTTGTGTG CTCTCCCCTTCTCCT TCACCACACC 40958 404 4.26e-08 AGTTTGCTGC CTCTCTCCTCCTCAC TGCCGTGTAA 36339 200 6.67e-08 CACTCACTCG CTCGCTCCTACACAT TGGCAAACCG 28544 435 1.65e-07 TGAGATCCAC CGCCCTCCTGCTCCT CGGTGCCATC 8777 385 1.84e-06 CCATCTGAAT CTCCTCCCTACACTT GGCTGTGGCG 10339 16 1.84e-06 AGTTCACATT CGCTCTCCTCAAAAT ATCTTCTTTG 12810 217 3.02e-06 TGAAATGATG CTTTCTTCTTCTCCG GAGGTGGGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5405 2e-08 290_[+2]_195 40958 4.3e-08 403_[+2]_82 36339 6.7e-08 199_[+2]_286 28544 1.6e-07 434_[+2]_51 8777 1.8e-06 384_[+2]_101 10339 1.8e-06 15_[+2]_470 12810 3e-06 216_[+2]_269 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=7 5405 ( 291) CTCTCCCCTTCTCCT 1 40958 ( 404) CTCTCTCCTCCTCAC 1 36339 ( 200) CTCGCTCCTACACAT 1 28544 ( 435) CGCCCTCCTGCTCCT 1 8777 ( 385) CTCCTCCCTACACTT 1 10339 ( 16) CGCTCTCCTCAAAAT 1 12810 ( 217) CTTTCTTCTTCTCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4374 bayes= 9.89159 E= 2.2e+000 -945 211 -945 -945 -945 -945 12 145 -945 189 -945 -87 -945 31 -88 113 -945 189 -945 -87 -945 31 -945 145 -945 189 -945 -87 -945 211 -945 -945 -945 -945 -945 194 22 31 -88 13 -78 189 -945 -945 81 -945 -945 113 -78 189 -945 -945 81 89 -945 -87 -945 -69 -88 145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 2.2e+000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.857143 0.000000 0.142857 0.000000 0.285714 0.142857 0.571429 0.000000 0.857143 0.000000 0.142857 0.000000 0.285714 0.000000 0.714286 0.000000 0.857143 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.285714 0.285714 0.142857 0.285714 0.142857 0.857143 0.000000 0.000000 0.428571 0.000000 0.000000 0.571429 0.142857 0.857143 0.000000 0.000000 0.428571 0.428571 0.000000 0.142857 0.000000 0.142857 0.142857 0.714286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[TG]C[TC]C[TC]CCT[ACT]C[TA]C[AC]T -------------------------------------------------------------------------------- Time 1.60 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 6 llr = 104 E-value = 4.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :723:37373387282:a5:a pos.-specific C 73778::5355::82:a:3a: probability G :::::22::2222:::::2:: matrix T 3:2:2522::::2::8::::: bits 2.1 ** ** 1.9 ** ** 1.7 ** ** 1.5 * ** ** ** Relative 1.3 ** * ***** ** Entropy 1.1 ** ** * * ***** ** (25.0 bits) 0.8 ***** * * ******* ** 0.6 ***** *************** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CACCCTACACCAACATCAACA consensus TC A A ACAA C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5405 312 9.97e-11 TCCTTCACCA CACCCTAAAACATCATCACCA GTCACCACAA 28544 403 1.18e-09 ACTTTCAACT TACACTTCAGCAACATCAACA ATGAGATCCA 36339 470 4.57e-09 CAGCTGTAGT CAACCTATCCAAACAACAACA AACGAACAGC 2938 476 9.62e-09 CTTTTGGGGG CACACAAACACAAACTCAACA CAAC 40958 370 1.50e-08 CTGTCTCGTC TCTCCAACACGGACATCACCA TGAAGTTTGC 12810 443 4.40e-08 CCACCACACA CCCCTGGCACAAGCATCAGCA GCTCCAATTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5405 1e-10 311_[+3]_168 28544 1.2e-09 402_[+3]_77 36339 4.6e-09 469_[+3]_10 2938 9.6e-09 475_[+3]_4 40958 1.5e-08 369_[+3]_110 12810 4.4e-08 442_[+3]_37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=6 5405 ( 312) CACCCTAAAACATCATCACCA 1 28544 ( 403) TACACTTCAGCAACATCAACA 1 36339 ( 470) CAACCTATCCAAACAACAACA 1 2938 ( 476) CACACAAACACAAACTCAACA 1 40958 ( 370) TCTCCAACACGGACATCACCA 1 12810 ( 443) CCCCTGGCACAAGCATCAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4320 bayes= 9.93784 E= 4.4e+000 -923 153 -923 35 144 53 -923 -923 -56 153 -923 -64 44 153 -923 -923 -923 185 -923 -64 44 -923 -66 94 144 -923 -66 -64 44 111 -923 -64 144 53 -923 -923 44 111 -66 -923 44 111 -66 -923 176 -923 -66 -923 144 -923 -66 -64 -56 185 -923 -923 176 -47 -923 -923 -56 -923 -923 168 -923 211 -923 -923 203 -923 -923 -923 103 53 -66 -923 -923 211 -923 -923 203 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 4.4e+000 0.000000 0.666667 0.000000 0.333333 0.666667 0.333333 0.000000 0.000000 0.166667 0.666667 0.000000 0.166667 0.333333 0.666667 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.333333 0.000000 0.166667 0.500000 0.666667 0.000000 0.166667 0.166667 0.333333 0.500000 0.000000 0.166667 0.666667 0.333333 0.000000 0.000000 0.333333 0.500000 0.166667 0.000000 0.333333 0.500000 0.166667 0.000000 0.833333 0.000000 0.166667 0.000000 0.666667 0.000000 0.166667 0.166667 0.166667 0.833333 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.333333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][AC]C[CA]C[TA]A[CA][AC][CA][CA]AACATCA[AC]CA -------------------------------------------------------------------------------- Time 2.35 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10339 1.78e-05 15_[+2(1.84e-06)]_124_\ [+1(5.29e-07)]_330 12810 1.10e-08 216_[+2(3.02e-06)]_211_\ [+3(4.40e-08)]_13_[+1(2.33e-06)]_8 25522 5.47e-02 21_[+1(8.50e-06)]_463 28544 4.49e-12 370_[+1(3.65e-07)]_16_\ [+3(1.18e-09)]_11_[+2(1.65e-07)]_51 2938 7.42e-08 439_[+1(4.42e-07)]_20_\ [+3(9.62e-09)]_4 36339 5.26e-12 199_[+2(6.67e-08)]_209_\ [+1(2.75e-07)]_30_[+3(4.57e-09)]_10 40958 1.95e-11 369_[+3(1.50e-08)]_13_\ [+2(4.26e-08)]_44_[+1(5.29e-07)]_22 5405 2.33e-14 19_[+1(1.33e-07)]_255_\ [+2(2.04e-08)]_6_[+3(9.97e-11)]_168 8777 1.43e-06 48_[+1(4.05e-08)]_320_\ [+2(1.84e-06)]_101 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************