******************************************************************************** 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/63/63.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42446 1.0000 500 13399 1.0000 500 54721 1.0000 500 33013 1.0000 500 49233 1.0000 500 49389 1.0000 500 41189 1.0000 500 41359 1.0000 500 45118 1.0000 500 45340 1.0000 500 42616 1.0000 500 42752 1.0000 500 45549 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/63/63.seqs.fa -oc motifs/63 -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 0.279 C 0.225 G 0.227 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.279 C 0.225 G 0.227 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 8 llr = 105 E-value = 1.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 9:::::63::5:9134 pos.-specific C :6:::93::61a:5:6 probability G 1:::3::::13:111: matrix T :4aa8118a31::36: bits 2.2 * 1.9 ** * * 1.7 ** * * 1.5 ** * * * Relative 1.3 * ** * * ** Entropy 1.1 ****** ** ** * (19.0 bits) 0.9 ****** *** ** * 0.6 ********** ** ** 0.4 ********** ** ** 0.2 **************** 0.0 ---------------- Multilevel ACTTTCATTCACACTC consensus T G CA TG TAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 41359 364 1.06e-08 GTTCCAACTA ACTTTCATTGACACTC TGTAGCTCTT 49389 264 2.72e-08 TTCCAGCAAG ACTTTCCTTCACAGTC AGTCAGTCAG 42752 36 2.06e-07 AGATAGTGCA ATTTTCATTCCCGCTC GCTCAACCTT 42616 47 3.67e-07 GCTATCTGAA ATTTGCAATCGCATTC CAAGAAGAAT 41189 417 4.04e-07 CCTCGATTGC GCTTGCATTCACACGC ACCCTTTACC 49233 228 8.41e-07 AATCCAATGA ACTTTCCTTTTCACAA ATCTCTCCGT 54721 116 1.97e-06 CAGGAGAGAC ACTTTTAATTACATTA ACGGCAATGT 45118 473 2.21e-06 TTGTGCATCG ATTTTCTTTCGCAAAA AAAAAATCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41359 1.1e-08 363_[+1]_121 49389 2.7e-08 263_[+1]_221 42752 2.1e-07 35_[+1]_449 42616 3.7e-07 46_[+1]_438 41189 4e-07 416_[+1]_68 49233 8.4e-07 227_[+1]_257 54721 2e-06 115_[+1]_369 45118 2.2e-06 472_[+1]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=8 41359 ( 364) ACTTTCATTGACACTC 1 49389 ( 264) ACTTTCCTTCACAGTC 1 42752 ( 36) ATTTTCATTCCCGCTC 1 42616 ( 47) ATTTGCAATCGCATTC 1 41189 ( 417) GCTTGCATTCACACGC 1 49233 ( 228) ACTTTCCTTTTCACAA 1 54721 ( 116) ACTTTTAATTACATTA 1 45118 ( 473) ATTTTCTTTCGCAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 10.3581 E= 1.5e+002 165 -965 -86 -965 -965 147 -965 48 -965 -965 -965 190 -965 -965 -965 190 -965 -965 14 148 -965 196 -965 -110 116 15 -965 -110 -16 -965 -965 148 -965 -965 -965 190 -965 147 -86 -10 84 -85 14 -110 -965 215 -965 -965 165 -965 -86 -965 -116 115 -86 -10 -16 -965 -86 122 43 147 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 1.5e+002 0.875000 0.000000 0.125000 0.000000 0.000000 0.625000 0.000000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.875000 0.000000 0.125000 0.625000 0.250000 0.000000 0.125000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.625000 0.125000 0.250000 0.500000 0.125000 0.250000 0.125000 0.000000 1.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.125000 0.500000 0.125000 0.250000 0.250000 0.000000 0.125000 0.625000 0.375000 0.625000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[CT]TT[TG]C[AC][TA]T[CT][AG]CA[CT][TA][CA] -------------------------------------------------------------------------------- Time 1.62 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 4 llr = 67 E-value = 1.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a83::a:::a3::::: pos.