******************************************************************************** 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/260/260.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 262031 1.0000 500 263284 1.0000 500 2956 1.0000 500 2959 1.0000 500 33376 1.0000 500 4865 1.0000 500 5777 1.0000 500 5779 1.0000 500 6657 1.0000 500 990 1.0000 500 992 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/260/260.seqs.fa -oc motifs/260 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.222 G 0.234 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.222 G 0.234 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 8 llr = 210 E-value = 1.6e-036 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::a:::a:::::a:::a:1: pos.-specific C ::a:::9::::a:::9a:9:a probability G ::::9:1:19::9::1::19: matrix T aa::1a::91a:1:a:::::: bits 2.2 * * * * 2.0 **** * * ** ** ** * 1.7 **** * * ** ** ** * 1.5 ******** ************ Relative 1.3 ********************* Entropy 1.1 ********************* (38.0 bits) 0.9 ********************* 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TTCAGTCATGTCGATCCACGC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 992 460 1.68e-13 GATACAACTT TTCAGTCATGTCGATCCACGC AGGATACCCG 990 460 1.68e-13 GATACAACTT TTCAGTCATGTCGATCCACGC AGGATACCCG 6657 466 1.68e-13 GATACAACTT TTCAGTCATGTCGATCCACGC AGGATACCCG 5779 369 1.68e-13 TACAAACATT TTCAGTCATGTCGATCCACGC AGGATACCCG 4865 460 1.68e-13 GATACAACTT TTCAGTCATGTCGATCCACGC AGGATACCCG 2959 460 1.68e-13 GATACAACTT TTCAGTCATGTCGATCCACGC AGGATACCCG 2956 372 8.44e-13 ACACAACATT TTCAGTCATGTCGATCCAGGC AGGATACCCG 262031 396 8.99e-10 GCATCCTCCA TTCATTGAGTTCTATGCACAC ATAGGCACAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 992 1.7e-13 459_[+1]_20 990 1.7e-13 459_[+1]_20 6657 1.7e-13 465_[+1]_14 5779 1.7e-13 368_[+1]_111 4865 1.7e-13 459_[+1]_20 2959 1.7e-13 459_[+1]_20 2956 8.4e-13 371_[+1]_108 262031 9e-10 395_[+1]_84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=8 992 ( 460) TTCAGTCATGTCGATCCACGC 1 990 ( 460) TTCAGTCATGTCGATCCACGC 1 6657 ( 466) TTCAGTCATGTCGATCCACGC 1 5779 ( 369) TTCAGTCATGTCGATCCACGC 1 4865 ( 460) TTCAGTCATGTCGATCCACGC 1 2959 ( 460) TTCAGTCATGTCGATCCACGC 1 2956 ( 372) TTCAGTCATGTCGATCCAGGC 1 262031 ( 396) TTCATTGAGTTCTATGCACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 9.36413 E= 1.6e-036 -965 -965 -965 190 -965 -965 -965 190 -965 217 -965 -965 186 -965 -965 -965 -965 -965 190 -109 -965 -965 -965 190 -965 197 -91 -965 186 -965 -965 -965 -965 -965 -91 171 -965 -965 190 -109 -965 -965 -965 190 -965 217 -965 -965 -965 -965 190 -109 186 -965 -965 -965 -965 -965 -965 190 -965 197 -91 -965 -965 217 -965 -965 186 -965 -965 -965 -965 197 -91 -965 -114 -965 190 -965 -965 217 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 1.6e-036 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.875000 0.125000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.125000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.875000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTCAGTCATGTCGATCCACGC -------------------------------------------------------------------------------- Time 0.99 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 173 E-value = 9.1e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::a::a::3a:3a:79:aa7a pos.