******************************************************************************** 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/463/463.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10378 1.0000 500 31508 1.0000 500 35855 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/463/463.seqs.fa -oc motifs/463 -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= 3 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= 1500 N= 3 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.238 C 0.247 G 0.236 T 0.279 Background letter frequencies (from dataset with add-one prior applied): A 0.238 C 0.247 G 0.236 T 0.279 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 18 sites = 3 llr = 62 E-value = 1.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 7a::a:7:::3:a:3:a: pos.-specific C ::a::a:33:3a::7::: probability G 3::a::3::::::a:a:: matrix T :::::::77a3::::::a bits 2.1 ***** *** ** 1.9 ***** * *** *** 1.7 ***** * *** *** 1.5 ***** * *** *** Relative 1.2 ******* * *** *** Entropy 1.0 ********** ******* (30.1 bits) 0.8 ********** ******* 0.6 ********** ******* 0.4 ****************** 0.2 ****************** 0.0 ------------------ Multilevel AACGACATTTACAGCGAT consensus G GCC C A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 31508 347 8.74e-11 AGCGACACGA AACGACACTTCCAGCGAT AGTACCGGAG 35855 299 2.35e-10 TGGATACCAC AACGACATTTTCAGAGAT CCCGATAGTT 10378 384 7.07e-10 AGACAGCGTT GACGACGTCTACAGCGAT GTACGGGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31508 8.7e-11 346_[+1]_136 35855 2.4e-10 298_[+1]_184 10378 7.1e-10 383_[+1]_99 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=18 seqs=3 31508 ( 347) AACGACACTTCCAGCGAT 1 35855 ( 299) AACGACATTTTCAGAGAT 1 10378 ( 384) GACGACGTCTACAGCGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 1449 bayes= 8.91289 E= 1.7e+001 148 -823 50 -823 207 -823 -823 -823 -823 201 -823 -823 -823 -823 208 -823 207 -823 -823 -823 -823 201 -823 -823 148 -823 50 -823 -823 43 -823 126 -823 43 -823 126 -823 -823 -823 184 48 43 -823 26 -823 201 -823 -823 207 -823 -823 -823 -823 -823 208 -823 48 143 -823 -823 -823 -823 208 -823 207 -823 -823 -823 -823 -823 -823 184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 3 E= 1.7e+001 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.333333 0.333333 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AG]ACGAC[AG][TC][TC]T[ACT]CAG[CA]GAT -------------------------------------------------------------------------------- Time 0.13 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 3 llr = 42 E-value = 5.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::7::::7:a pos.-specific C :::::::::::: probability G a:aa3::333a: matrix T :a:::aa77::: bits 2.1 * ** ** 1.9 **** ** ** 1.7 **** ** ** 1.5 **** ** ** Relative 1.2 ******* *** Entropy 1.0 ************ (20.3 bits) 0.8 ************ 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GTGGATTTTAGA consensus G GGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 10378 70 1.90e-07 ACATTAGTTC GTGGATTGTAGA AGCCGTCTCG 35855 36 3.31e-07 TAATCGTTCT GTGGATTTTGGA ACCAAAATTC 31508 220 6.18e-07 AAAAGTAGGG GTGGGTTTGAGA CGTTTGGAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10378 1.9e-07 69_[+2]_419 35855 3.3e-07 35_[+2]_453 31508 6.2e-07 219_[+2]_269 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=3 10378 ( 70) GTGGATTGTAGA 1 35855 ( 36) GTGGATTTTGGA 1 31508 ( 220) GTGGGTTTGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1467 bayes= 8.93074 E= 5.3e+002 -823 -823 208 -823 -823 -823 -823 184 -823 -823 208 -823 -823 -823 208 -823 148 -823 50 -823 -823 -823 -823 184 -823 -823 -823 184 -823 -823 50 126 -823 -823 50 126 148 -823 50 -823 -823 -823 208 -823 207 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 3 E= 5.3e+002 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 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.666667 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GTGG[AG]TT[TG][TG][AG]GA -------------------------------------------------------------------------------- Time 0.22 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 14 sites = 3 llr = 46 E-value = 5.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a:33a7a::a3a:3 pos.-specific C :a3::::a::3:a: probability G ::33:3::a::::7 matrix T :::3::::::3::: bits 2.1 ** * **** ** 1.9 ** * **** ** 1.7 ** * **** ** 1.5 ** * **** ** Relative 1.2 ** ****** *** Entropy 1.0 ** ****** *** (22.1 bits) 0.8 ** ****** *** 0.6 ** ****** *** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel ACAAAAACGAAACG consensus CG G C A sequence GT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 31508 480 5.47e-08 CTTTCTACAA ACATAAACGAAACG CCCCGGT 35855 378 1.08e-07 GTTTGGACCG ACCGAAACGACACA TTCACACATC 10378 322 1.31e-07 TCGTTGAGTT ACGAAGACGATACG GCTTCTACTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31508 5.5e-08 479_[+3]_7 35855 1.1e-07 377_[+3]_109 10378 1.3e-07 321_[+3]_165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=14 seqs=3 31508 ( 480) ACATAAACGAAACG 1 35855 ( 378) ACCGAAACGACACA 1 10378 ( 322) ACGAAGACGATACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 1461 bayes= 8.92481 E= 5.5e+002 207 -823 -823 -823 -823 201 -823 -823 48 43 50 -823 48 -823 50 26 207 -823 -823 -823 148 -823 50 -823 207 -823 -823 -823 -823 201 -823 -823 -823 -823 208 -823 207 -823 -823 -823 48 43 -823 26 207 -823 -823 -823 -823 201 -823 -823 48 -823 149 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 3 E= 5.5e+002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.333333 0.000000 0.333333 0.333333 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.333333 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AC[ACG][AGT]A[AG]ACGA[ACT]AC[GA] -------------------------------------------------------------------------------- Time 0.30 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10378 1.23e-12 69_[+2(1.90e-07)]_240_\ [+3(1.31e-07)]_48_[+1(7.07e-10)]_99 31508 2.28e-13 77_[+1(7.82e-05)]_124_\ [+2(6.18e-07)]_115_[+1(8.74e-11)]_115_[+3(5.47e-08)]_7 35855 6.10e-13 35_[+2(3.31e-07)]_251_\ [+1(2.35e-10)]_61_[+3(1.08e-07)]_109 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************