-specific C :::33::53:8::8a3 probability G :3::8::38::aa3:8 matrix T ::88::a3:::::::: bits 2.2 ** * 1.9 * ** * ** * 1.7 * ** * ** * 1.5 * ** * ** * Relative 1.3 * *** ******** Entropy 1.1 ******* ******** (24.3 bits) 0.9 ******* ******** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel AATTGATCGACGGCCG consensus GACC GC A G C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 49233 163 1.80e-09 TACCGTGAAC AATTCATCGACGGCCG AAAATAGAGA 41359 122 5.80e-09 ATAATTGCAC AATTGATGGAAGGCCG GGGCTGCAGA 42446 236 2.87e-08 AGTTCGTCCA AAATGATCGACGGGCC TAGCCCGAGT 49389 225 3.40e-08 CTAGTTTCCG AGTCGATTCACGGCCG TGTGACTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49233 1.8e-09 162_[+2]_322 41359 5.8e-09 121_[+2]_363 42446 2.9e-08 235_[+2]_249 49389 3.4e-08 224_[+2]_260 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=4 49233 ( 163) AATTCATCGACGGCCG 1 41359 ( 122) AATTGATGGAAGGCCG 1 42446 ( 236) AAATGATCGACGGGCC 1 49389 ( 225) AGTCGATTCACGGCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 10.6214 E= 1.7e+003 184 -865 -865 -865 142 -865 14 -865 -16 -865 -865 148 -865 15 -865 148 -865 15 172 -865 184 -865 -865 -865 -865 -865 -865 189 -865 115 14 -10 -865 15 172 -865 184 -865 -865 -865 -16 173 -865 -865 -865 -865 213 -865 -865 -865 213 -865 -865 173 14 -865 -865 215 -865 -865 -865 15 172 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 4 E= 1.7e+003 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[AG][TA][TC][GC]AT[CGT][GC]A[CA]GG[CG]C[GC] -------------------------------------------------------------------------------- Time 3.07 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 4 llr = 67 E-value = 1.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3::a:3::::3::::: pos.-specific C 8:::58333:5:::a3 probability G ::a:::888:35:::8 matrix T :a::5::::a:5aa:: bits 2.2 * * 1.9 *** * *** 1.7 *** * *** 1.5 *** * *** Relative 1.3 **** ***** **** Entropy 1.1 ********** ***** (24.2 bits) 0.9 ********** ***** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CTGACCGGGTCGTTCG consensus A TACCC AT C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 45118 83 3.90e-10 ACATTAATTT CTGACCGGGTCTTTCG TTATACCGTT 45340 156 1.08e-08 GTAAACGTCG CTGACCGCGTCGTTCC GAGAGCAAAG 42446 216 4.06e-08 TATACTGCAA ATGATCCGGTAGTTCG TCCAAAATGA 49389 427 4.45e-08 CCGTCCGGTA CTGATAGGCTGTTTCG GAATCAGTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45118 3.9e-10 82_[+3]_402 45340 1.1e-08 155_[+3]_329 42446 4.1e-08 215_[+3]_269 49389 4.5e-08 426_[+3]_58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=4 45118 ( 83) CTGACCGGGTCTTTCG 1 45340 ( 156) CTGACCGCGTCGTTCC 1 42446 ( 216) ATGATCCGGTAGTTCG 1 49389 ( 427) CTGATAGGCTGTTTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 11.3587 E= 1.8e+003 -16 173 -865 -865 -865 -865 -865 189 -865 -865 213 -865 184 -865 -865 -865 -865 115 -865 89 -16 173 -865 -865 -865 15 172 -865 -865 15 172 -865 -865 15 172 -865 -865 -865 -865 189 -16 115 14 -865 -865 -865 113 89 -865 -865 -865 189 -865 -865 -865 189 -865 215 -865 -865 -865 15 172 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 4 E= 1.8e+003 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.250000 0.750000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.500000 0.250000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CA]TGA[CT][CA][GC][GC][GC]T[CAG][GT]TTC[GC] -------------------------------------------------------------------------------- Time 4.34 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42446 2.49e-08 215_[+3(4.06e-08)]_4_[+2(2.87e-08)]_\ 249 13399 9.58e-01 500 54721 1.67e-02 115_[+1(1.97e-06)]_369 33013 1.12e-01 500 49233 6.19e-08 162_[+2(1.80e-09)]_49_\ [+1(8.41e-07)]_257 49389 2.72e-12 224_[+2(3.40e-08)]_23_\ [+1(2.72e-08)]_147_[+3(4.45e-08)]_58 41189 4.39e-03 416_[+1(4.04e-07)]_68 41359 7.51e-10 121_[+2(5.80e-09)]_226_\ [+1(1.06e-08)]_121 45118 3.04e-08 82_[+3(3.90e-10)]_374_\ [+1(2.21e-06)]_12 45340 1.71e-04 155_[+3(1.08e-08)]_329 42616 6.08e-03 46_[+1(3.67e-07)]_438 42752 4.18e-03 35_[+1(2.06e-07)]_449 45549 9.80e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************