******************************************************************************** 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/382/382.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21983 1.0000 500 49666 1.0000 500 44887 1.0000 500 41116 1.0000 500 35854 1.0000 500 45043 1.0000 500 34985 1.0000 500 33637 1.0000 500 43987 1.0000 500 45057 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/382/382.seqs.fa -oc motifs/382 -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= 10 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= 5000 N= 10 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.277 C 0.243 G 0.197 T 0.284 Background letter frequencies (from dataset with add-one prior applied): A 0.277 C 0.243 G 0.197 T 0.284 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 5 llr = 105 E-value = 2.7e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::626:4a2:::2::::::: pos.-specific C 824:2a::::a4::aa8aa8 probability G 2:::2:6:8a::2::::::2 matrix T :8:8:::::::66a::2::: bits 2.3 * 2.1 * ** ** ** 1.9 * * ** *** ** 1.6 * **** *** ** Relative 1.4 * * **** *** *** Entropy 1.2 ** * ****** ******* (30.3 bits) 0.9 **** ******* ******* 0.7 ************ ******* 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CTATACGAGGCTTTCCCCCC consensus GCCAC A A CA T G sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 35854 416 2.42e-12 CAATCGGAGC CTCTACGAGGCTTTCCCCCC AACTTCTACT 41116 386 4.34e-12 CAATTGGAGC CTATACAAGGCTTTCCCCCC AAAAGTTCTA 33637 369 5.22e-11 CACTCGGAGC CTCTACGAAGCTTTCCCCCC AACTTCTACT 45057 408 4.48e-10 CTGGGATTCA CTATCCGAGGCCATCCTCCC GCTGTGACTG 45043 18 2.62e-09 GAGCGCAACG GCAAGCAAGGCCGTCCCCCG CCCCGGAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35854 2.4e-12 415_[+1]_65 41116 4.3e-12 385_[+1]_95 33637 5.2e-11 368_[+1]_112 45057 4.5e-10 407_[+1]_73 45043 2.6e-09 17_[+1]_463 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=5 35854 ( 416) CTCTACGAGGCTTTCCCCCC 1 41116 ( 386) CTATACAAGGCTTTCCCCCC 1 33637 ( 369) CTCTACGAAGCTTTCCCCCC 1 45057 ( 408) CTATCCGAGGCCATCCTCCC 1 45043 ( 18) GCAAGCAAGGCCGTCCCCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 4810 bayes= 10.1602 E= 2.7e-004 -897 172 2 -897 -897 -28 -897 149 112 72 -897 -897 -47 -897 -897 149 112 -28 2 -897 -897 204 -897 -897 53 -897 160 -897 185 -897 -897 -897 -47 -897 202 -897 -897 -897 234 -897 -897 204 -897 -897 -897 72 -897 108 -47 -897 2 108 -897 -897 -897 182 -897 204 -897 -897 -897 204 -897 -897 -897 172 -897 -50 -897 204 -897 -897 -897 204 -897 -897 -897 172 2 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 5 E= 2.7e-004 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.000000 0.800000 0.600000 0.400000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.600000 0.200000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.200000 0.000000 0.200000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][TC][AC][TA][ACG]C[GA]A[GA]GC[TC][TAG]TCC[CT]CC[CG] -------------------------------------------------------------------------------- Time 0.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 3 llr = 84 E-value = 2.4e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::a::a:a::::::a:3::: pos.-specific C :a7::::a:::::7::a:::: probability G a:::a::::::aa::::7aaa matrix T ::3::a:::aa::3a:::::: bits 2.3 * * ** *** 2.1 ** * * ** * *** 1.9 ** ********** *** *** 1.6 ** ********** *** *** Relative 1.4 ** ********** *** *** Entropy 1.2 ** ********** ******* (40.6 bits) 0.9 ********************* 0.7 ********************* 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GCCAGTACATTGGCTACGGGG consensus T T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 33637 240 7.36e-14 TGGTTCGATA GCCAGTACATTGGCTACGGGG TTTCTACGTT 35854 287 7.36e-14 TGGTTCGATA GCCAGTACATTGGCTACGGGG TTTCTACGTT 41116 131 8.33e-13 AGATTGCACA GCTAGTACATTGGTTACAGGG TTCTATGTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 33637 7.4e-14 239_[+2]_240 35854 7.4e-14 286_[+2]_193 41116 8.3e-13 130_[+2]_349 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=3 33637 ( 240) GCCAGTACATTGGCTACGGGG 1 35854 ( 287) GCCAGTACATTGGCTACGGGG 1 41116 ( 131) GCTAGTACATTGGTTACAGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 11.0907 E= 2.4e-003 -823 -823 234 -823 -823 204 -823 -823 -823 146 -823 23 185 -823 -823 -823 -823 -823 234 -823 -823 -823 -823 181 185 -823 -823 -823 -823 204 -823 -823 185 -823 -823 -823 -823 -823 -823 181 -823 -823 -823 181 -823 -823 234 -823 -823 -823 234 -823 -823 146 -823 23 -823 -823 -823 181 185 -823 -823 -823 -823 204 -823 -823 27 -823 176 -823 -823 -823 234 -823 -823 -823 234 -823 -823 -823 234 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 3 E= 2.4e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GC[CT]AGTACATTGG[CT]TAC[GA]GGG -------------------------------------------------------------------------------- Time 1.71 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 8 llr = 127 E-value = 1.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 9::::4:13:461:9:5:4:: pos.-specific C ::3:5:4:191:36:9::11: probability G ::35:::8615:311:5:18a matrix T 1a555661:::443:1:a41: bits 2.3 * 2.1 * 1.9 * * * 1.6 * * * * Relative 1.4 ** * ** * * Entropy 1.2 ** * * * **** ** (22.9 bits) 0.9 ** ******* * **** ** 0.7 ** ********* ***** ** 0.5 ************ ***** ** 0.2 ************ ***** ** 0.0 --------------------- Multilevel ATTGCTTGGCGATCACATAGG consensus CTTAC A ATCT G T sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 33637 178 1.77e-11 TCCGAACTCG ATGGTTTGGCGATCACATAGG TGATCCAATC 35854 224 1.77e-11 TCCGAACTCG ATGGTTTGGCGATCACATAGG TGATCCAATC 34985 122 3.71e-10 CCTGATTCAA ATTTTTTGGCAAGCACGTGGG TTGCTCCCCC 45057 265 3.25e-09 TCCGCGGCCA ATCTTTCGACGTCCACGTTGG TTGCTGCGTT 41116 252 4.81e-08 CTGTCAAAAG ATTGCATTGCCAGTACATTGG TCACAGGTTT 43987 188 2.40e-07 GTACATGAAA ATTTCACAACGTCGACGTCGG CCTAAGCCCG 45043 208 5.13e-07 AAGCATTTCT ATTTCACGCGATACACGTTCG CGCAAGATCT 49666 95 9.77e-07 TGGACAGCAA TTCGCTTGGCAATTGTATATG CGAGTAAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 33637 1.8e-11 177_[+3]_302 35854 1.8e-11 223_[+3]_256 34985 3.7e-10 121_[+3]_358 45057 3.2e-09 264_[+3]_215 41116 4.8e-08 251_[+3]_228 43987 2.4e-07 187_[+3]_292 45043 5.1e-07 207_[+3]_272 49666 9.8e-07 94_[+3]_385 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=8 33637 ( 178) ATGGTTTGGCGATCACATAGG 1 35854 ( 224) ATGGTTTGGCGATCACATAGG 1 34985 ( 122) ATTTTTTGGCAAGCACGTGGG 1 45057 ( 265) ATCTTTCGACGTCCACGTTGG 1 41116 ( 252) ATTGCATTGCCAGTACATTGG 1 43987 ( 188) ATTTCACAACGTCGACGTCGG 1 45043 ( 208) ATTTCACGCGATACACGTTCG 1 49666 ( 95) TTCGCTTGGCAATTGTATATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 9.96434 E= 1.8e-001 166 -965 -965 -118 -965 -965 -965 182 -965 4 34 82 -965 -965 134 82 -965 104 -965 82 44 -965 -965 114 -965 63 -965 114 -114 -965 193 -118 -15 -95 166 -965 -965 185 -66 -965 44 -95 134 -965 118 -965 -965 40 -114 4 34 40 -965 136 -66 -18 166 -965 -66 -965 -965 185 -965 -118 85 -965 134 -965 -965 -965 -965 182 44 -95 -66 40 -965 -95 193 -118 -965 -965 234 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 1.8e-001 0.875000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.000000 0.500000 0.375000 0.000000 0.000000 0.625000 0.000000 0.375000 0.000000 0.625000 0.125000 0.000000 0.750000 0.125000 0.250000 0.125000 0.625000 0.000000 0.000000 0.875000 0.125000 0.000000 0.375000 0.125000 0.500000 0.000000 0.625000 0.000000 0.000000 0.375000 0.125000 0.250000 0.250000 0.375000 0.000000 0.625000 0.125000 0.250000 0.875000 0.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.125000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.375000 0.125000 0.125000 0.375000 0.000000 0.125000 0.750000 0.125000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AT[TCG][GT][CT][TA][TC]G[GA]C[GA][AT][TCG][CT]AC[AG]T[AT]GG -------------------------------------------------------------------------------- Time 2.55 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21983 3.23e-01 500 49666 4.60e-03 94_[+3(9.77e-07)]_385 44887 9.35e-01 500 41116 2.73e-20 130_[+2(8.33e-13)]_108_\ [+2(1.13e-09)]_105_[+1(4.34e-12)]_95 35854 7.21e-25 223_[+3(1.77e-11)]_42_\ [+2(7.36e-14)]_108_[+1(2.42e-12)]_65 45043 4.40e-08 17_[+1(2.62e-09)]_170_\ [+3(5.13e-07)]_272 34985 1.06e-05 121_[+3(3.71e-10)]_358 33637 1.41e-23 177_[+3(1.77e-11)]_41_\ [+2(7.36e-14)]_108_[+1(5.22e-11)]_112 43987 3.35e-03 187_[+3(2.40e-07)]_292 45057 7.91e-11 264_[+3(3.25e-09)]_122_\ [+1(4.48e-10)]_73 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************