******************************************************************************** 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/13/13.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 48915 1.0000 500 50357 1.0000 500 41599 1.0000 500 50621 1.0000 500 45389 1.0000 500 45393 1.0000 500 43325 1.0000 500 55138 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/13/13.seqs.fa -oc motifs/13 -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= 8 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= 4000 N= 8 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.291 C 0.222 G 0.198 T 0.289 Background letter frequencies (from dataset with add-one prior applied): A 0.291 C 0.222 G 0.198 T 0.289 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 5 llr = 94 E-value = 1.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::6a248::2a:64aa4::: pos.-specific C 262:8::22::a:4:::::: probability G 822::62448::42::6::a matrix T :2:::::44::::::::aa: bits 2.3 * 2.1 * * 1.9 * ** ** *** 1.6 * * ** ** *** Relative 1.4 * ** *** ** *** Entropy 1.2 * **** *** ****** (27.2 bits) 0.9 * **** **** ****** 0.7 ******* **** ****** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GCAACGAGGGACAAAAGTTG consensus CGC AAGTTA GC A sequence TG CC G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 45389 44 8.68e-12 ATCCGCTGGT GCAACGAGTGACGAAAGTTG CAATTTGCGT 50621 91 1.57e-11 ACCCAATAGT GCAACGAGTGACAGAAGTTG TGCTTGTGAC 45393 71 1.01e-09 GCCATGCGTT GGAACGGTCGACGCAAGTTG CCTTCCCAGA 55138 78 1.06e-08 GTGTCCGTGC CTGACAATGGACAAAAATTG CAATTATCAT 48915 451 1.53e-08 CACAAATCCT GCCAAAACGAACACAAATTG ATTGTGGCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45389 8.7e-12 43_[+1]_437 50621 1.6e-11 90_[+1]_390 45393 1e-09 70_[+1]_410 55138 1.1e-08 77_[+1]_403 48915 1.5e-08 450_[+1]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=5 45389 ( 44) GCAACGAGTGACGAAAGTTG 1 50621 ( 91) GCAACGAGTGACAGAAGTTG 1 45393 ( 71) GGAACGGTCGACGCAAGTTG 1 55138 ( 78) CTGACAATGGACAAAAATTG 1 48915 ( 451) GCCAAAACGAACACAAATTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 3848 bayes= 9.83793 E= 1.5e+000 -897 -15 201 -897 -897 143 1 -53 104 -15 1 -897 178 -897 -897 -897 -54 185 -897 -897 46 -897 160 -897 146 -897 1 -897 -897 -15 101 47 -897 -15 101 47 -54 -897 201 -897 178 -897 -897 -897 -897 217 -897 -897 104 -897 101 -897 46 85 1 -897 178 -897 -897 -897 178 -897 -897 -897 46 -897 160 -897 -897 -897 -897 179 -897 -897 -897 179 -897 -897 233 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 5 E= 1.5e+000 0.000000 0.200000 0.800000 0.000000 0.000000 0.600000 0.200000 0.200000 0.600000 0.200000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.200000 0.400000 0.400000 0.000000 0.200000 0.400000 0.400000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.400000 0.400000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC][CGT][ACG]A[CA][GA][AG][GTC][GTC][GA]AC[AG][ACG]AA[GA]TTG -------------------------------------------------------------------------------- Time 0.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 96 E-value = 7.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :22:::2:2:::::::2::a: pos.-specific C 2:4::44a6:6:2284::8:a probability G :8:a2:::::24::26::2:: matrix T 8:4:864:2a2688::8a::: bits 2.3 * 2.1 * * * 1.9 * * * * ** 1.6 * * * * ** Relative 1.4 * * * * ** **** Entropy 1.2 ** ** * * ********* (27.7 bits) 0.9 ** *** * * ********** 0.7 ** *** ************** 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TGCGTTCCCTCTTTCGTTCAC consensus CAT GCT A GGCCGCA G sequence A A T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 45389 437 1.05e-12 GAATCGTTGC TGCGTTTCCTCTTTCGTTCAC CACACTAGAG 50621 436 1.15e-11 GAATGGTTGC TGCGTTTCCTGTTTCGTTCAC CACACTAGAT 48915 473 1.18e-09 ACAAATTGAT TGTGGCCCATTGTTCGTTCAC TGTCCTC 50357 380 9.47e-09 TTCTTGTTGC CAAGTTCCTTCGCTCCTTCAC GACTGCTAAA 55138 241 1.03e-08 TCCCTTCTAC TGTGTCACCTCTTCGCATGAC CCGGACAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45389 