******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ 8663 1.0000 500 13158 1.0000 500 36468 1.0000 500 13418 1.0000 500 47390 1.0000 500 14937 1.0000 500 38899 1.0000 500 15960 1.0000 500 45202 1.0000 500 45226 1.0000 500 12113 1.0000 500 45807 1.0000 500 48273 1.0000 500 47252 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= 14 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= 7000 N= 14 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.273 C 0.251 G 0.215 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.251 G 0.215 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 7 llr = 94 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a1::a:6:1:a9 pos.-specific C :91::9:::::: probability G ::3a:1:a:a:: matrix T ::6:::4:9::1 bits 2.2 * * * 2.0 * * * 1.8 * ** * ** 1.6 * ** * ** Relative 1.3 ** *** ***** Entropy 1.1 ** *** ***** (19.3 bits) 0.9 ** ********* 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel ACTGACAGTGAA consensus G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 12113 1 6.47e-08 . ACTGACAGTGAA ACATCATCTT 47252 90 1.80e-07 TTGTCGTTCC ACGGACAGTGAA AATGACCAGT 38899 264 4.08e-07 TTCACGCCTA ACCGACTGTGAA GGAAAAAAGA 45226 343 6.61e-07 TCGTAATGGC ACTGACAGAGAA CTAGTTTTGG 47390 205 6.61e-07 AAACGTCACT ACTGAGTGTGAA CGACAGACAA 8663 167 6.61e-07 TGACATTGGA AATGACAGTGAA TCGCCTTTTT 13418 134 1.15e-06 ACCGGATCTA ACGGACTGTGAT TGTGACGGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12113 6.5e-08 [+1]_488 47252 1.8e-07 89_[+1]_399 38899 4.1e-07 263_[+1]_225 45226 6.6e-07 342_[+1]_146 47390 6.6e-07 204_[+1]_284 8663 6.6e-07 166_[+1]_322 13418 1.2e-06 133_[+1]_355 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=7 12113 ( 1) ACTGACAGTGAA 1 47252 ( 90) ACGGACAGTGAA 1 38899 ( 264) ACCGACTGTGAA 1 45226 ( 343) ACTGACAGAGAA 1 47390 ( 205) ACTGAGTGTGAA 1 8663 ( 167) AATGACAGTGAA 1 13418 ( 134) ACGGACTGTGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6846 bayes= 10.5384 E= 1.4e-001 187 -945 -945 -945 -93 177 -945 -945 -945 -81 41 113 -945 -945 222 -945 187 -945 -945 -945 -945 177 -59 -945 106 -945 -945 72 -945 -945 222 -945 -93 -945 -945 171 -945 -945 222 -945 187 -945 -945 -945 165 -945 -945 -87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 1.4e-001 1.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.142857 0.285714 0.571429 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.571429 0.000000 0.000000 0.428571 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.000000 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- AC[TG]GAC[AT]GTGAA -------------------------------------------------------------------------------- Time 1.80 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 7 llr = 97 E-value = 3.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::73::::::4:: pos.-specific C ::919:3::::3:1:: probability G 9719:3:a3371a376 matrix T 13::1:4:7736:134 bits 2.2 * * 2.0 * * 1.8 * * 1.6 * * * * Relative 1.3 ***** * * * * Entropy 1.1 ****** **** * ** (20.0 bits) 0.9 ****** **** * ** 0.7 ****** ****** ** 0.4 ************* ** 0.2 **************** 0.0 ---------------- Multilevel GGCGCATGTTGTGAGG consensus T GA GGTC GTT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 45807 99 1.69e-09 AAGTTGCAAT GGCGCATGGTGTGGGG TGCCAACACA 14937 312 3.25e-08 CATAGGAGGA GGCGCGAGTGGTGAGT GCCTGTGACA 13418 320 5.25e-08 CAATCGCTTT GGCGCAAGTTTCGAGT GCTGCCTACT 36468 176 2.34e-07 ATACTTGTGG GTCGTACGTGGTGAGG TTTCTAGATC 13158 154 7.72e-07 GTACCTGGTT GTCGCGTGTTGGGTTG GCATTAGGCC 47252 148 9.23e-07 TGTTGCAAAG GGGGCACGGTTCGCGG AAGGATCGGG 45202 93 1.10e-06 GACTGCATCC TGCCCATGTTGTGGTT CGAAGAACAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45807 1.7e-09 98_[+2]_386 14937 3.3e-08 311_[+2]_173 13418 5.3e-08 319_[+2]_165 36468 2.3e-07 175_[+2]_309 13158 7.7e-07 153_[+2]_331 47252 9.2e-07 147_[+2]_337 45202 1.1e-06 92_[+2]_392 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=7 45807 ( 99) GGCGCATGGTGTGGGG 1 14937 ( 312) GGCGCGAGTGGTGAGT 1 13418 ( 320) GGCGCAAGTTTCGAGT 1 36468 ( 176) GTCGTACGTGGTGAGG 1 13158 ( 154) GTCGCGTGTTGGGTTG 1 47252 ( 148) GGGGCACGGTTCGCGG 1 45202 ( 93) TGCCCATGTTGTGGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6790 bayes= 11.1436 E= 3.0e+002 -945 -945 200 -87 -945 -945 173 13 -945 177 -59 -945 -945 -81 200 -945 -945 177 -945 -87 139 -945 41 -945 6 19 -945 72 -945 -945 222 -945 -945 -945 41 145 -945 -945 41 145 -945 -945 173 13 -945 19 -59 113 -945 -945 222 -945 65 -81 41 -87 -945 -945 173 13 -945 -945 141 72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 7 E= 3.0e+002 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.714286 0.285714 0.000000 0.857143 0.142857 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.857143 0.000000 0.142857 0.714286 0.000000 0.285714 0.000000 0.285714 0.285714 0.000000 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.714286 0.285714 0.000000 0.285714 0.142857 0.571429 0.000000 0.000000 1.000000 0.000000 0.428571 0.142857 0.285714 0.142857 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.571429 0.428571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[GT]CGC[AG][TAC]G[TG][TG][GT][TC]G[AG][GT][GT] -------------------------------------------------------------------------------- Time 3.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 94 E-value = 3.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2:::::::4:::2:2:::2 pos.-specific C :a84:::624222a4::::8: probability G :::2:4428:28:::::2a:: matrix T a::4a662:62:8:4a88:28 bits 2.2 * 2.0 ** * * * * 1.8 ** * * * * 1.6 ** * * * * * * Relative 1.3 *** * * *** * *** Entropy 1.1 *** *** * *** ****** (27.1 bits) 0.9 *** *** ** *** ****** 0.7 *** ****** *** ****** 0.4 ********** ********** 0.2 ********** ********** 0.0 --------------------- Multilevel TCCCTTTCGTAGTCCTTTGCT consensus AT GGGCCCCC T AG TA sequence G T G A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8663 222 2.52e-10 GCTCTCTTCA TCACTTGCGTCGTCTTTTGCT ACGCCTCCTA 15960 229 9.42e-10 GTTGAGTGTG TCCTTTTCGCAGTCCTATGCA GTTGTGTCAG 45202 454 1.50e-09 TATATTTCCA TCCCTTGGCCTGTCCTTTGCT ATCTCAAAAA 45226 34 1.78e-09 AGGAATTGCT TCCGTGTTGTGCTCTTTTGCT GGCAATCCGT 47252 438 5.10e-09 GACATGGACC TCCTTGTCGTAGCCATTGGTT AGACAAACGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8663 2.5e-10 221_[+3]_258 15960 9.4e-10 228_[+3]_251 45202 1.5e-09 453_[+3]_26 45226 1.8e-09 33_[+3]_446 47252 5.1e-09 437_[+3]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 8663 ( 222) TCACTTGCGTCGTCTTTTGCT 1 15960 ( 229) TCCTTTTCGCAGTCCTATGCA 1 45202 ( 454) TCCCTTGGCCTGTCCTTTGCT 1 45226 ( 34) TCCGTGTTGTGCTCTTTTGCT 1 47252 ( 438) TCCTTGTCGTAGCCATTGGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6720 bayes= 9.82513 E= 3.3e+002 -897 -897 -897 194 -897 199 -897 -897 -45 167 -897 -897 -897 67 -10 62 -897 -897 -897 194 -897 -897 90 120 -897 -897 90 120 -897 125 -10 -38 -897 -33 190 -897 -897 67 -897 120 55 -33 -10 -38 -897 -33 190 -897 -897 -33 -897 161 -897 199 -897 -897 -45 67 -897 62 -897 -897 -897 194 -45 -897 -897 161 -897 -897 -10 161 -897 -897 222 -897 -897 167 -897 -38 -45 -897 -897 161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 3.3e+002 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.400000 0.200000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.400000 0.600000 0.000000 0.600000 0.200000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 0.400000 0.000000 0.600000 0.400000 0.200000 0.200000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.200000 0.400000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.200000 0.000000 0.000000 0.800000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TC[CA][CTG]T[TG][TG][CGT][GC][TC][ACGT][GC][TC]C[CTA]T[TA][TG]G[CT][TA] -------------------------------------------------------------------------------- Time 5.62 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8663 1.17e-08 28_[+3(2.90e-05)]_117_\ [+1(6.61e-07)]_43_[+3(2.52e-10)]_144_[+3(2.90e-05)]_93 13158 1.25e-03 153_[+2(7.72e-07)]_331 36468 4.04e-03 175_[+2(2.34e-07)]_309 13418 2.19e-06 133_[+1(1.15e-06)]_174_\ [+2(5.25e-08)]_165 47390 8.91e-03 204_[+1(6.61e-07)]_284 14937 6.08e-04 311_[+2(3.25e-08)]_173 38899 1.38e-03 263_[+1(4.08e-07)]_225 15960 1.26e-05 228_[+3(9.42e-10)]_251 45202 3.57e-08 92_[+2(1.10e-06)]_345_\ [+3(1.50e-09)]_26 45226 6.28e-08 33_[+3(1.78e-09)]_288_\ [+1(6.61e-07)]_146 12113 2.54e-04 [+1(6.47e-08)]_488 45807 1.42e-05 98_[+2(1.69e-09)]_386 48273 5.33e-01 500 47252 4.62e-11 89_[+1(1.80e-07)]_46_[+2(9.23e-07)]_\ 274_[+3(5.10e-09)]_42 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************