-specific C ::::a::a::3::a::7::3: probability G a:::::::7:77::31::::: matrix T :a:a::a:::::::::3:::: bits 2.2 * * * * 2.0 ******** * ** ** * 1.7 ******** * ** ** * 1.5 ******** * ** ** * Relative 1.3 ******** ** ** **** * Entropy 1.1 ********************* (35.6 bits) 0.9 ********************* 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTATCATCGAGGACAACAAAA consensus A CA G T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 992 101 3.56e-13 ATGCACTCTG GTATCATCGAGGACAACAAAA AGTCGTGGTC 990 101 3.56e-13 ATGCACTCTG GTATCATCGAGGACAACAAAA AGTCGTGGTC 6657 109 3.56e-13 ATGCACTCTG GTATCATCGAGGACAACAAAA AGTCGTGGTC 2959 101 3.56e-13 ATGCACTCTG GTATCATCGAGGACAACAAAA AGTCGTGATC 4865 102 3.65e-12 ATGCACTCTG GTATCATCGAGGACAGCAAAA AGTCGTGGTC 5779 469 4.19e-11 ACTCAAAACA GTATCATCAACAACGATAACA AGAACAACAA 2956 469 4.19e-11 ATTCAAAACA GTATCATCAACAACGATAACA AGAACAACAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 992 3.6e-13 100_[+2]_379 990 3.6e-13 100_[+2]_379 6657 3.6e-13 108_[+2]_371 2959 3.6e-13 100_[+2]_379 4865 3.6e-12 101_[+2]_378 5779 4.2e-11 468_[+2]_11 2956 4.2e-11 468_[+2]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 992 ( 101) GTATCATCGAGGACAACAAAA 1 990 ( 101) GTATCATCGAGGACAACAAAA 1 6657 ( 109) GTATCATCGAGGACAACAAAA 1 2959 ( 101) GTATCATCGAGGACAACAAAA 1 4865 ( 102) GTATCATCGAGGACAGCAAAA 1 5779 ( 469) GTATCATCAACAACGATAACA 1 2956 ( 469) GTATCATCAACAACGATAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 9.40072 E= 9.1e-022 -945 -945 209 -945 -945 -945 -945 190 185 -945 -945 -945 -945 -945 -945 190 -945 217 -945 -945 185 -945 -945 -945 -945 -945 -945 190 -945 217 -945 -945 5 -945 161 -945 185 -945 -945 -945 -945 36 161 -945 5 -945 161 -945 185 -945 -945 -945 -945 217 -945 -945 137 -945 29 -945 163 -945 -71 -945 -945 168 -945 10 185 -945 -945 -945 185 -945 -945 -945 137 36 -945 -945 185 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 9.1e-022 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.285714 0.000000 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.714286 0.000000 0.285714 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.714286 0.000000 0.285714 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GTATCATC[GA]A[GC][GA]AC[AG]A[CT]AA[AC]A -------------------------------------------------------------------------------- Time 1.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 9 llr = 187 E-value = 8.6e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2:48:21a:8:37::::2: pos.-specific C :::2:2a8::9::6::::::: probability G 937:::::9:12a1:a9:38: matrix T 17186:::::::::3:1a7:a bits 2.2 * * * 2.0 * * * * * * 1.7 * ** * * * * 1.5 * * *** * *** * Relative 1.3 * * ***** * *** ** Entropy 1.1 ** * ******** ****** (29.9 bits) 0.9 ************* ******* 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTGTTACCGACAGCAGGTTGT consensus GACAC A G AT GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 992 197 1.96e-13 ACAGCTTATC GTGTTACCGACAGCAGGTTGT AGTGGGGAAT 990 197 