1e-12 436_[+2]_43 50621 1.2e-11 435_[+2]_44 48915 1.2e-09 472_[+2]_7 50357 9.5e-09 379_[+2]_100 55138 1e-08 240_[+2]_239 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 45389 ( 437) TGCGTTTCCTCTTTCGTTCAC 1 50621 ( 436) TGCGTTTCCTGTTTCGTTCAC 1 48915 ( 473) TGTGGCCCATTGTTCGTTCAC 1 50357 ( 380) CAAGTTCCTTCGCTCCTTCAC 1 55138 ( 241) TGTGTCACCTCTTCGCATGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3840 bayes= 9.83492 E= 7.0e+000 -897 -15 -897 147 -54 -897 201 -897 -54 85 -897 47 -897 -897 233 -897 -897 -897 1 147 -897 85 -897 105 -54 85 -897 47 -897 217 -897 -897 -54 143 -897 -53 -897 -897 -897 179 -897 143 1 -53 -897 -897 101 105 -897 -15 -897 147 -897 -15 -897 147 -897 185 1 -897 -897 85 160 -897 -54 -897 -897 147 -897 -897 -897 179 -897 185 1 -897 178 -897 -897 -897 -897 217 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 7.0e+000 0.000000 0.200000 0.000000 0.800000 0.200000 0.000000 0.800000 0.000000 0.200000 0.400000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.400000 0.000000 0.600000 0.200000 0.400000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.200000 0.200000 0.000000 0.000000 0.400000 0.600000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.400000 0.600000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC][GA][CTA]G[TG][TC][CTA]C[CAT]T[CGT][TG][TC][TC][CG][GC][TA]T[CG]AC -------------------------------------------------------------------------------- Time 1.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 3 llr = 72 E-value = 1.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::7:::::7:::::37::::3 pos.-specific C a::a::33:::7::7::a::: probability G :a:::a373::3aa::::3a7 matrix T ::3:a:3::aa::::3a:7:: bits 2.3 * * ** * 2.1 ** * * ** * * 1.9 ** *** ** ** ** * 1.6 ** *** ** ** ** * Relative 1.4 ** *** * ***** ** * Entropy 1.2 ** *** * ****** ***** (34.7 bits) 0.9 ****** ************** 0.7 ****** ************** 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CGACTGCGATTCGGCATCTGG consensus T GCG G AT G A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 50621 350 1.34e-13 AACAAAATGA CGACTGCGATTCGGCATCTGG TTACATCCAT 45389 351 3.13e-13 ACCAAAATGA CGACTGTGATTCGGCATCTGG TTCTATCCAT 50357 344 5.80e-11 TGTAAAAGCT CGTCTGGCGTTGGGATTCGGA ATTCATTCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50621 1.3e-13 349_[+3]_130 45389 3.1e-13 350_[+3]_129 50357 5.8e-11 343_[+3]_136 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=3 50621 ( 350) CGACTGCGATTCGGCATCTGG 1 45389 ( 351) CGACTGTGATTCGGCATCTGG 1 50357 ( 344) CGTCTGGCGTTGGGATTCGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3840 bayes= 10.7686 E= 1.4e+001 -823 217 -823 -823 -823 -823 233 -823 119 -823 -823 21 -823 217 -823 -823 -823 -823 -823 179 -823 -823 233 -823 -823 58 75 21 -823 58 175 -823 119 -823 75 -823 -823 -823 -823 179 -823 -823 -823 179 -823 158 75 -823 -823 -823 233 -823 -823 -823 233 -823 20 158 -823 -823 119 -823 -823 21 -823 -823 -823 179 -823 217 -823 -823 -823 -823 75 120 -823 -823 233 -823 20 -823 175 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 3 E= 1.4e+001 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.333333 0.666667 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 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CG[AT]CTG[CGT][GC][AG]TT[CG]GG[CA][AT]TC[TG]G[GA] -------------------------------------------------------------------------------- Time 2.24 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48915 8.51e-10 450_[+1(1.53e-08)]_2_[+2(1.18e-09)]_\ 7 50357 5.82e-11 343_[+3(5.80e-11)]_15_\ [+2(9.47e-09)]_100 41599 4.37e-01 500 50621 5.22e-24 90_[+1(1.57e-11)]_239_\ [+3(1.34e-13)]_65_[+2(1.15e-11)]_44 45389 6.52e-25 43_[+1(8.68e-12)]_287_\ [+3(3.13e-13)]_65_[+2(1.05e-12)]_43 45393 4.40e-05 70_[+1(1.01e-09)]_410 43325 5.16e-01 500 55138 4.50e-09 77_[+1(1.06e-08)]_143_\ [+2(1.03e-08)]_239 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************