******************************************************************************** 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/348/348.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 17936 1.0000 500 37144 1.0000 500 31254 1.0000 500 44708 1.0000 500 45116 1.0000 500 39901 1.0000 500 32327 1.0000 500 46339 1.0000 500 46445 1.0000 500 43621 1.0000 500 45341 1.0000 500 44613 1.0000 500 41286 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/348/348.seqs.fa -oc motifs/348 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.263 C 0.232 G 0.213 T 0.293 Background letter frequencies (from dataset with add-one prior applied): A 0.263 C 0.232 G 0.213 T 0.293 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 13 llr = 131 E-value = 1.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 8::49:5:15a2 pos.-specific C :5:6:8:::5:3 probability G 11:::::8:1:5 matrix T 15a:12529::: bits 2.2 2.0 * 1.8 * * 1.6 * * * * Relative 1.3 * ** ** * Entropy 1.1 * **** ** * (14.5 bits) 0.9 * ******* * 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACTCACAGTAAG consensus T A TT C C sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46339 341 5.24e-07 GTGACGACCG ATTCACTGTCAG CCGAGAACAG 17936 369 9.47e-07 CACTCATATC ACTCACTGTCAC ACACACATCA 41286 59 1.57e-06 ATCAAGATTT ACTAACTGTAAG TTCCTTCGTC 45116 261 2.05e-06 ACTGACTGTG ATTCACTGTAAC TGTAACTGTA 32327 130 2.72e-06 AGTTGTTTGT ACTCATAGTCAG CCCGGGAGGC 45341 334 2.97e-06 AGTACCATAC ATTAACAGTAAC TGTAAAACAA 31254 104 4.67e-06 TTCACTGTCG ATTCACAGTGAG TCAAAATAAA 37144 362 1.16e-05 GATGCGATGG ACTCACAGACAC AAATAGAAAA 43621 393 1.78e-05 GTAAATTCTC ACTCACTTTCAA CGCATCAATA 46445 102 3.03e-05 TAATTTTCGG GCTAACAGTAAA CCCCTCACAA 44613 109 3.83e-05 AAATGTTCTG TTTCATAGTCAG CGAAAGACGG 44708 174 7.82e-05 TGCAAAAGAG ATTATTTGTAAG GGAGACAGTT 39901 353 8.27e-05 GAAGCCTATT AGTAACATTAAA CAAAAGTTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46339 5.2e-07 340_[+1]_148 17936 9.5e-07 368_[+1]_120 41286 1.6e-06 58_[+1]_430 45116 2e-06 260_[+1]_228 32327 2.7e-06 129_[+1]_359 45341 3e-06 333_[+1]_155 31254 4.7e-06 103_[+1]_385 37144 1.2e-05 361_[+1]_127 43621 1.8e-05 392_[+1]_96 46445 3e-05 101_[+1]_387 44613 3.8e-05 108_[+1]_380 44708 7.8e-05 173_[+1]_315 39901 8.3e-05 352_[+1]_136 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=13 46339 ( 341) ATTCACTGTCAG 1 17936 ( 369) ACTCACTGTCAC 1 41286 ( 59) ACTAACTGTAAG 1 45116 ( 261) ATTCACTGTAAC 1 32327 ( 130) ACTCATAGTCAG 1 45341 ( 334) ATTAACAGTAAC 1 31254 ( 104) ATTCACAGTGAG 1 37144 ( 362) ACTCACAGACAC 1 43621 ( 393) ACTCACTTTCAA 1 46445 ( 102) GCTAACAGTAAA 1 44613 ( 109) TTTCATAGTCAG 1 44708 ( 174) ATTATTTGTAAG 1 39901 ( 353) AGTAACATTAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 8.93074 E= 1.7e-001 169 -1035 -146 -193 -1035 99 -146 66 -1035 -1035 -1035 177 55 141 -1035 -1035 181 -1035 -1035 -193 -1035 173 -1035 -34 104 -1035 -1035 66 -1035 -1035 199 -93 -177 -1035 -1035 166 81 99 -146 -1035 193 -1035 -1035 -1035 -19 41 112 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 13 E= 