1.96e-13 ACAGCTTATC GTGTTACCGACAGCAGGTTGT AGTGGGGAAT 6657 205 1.96e-13 ACAGCTTATC GTGTTACCGACAGCAGGTTGT AGTGGGGAAT 4865 198 1.96e-13 ACAGCTTATC GTGTTACCGACAGCAGGTTGT AGTGGGGAAT 2959 197 1.96e-13 ACAGCTTATC GTGTTACCGACAGCAGGTTGT AGTGGGGAAT 5779 391 2.66e-09 GATCCACGCA GGATACCCGACGGATGGTGAT GCACCGTCAC 2956 394 2.66e-09 GATCCAGGCA GGATACCCGACGGATGGTGAT GCACCATCAC 33376 347 7.73e-09 TGTTGTGTTG TGGCAACAGACAGATGTTGGT TGTTGTTTTT 262031 194 1.16e-08 GTACGAAATT GTTCAACAAAGAGGAGGTTGT TGGCATCACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 992 2e-13 196_[+3]_283 990 2e-13 196_[+3]_283 6657 2e-13 204_[+3]_275 4865 2e-13 197_[+3]_282 2959 2e-13 196_[+3]_283 5779 2.7e-09 390_[+3]_89 2956 2.7e-09 393_[+3]_86 33376 7.7e-09 346_[+3]_133 262031 1.2e-08 193_[+3]_286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=9 992 ( 197) GTGTTACCGACAGCAGGTTGT 1 990 ( 197) GTGTTACCGACAGCAGGTTGT 1 6657 ( 205) GTGTTACCGACAGCAGGTTGT 1 4865 ( 198) GTGTTACCGACAGCAGGTTGT 1 2959 ( 197) GTGTTACCGACAGCAGGTTGT 1 5779 ( 391) GGATACCCGACGGATGGTGAT 1 2956 ( 394) GGATACCCGACGGATGGTGAT 1 33376 ( 347) TGGCAACAGACAGATGTTGGT 1 262031 ( 194) GTTCAACAAAGAGGAGGTTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 9.32846 E= 8.6e-022 -982 -982 192 -126 -982 -982 51 132 -31 -982 151 -126 -982 0 -982 154 69 -982 -982 106 149 0 -982 -982 -982 217 -982 -982 -31 181 -982 -982 -131 -982 192 -982 186 -982 -982 -982 -982 200 -108 -982 149 -982 -8 -982 -982 -982 209 -982 27 132 -108 -982 127 -982 -982 32 -982 -982 209 -982 -982 -982 192 -126 -982 -982 -982 190 -982 -982 51 132 -31 -982 173 -982 -982 -982 -982 190 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 9 E= 8.6e-022 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.333333 0.666667 0.222222 0.000000 0.666667 0.111111 0.000000 0.222222 0.000000 0.777778 0.444444 0.000000 0.000000 0.555556 0.777778 0.222222 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.222222 0.777778 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.777778 0.000000 0.222222 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.555556 0.111111 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.222222 0.000000 0.777778 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[TG][GA][TC][TA][AC]C[CA]GAC[AG]G[CA][AT]GGT[TG][GA]T -------------------------------------------------------------------------------- Time 2.85 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262031 7.71e-10 193_[+3(1.16e-08)]_181_\ [+1(8.99e-10)]_84 263284 9.64e-01 500 2956 1.51e-20 371_[+1(8.44e-13)]_1_[+3(2.66e-09)]_\ 54_[+2(4.19e-11)]_11 2959 3.15e-27 100_[+2(3.56e-13)]_75_\ [+3(1.96e-13)]_242_[+1(1.68e-13)]_20 33376 1.95e-05 346_[+3(7.73e-09)]_133 4865 3.02e-26 101_[+2(3.65e-12)]_75_\ [+3(1.96e-13)]_241_[+1(1.68e-13)]_20 5777 7.32e-01 500 5779 3.19e-21 368_[+1(1.68e-13)]_1_[+3(2.66e-09)]_\ 57_[+2(4.19e-11)]_11 6657 3.15e-27 108_[+2(3.56e-13)]_75_\ [+3(1.96e-13)]_240_[+1(1.68e-13)]_14 990 3.15e-27 100_[+2(3.56e-13)]_75_\ [+3(1.96e-13)]_242_[+1(1.68e-13)]_20 992 3.15e-27 100_[+2(3.56e-13)]_75_\ [+3(1.96e-13)]_242_[+1(1.68e-13)]_20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************