******************************************************************************** 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/493/493.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 21663 1.0000 500 24521 1.0000 500 262146 1.0000 500 262148 1.0000 500 262149 1.0000 500 262151 1.0000 500 263298 1.0000 500 263301 1.0000 500 264337 1.0000 500 27836 1.0000 500 42123 1.0000 500 42447 1.0000 500 6914 1.0000 500 7256 1.0000 500 8952 1.0000 500 9152 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/493/493.seqs.fa -oc motifs/493 -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= 16 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= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.268 C 0.240 G 0.231 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.268 C 0.241 G 0.231 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 4 llr = 114 E-value = 3.6e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :aa:aa::a::aa:a:::a:: pos.-specific C :::a::::::a::a::aa::a probability G a:::::::::::::::::::: matrix T ::::::aa:a:::::a:::a: bits 2.1 * * * * ** * 1.9 ********************* 1.7 ********************* 1.5 ********************* Relative 1.3 ********************* Entropy 1.1 ********************* (41.3 bits) 0.8 ********************* 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GAACAATTATCAACATCCATC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 262151 480 3.91e-13 ACACTTCAAA GAACAATTATCAACATCCATC 262149 480 3.91e-13 ACACTTCAAA GAACAATTATCAACATCCATC 262148 480 3.91e-13 CAACTTCAAA GAACAATTATCAACATCCATC 262146 480 3.91e-13 CAACTTCAAA GAACAATTATCAACATCCATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262151 3.9e-13 479_[+1] 262149 3.9e-13 479_[+1] 262148 3.9e-13 479_[+1] 262146 3.9e-13 479_[+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=4 262151 ( 480) GAACAATTATCAACATCCATC 1 262149 ( 480) GAACAATTATCAACATCCATC 1 262148 ( 480) GAACAATTATCAACATCCATC 1 262146 ( 480) GAACAATTATCAACATCCATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 10.9061 E= 3.6e-007 -865 -865 211 -865 190 -865 -865 -865 190 -865 -865 -865 -865 205 -865 -865 190 -865 -865 -865 190 -865 -865 -865 -865 -865 -865 194 -865 -865 -865 194 190 -865 -865 -865 -865 -865 -865 194 -865 205 -865 -865 190 -865 -865 -865 190 -865 -865 -865 -865 205 -865 -865 190 -865 -865 -865 -865 -865 -865 194 -865 205 -865 -865 -865 205 -865 -865 190 -865 -865 -865 -865 -865 -865 194 -865 205 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 3.6e-007 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 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 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 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 1.000000 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 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GAACAATTATCAACATCCATC -------------------------------------------------------------------------------- Time 1.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 8 llr = 143 E-value = 9.0e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::3:::::5:3::8a3:81: pos.