1.7e-001 0.846154 0.000000 0.076923 0.076923 0.000000 0.461538 0.076923 0.461538 0.000000 0.000000 0.000000 1.000000 0.384615 0.615385 0.000000 0.000000 0.923077 0.000000 0.000000 0.076923 0.000000 0.769231 0.000000 0.230769 0.538462 0.000000 0.000000 0.461538 0.000000 0.000000 0.846154 0.153846 0.076923 0.000000 0.000000 0.923077 0.461538 0.461538 0.076923 0.000000 1.000000 0.000000 0.000000 0.000000 0.230769 0.307692 0.461538 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[CT]T[CA]A[CT][AT]GT[AC]A[GCA] -------------------------------------------------------------------------------- Time 1.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 92 E-value = 5.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::2::4::2:::6:2:::::: pos.-specific C :82:2:8::6:62:2::::2: probability G 2:::8428:4a::84a8:22a matrix T 826a:2:28::4222:2a86: bits 2.2 * * * 2.0 * * * 1.8 * * * * * 1.6 ** * * * * Relative 1.3 * ** ** * * *** * Entropy 1.1 ** ** ***** * **** * (26.5 bits) 0.9 ** ** ****** * **** * 0.7 ** ** ******** ****** 0.4 ************** ****** 0.2 ********************* 0.0 --------------------- Multilevel TCTTGACGTCGCAGGGGTTTG consensus GTA CGGTAG TCTA T GC sequence C T T C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 41286 304 1.27e-10 CGTTTGTAGT GCCTGACGTCGCAGCGGTTTG TTGCCTCCCA 31254 31 1.63e-10 CATGTCTGTA TCTTGTCGTGGTAGGGGTGTG TCAATCCATA 37144 28 7.55e-10 ATTCGCGATT TCTTGGCTTCGTCGGGGTTGG CGAGCAATCT 46445 403 9.95e-09 TATACATATA TCATCACGTGGCTTAGGTTTG GCGTTGTGGC 32327 26 2.12e-08 GCAAAAACTG TTTTGGGGACGCAGTGTTTCG GGCTGAAGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41286 1.3e-10 303_[+2]_176 31254 1.6e-10 30_[+2]_449 37144 7.5e-10 27_[+2]_452 46445 1e-08 402_[+2]_77 32327 2.1e-08 25_[+2]_454 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 41286 ( 304) GCCTGACGTCGCAGCGGTTTG 1 31254 ( 31) TCTTGTCGTGGTAGGGGTGTG 1 37144 ( 28) TCTTGGCTTCGTCGGGGTTGG 1 46445 ( 403) TCATCACGTGGCTTAGGTTTG 1 32327 ( 26) TTTTGGGGACGCAGTGTTTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6240 bayes= 10.536 E= 5.5e+002 -897 -897 -9 145 -897 178 -897 -55 -39 -21 -897 103 -897 -897 -897 177 -897 -21 191 -897 61 -897 91 -55 -897 178 -9 -897 -897 -897 191 -55 -39 -897 -897 145 -897 137 91 -897 -897 -897 223 -897 -897 137 -897 45 119 -21 -897 -55 -897 -897 191 -55 -39 -21 91 -55 -897 -897 223 -897 -897 -897 191 -55 -897 -897 -897 177 -897 -897 -9 145 -897 -21 -9 103 -897 -897 223 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 5.5e+002 0.000000 0.000000 0.200000 0.800000 0.000000 0.800000 0.000000 0.200000 0.200000 0.200000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.800000 0.000000 0.400000 0.000000 0.400000 0.200000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.800000 0.200000 0.200000 0.000000 0.000000 0.800000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.600000 0.200000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.200000 0.200000 0.400000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.200000 0.200000 0.600000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][CT][TAC]T[GC][AGT][CG][GT][TA][CG]G[CT][ACT][GT][GACT]G[GT]T[TG][TCG]G -------------------------------------------------------------------------------- Time 3.03 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 4 llr = 81 E-value = 5.