-specific C 1:::5:::4:13:3:31::: probability G 3::a33:81:5:a::59:96 matrix T 6a8:38a3:a18:::::3:4 bits 2.1 * * 1.9 * * * * * * 1.7 * * * * * * 1.5 * * * * * * * * Relative 1.3 * * *** * * * * * Entropy 1.1 *** *** * **** **** (25.7 bits) 0.8 *** *** * **** **** 0.6 ********** ********* 0.4 ********** ********* 0.2 ******************** 0.0 -------------------- Multilevel TTTGCTTGATGTGAAGGAGG consensus G A GG TC AC C A T T sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 262151 20 4.18e-12 AGGTGTGGTG TTTGGTTGATGTGAAGGAGG GCTGGTTGTG 262149 20 4.18e-12 AGGTGTGGTG TTTGGTTGATGTGAAGGAGG GCTGGTTGTG 262148 63 1.42e-09 CCAACGTTGT TTAGCTTGATGTGAACGTGT GCGGACGCCG 262146 63 1.42e-09 CCAACGTTGT TTAGCTTGATGTGAACGTGT GCGGACGCCG 263301 123 7.04e-09 ATCAGAGCAC GTTGCGTTCTATGAAAGAGG AAGAATCGTA 263298 123 7.04e-09 ATCAGAGCAC GTTGCGTTCTATGAAAGAGG AAGAATCGTA 27836 227 4.75e-08 TGTACGAAGC CTTGTTTGGTTCGCAGGAGT ATCTCTTATG 24521 156 6.56e-08 GGAGGGCGTC TTTGTTTGCTCCGCAGCAAG CCTGATGGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262151 4.2e-12 19_[+2]_461 262149 4.2e-12 19_[+2]_461 262148 1.4e-09 62_[+2]_418 262146 1.4e-09 62_[+2]_418 263301 7e-09 122_[+2]_358 263298 7e-09 122_[+2]_358 27836 4.8e-08 226_[+2]_254 24521 6.6e-08 155_[+2]_325 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=8 262151 ( 20) TTTGGTTGATGTGAAGGAGG 1 262149 ( 20) TTTGGTTGATGTGAAGGAGG 1 262148 ( 63) TTAGCTTGATGTGAACGTGT 1 262146 ( 63) TTAGCTTGATGTGAACGTGT 1 263301 ( 123) GTTGCGTTCTATGAAAGAGG 1 263298 ( 123) GTTGCGTTCTATGAAAGAGG 1 27836 ( 227) CTTGTTTGGTTCGCAGGAGT 1 24521 ( 156) TTTGTTTGCTCCGCAGCAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 7696 bayes= 9.90839 E= 9.0e-007 -965 -94 11 126 -965 -965 -965 194 -10 -965 -965 152 -965 -965 211 -965 -965 105 11 -6 -965 -965 11 152 -965 -965 -965 194 -965 -965 170 -6 90 64 -88 -965 -965 -965 -965 194 -10 -94 111 -106 -965 6 -965 152 -965 -965 211 -965 148 6 -965 -965 190 -965 -965 -965 -10 6 111 -965 -965 -94 192 -965 148 -965 -965 -6 -110 -965 192 -965 -965 -965 144 52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 9.0e-007 0.000000 0.125000 0.250000 0.625000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.500000 0.375000 0.125000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.125000 0.500000 0.125000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.125000 0.875000 0.000000 0.750000 0.000000 0.000000 0.250000 0.125000 0.000000 0.875000 0.000000 0.000000 0.000000 0.625000 0.375000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG]T[TA]G[CGT][TG]T[GT][AC]T[GA][TC]G[AC]A[GAC]G[AT]G[GT] -------------------------------------------------------------------------------- Time 3.79 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 8 llr = 141 E-value = 5.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::1::3::1:414:::::11: pos.-specific C :::::1::::3::::8:3::: probability G 198:45:93::6:81::634a matrix T 911a61a16a436393a165: bits 2.1 * 1.9 * * * * * 1.7 * * * * * 1.5 ** * ** * * * * Relative 1.3 ** * ** * **** * Entropy 1.1 ***** ** * ***** * (25.5 bits) 0.8 ***** ** * ******* * 0.6 ***** **** ********** 0.4 ***** *************** 0.2 ********************* 0.0 --------------------- Multilevel TGGTTGTGTTAGTGTCTGTTG consensus GA G TTAT T CGG sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 262151 42 1.44e-12 GAAGGAGGGC TGGTTGTGTTCGTGTCTGTGG CTCAGTTAGT 262149 42 1.44e-12 GAAGGAGGGC TGGTTGTGTTCGTGTCTGTGG CTCAGTTAGT 263301 370 4.28e-10 TTCTATCTTC TGGTTATGTTATAGTCTCTTG TCTGTCATGT 263298 370 4.28e-10 TTCTATGTTC TGGTTATGTTATAGTCTCTTG TCTGTCATGT 7256 78 2.72e-08 ACGGTGTACG TGGTGTTGGTAATGTTTGATG ACGAATCTGT 9152 352 4.10e-08 ATTTGCAACA GGTTGCTGTTTGTGTCTGGAG GGTGGGTGGC 24521 178 6.56e-08 GCAGCAAGCC TGATGGTGATTGATTCTTGGG CCGTTCGGGA 42123 1 9.09e-08 . TTGTTGTTGTTGTTGTTGTTG TTGTTGTTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262151 1.4e-12 41_[+3]_438 262149 1.4e-12 41_[+3]_438 263301 4.3e-10 369_[+3]_110 263298 4.3e-10 369_[+3]_110 7256 2.7e-08 77_[+3]_402 9152 4.1e-08 351_[+3]_128 24521 6.6e-08 177_[+3]_302 42123 9.1e-08 [+3]_479 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=8 262151 ( 42) TGGTTGTGTTCGTGTCTGTGG 1 262149 ( 42) TGGTTGTGTTCGTGTCTGTGG 1 263301 ( 370) TGGTTATGTTATAGTCTCTTG 1 263298 ( 370) TGGTTATGTTATAGTCTCTTG 1 7256 ( 78) TGGTGTTGGTAATGTTTGATG 1 9152 ( 352) GGTTGCTGTTTGTGTCTGGAG 1 24521 ( 178) TGATGGTGATTGATTCTTGGG 1 42123 ( 1) TTGTTGTTGTTGTTGTTGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 9.90539 E= 5.6e-005 -965 -965 -88 175 -965 -965 192 -106 -110 -965 170 -106 -965 -965 -965 194 -965 -965 70 126 -10 -94 111 -106 -965 -965 -965 194 -965 -965 192 -106 -110 -965 11 126 -965 -965 -965 194 48 6 -965 52 -110 -965 144 -6 48 -965 -965 126 -965 -965 170 -6 -965 -965 -88 175 -965 164 -965 -6 -965 -965 -965 194 -965 6 144 -106 -110 -965 11 126 -110 -965 70 94 -965 -965 211 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 5.6e-005 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.875000 0.125000 0.125000 0.000000 0.750000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.625000 0.250000 0.125000 0.500000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.125000 0.000000 0.250000 0.625000 0.000000 0.000000 0.000000 1.000000 0.375000 0.250000 0.000000 0.375000 0.125000 0.000000 0.625000 0.250000 0.375000 0.000000 0.000000 0.625000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.125000 0.875000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.625000 0.125000 0.125000 0.000000 0.250000 0.625000 0.125000 0.000000 0.375000 0.500000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TGGT[TG][GA]TG[TG]T[ATC][GT][TA][GT]T[CT]T[GC][TG][TG]G -------------------------------------------------------------------------------- Time 5.67 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21663 4.17e-01 500 24521 5.05e-08 155_[+2(6.56e-08)]_2_[+3(6.56e-08)]_\ 302 262146 8.89e-14 62_[+2(1.42e-09)]_397_\ [+1(3.91e-13)] 262148 8.89e-14 62_[+2(1.42e-09)]_397_\ [+1(3.91e-13)] 262149 5.42e-25 19_[+2(4.18e-12)]_2_[+3(1.44e-12)]_\ 417_[+1(3.91e-13)] 262151 5.42e-25 19_[+2(4.18e-12)]_2_[+3(1.44e-12)]_\ 417_[+1(3.91e-13)] 263298 2.03e-10 122_[+2(7.04e-09)]_227_\ [+3(4.28e-10)]_110 263301 2.03e-10 122_[+2(7.04e-09)]_227_\ [+3(4.28e-10)]_110 264337 9.55e-01 500 27836 6.33e-04 226_[+2(4.75e-08)]_254 42123 2.73e-04 [+3(9.09e-08)]_[+3(3.50e-06)]_458 42447 4.29e-01 500 6914 2.99e-01 500 7256 3.88e-04 77_[+3(2.72e-08)]_402 8952 6.61e-01 500 9152 2.00e-05 351_[+3(4.10e-08)]_128 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************