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3:5:a5a5:::335::333 pos.-specific C ::::a::::3aa:5::38:8 probability G ::a:::5::8::8::a8::: matrix T a8:5::::5::::35:::8: bits 2.2 * * 2.0 * ** * ** * 1.8 * * ** * ** * 1.6 * * ** * ** * Relative 1.3 * * ** * **** *** * Entropy 1.1 * * **** **** *** * (29.2 bits) 0.9 ************* ****** 0.7 ************* ****** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TTGACAAAAGCCGCAGGCTC consensus A T G TC AAT CAAA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 45341 384 3.72e-12 TCTTGTTTCC TTGACAGATGCCGCTGGCTC ACCCTTTGTA 39901 331 6.51e-10 TTGGTTTGCT TTGTCAGAAGCCGAAGCCTA TTAGTAACAT 41286 432 8.36e-10 TAATCAATAC TAGTCAAAACCCGCAGGCAC TGTGTACCTT 43621 53 1.42e-09 CGTCAATTGT TTGACAAATGCCATTGGATC TCATCATCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45341 3.7e-12 383_[+3]_97 39901 6.5e-10 330_[+3]_150 41286 8.4e-10 431_[+3]_49 43621 1.4e-09 52_[+3]_428 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=4 45341 ( 384) TTGACAGATGCCGCTGGCTC 1 39901 ( 331) TTGTCAGAAGCCGAAGCCTA 1 41286 ( 432) TAGTCAAAACCCGCAGGCAC 1 43621 ( 53) TTGACAAATGCCATTGGATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 6253 bayes= 10.6094 E= 5.3e+002 -865 -865 -865 177 -7 -865 -865 135 -865 -865 223 -865 93 -865 -865 77 -865 211 -865 -865 193 -865 -865 -865 93 -865 123 -865 193 -865 -865 -865 93 -865 -865 77 -865 11 182 -865 -865 211 -865 -865 -865 211 -865 -865 -7 -865 182 -865 -7 111 -865 -23 93 -865 -865 77 -865 -865 223 -865 -865 11 182 -865 -7 169 -865 -865 -7 -865 -865 135 -7 169 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 4 E= 5.3e+002 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.500000 0.000000 0.250000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.750000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TA]G[AT]CA[AG]A[AT][GC]CC[GA][CAT][AT]G[GC][CA][TA][CA] -------------------------------------------------------------------------------- Time 4.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17936 1.39e-03 368_[+1(9.47e-07)]_120 37144 1.56e-07 27_[+2(7.55e-10)]_313_\ [+1(1.16e-05)]_127 31254 3.91e-08 30_[+2(1.63e-10)]_52_[+1(4.67e-06)]_\ 385 44708 2.08e-01 173_[+1(7.82e-05)]_315 45116 2.55e-02 260_[+1(2.05e-06)]_[+1(9.89e-05)]_\ 216 39901 2.92e-07 330_[+3(6.51e-10)]_2_[+1(8.27e-05)]_\ 136 32327 2.25e-06 25_[+2(2.12e-08)]_83_[+1(2.72e-06)]_\ 359 46339 6.78e-03 340_[+1(5.24e-07)]_148 46445 4.66e-06 101_[+1(3.03e-05)]_289_\ [+2(9.95e-09)]_77 43621 4.61e-07 52_[+3(1.42e-09)]_320_\ [+1(1.78e-05)]_96 45341 5.55e-10 333_[+1(2.97e-06)]_3_[+3(4.54e-05)]_\ 15_[+3(3.72e-12)]_97 44613 5.33e-02 108_[+1(3.83e-05)]_380 41286 1.47e-14 58_[+1(1.57e-06)]_233_\ [+2(1.27e-10)]_107_[+3(8.36e-10)]_49 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************