******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009) 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= chrew.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ upstream_region_"ORF1ab" 1.0000 338 "S" 1.0000 100 "E" 1.0000 85 "M" 1.0000 100 "N" 1.0000 107 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme chrew.fasta -dna -mod zoops -revcomp -minw 6 -nmotifs 3 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 5 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= 730 N= 5 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.303 C 0.197 G 0.197 T 0.303 Background letter frequencies (from dataset with add-one prior applied): A 0.303 C 0.197 G 0.197 T 0.303 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 39 sites = 3 llr = 127 E-value = 2.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :a7:3a73a:3:a:7:7::7:::3::::::::::a773: pos.-specific C a:3::::::a7a:a:7:::3:3::3:7:::::a3::37a probability G :::a:::::::::::3:aa::7:::7:3:aa::::3::: matrix T ::::7:37::::::3:3:::a:a77337a::a:7::::: bits 2.3 * * * * * ** ** * * 2.1 * * * * * ** ** * * 1.9 * * * * * ** ** * * 1.6 ** * * ** *** ** * * ***** * * Relative 1.4 ** * * ** *** * ** *** ***** * * Entropy 1.2 ** * * ****** * ** *** ** ***** * ** (60.9 bits) 0.9 **** * ****** * ****** *************** 0.7 *************************************** 0.5 *************************************** 0.2 *************************************** 0.0 --------------------------------------- Multilevel CAAGTAATACCCACACAGGATGTTTGCTTGGTCTAAACC consensus C A TA A TGT C C ACTTG C GCA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------------------------- "N" + 66 3.96e-24 AGTTTATAAA CAAGTAATACCCACACAGGATGTTTGCTTGGTCTAAACC AAA "M" + 59 3.96e-24 AGTTTATAAA CAAGTAATACCCACACAGGATGTTTGCTTGGTCTAAACC AAA upstream_region_"ORF1ab" + 278 3.44e-17 CCGTCGCTGT CACGAATAACACACTGTGGCTCTACTTGTGGTCCAGCAC AAGTATCCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "N" 4e-24 65_[+1]_3 "M" 4e-24 58_[+1]_3 upstream_region_"ORF1ab" 3.4e-17 277_[+1]_22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=39 seqs=3 "N" ( 66) CAAGTAATACCCACACAGGATGTTTGCTTGGTCTAAACC 1 "M" ( 59) CAAGTAATACCCACACAGGATGTTTGCTTGGTCTAAACC 1 upstream_region_"ORF1ab" ( 278) CACGAATAACACACTGTGGCTCTACTTGTGGTCCAGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 39 n= 540 bayes= 7.93342 E= 2.3e-001 -823 234 -823 -823 172 -823 -823 -823 113 76 -823 -823 -823 -823 234 -823 14 -823 -823 113 172 -823 -823 -823 113 -823 -823 14 14 -823 -823 113 172 -823 -823 -823 -823 234 -823 -823 14 176 -823 -823 -823 234 -823 -823 172 -823 -823 -823 -823 234 -823 -823 113 -823 -823 14 -823 176 76 -823 113 -823 -823 14 -823 -823 234 -823 -823 -823 234 -823 113 76 -823 -823 -823 -823 -823 172 -823 76 176 -823 -823 -823 -823 172 14 -823 -823 113 -823 76 -823 113 -823 -823 176 14 -823 176 -823 14 -823 -823 76 113 -823 -823 -823 172 -823 -823 234 -823 -823 -823 234 -823 -823 -823 -823 172 -823 234 -823 -823 -823 76 -823 113 172 -823 -823 -823 113 -823 76 -823 113 76 -823 -823 14 176 -823 -823 -823 234 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 39 nsites= 3 E= 2.3e-001 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.333333 0.000000 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.000000 0.333333 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 0.000000 0.000000 1.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.666667 0.333333 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.333333 0.666667 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[AC]G[TA]A[AT][TA]AC[CA]CAC[AT][CG][AT]GG[AC]T[GC]T[TA][TC][GT][CT][TG]TGGTC[TC]A[AG][AC][CA]C -------------------------------------------------------------------------------- Time 0.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 38 sites = 5 llr = 139 E-value = 2.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 8::a42422:668::248:6868246:64:48:622:: pos.-specific C :66:::::2::22::4::6::2262:4::8226::::: probability G 24::68:82242:aa:::2::::::2:::2::428::: matrix T ::4:::6:48:::::4622422:242646:4::2:8aa bits 2.3 ** 2.1 ** 1.9 ** 1.6 * ** * ** Relative 1.4 * * * * ** * * * ** Entropy 1.2 ****** * * *** * * ** * ** (40.1 bits) 0.9 ****** * ** *** ** * * * * ** **** 0.7 ******** ****** ***** ** **** ** **** 0.5 ******** *************** ***** ******* 0.2 ******** ***************************** 0.0 -------------------------------------- Multilevel ACCAGGTGTTAAAGGCTACAAAACAATATCAACAGTTT consensus GGT AAAAAGGCC TATGTTCCATGCTAGTCGGAA sequence C G A T T TCT C T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------------------------------- "N" + 23 5.35e-20 TTATAATAGT ACCAGGTGTTAAAGGCTACAAAACAATTTCTAGAGTTT ATAAACAAGT "M" + 16 5.35e-20 TTATAATAGT ACCAGGTGTTAAAGGCTACAAAACAATTTCTAGAGTTT ATAAACAAGT "E" + 34 2.79e-12 GCAAATTGTT AGTAAGAGATAACGGTAAGTTACTTATATCAACAGATT CATTAGTAAA "S" + 1 7.60e-12 . ACCAAGAACTGCAGGAAATTATAATGCAAGAACTGTTT CTAAAAACAG upstream_region_"ORF1ab" - 78 1.01e-11 TTGGCAAGTG GGTAGATGGGGGAGGTTTCAACACCTCAACCCCGATTT TAGTTTAGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "N" 5.4e-20 22_[+2]_47 "M" 5.4e-20 15_[+2]_47 "E" 2.8e-12 33_[+2]_14 "S" 7.6e-12 [+2]_62 upstream_region_"ORF1ab" 1e-11 77_[-2]_223 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=38 seqs=5 "N" ( 23) ACCAGGTGTTAAAGGCTACAAAACAATTTCTAGAGTTT 1 "M" ( 16) ACCAGGTGTTAAAGGCTACAAAACAATTTCTAGAGTTT 1 "E" ( 34) AGTAAGAGATAACGGTAAGTTACTTATATCAACAGATT 1 "S" ( 1) ACCAAGAACTGCAGGAAATTATAATGCAAGAACTGTTT 1 upstream_region_"ORF1ab" ( 78) GGTAGATGGGGGAGGTTTCAACACCTCAACCCCGATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 38 n= 545 bayes= 7.00856 E= 2.3e-001 140 -897 2 -897 -897 161 102 -897 -897 161 -897 40 172 -897 -897 -897 40 -897 161 -897 -60 -897 202 -897 40 -897 -897 98 -60 -897 202 -897 -60 2 2 40 -897 -897 2 140 98 -897 102 -897 98 2 2 -897 140 2 -897 -897 -897 -897 234 -897 -897 -897 234 -897 -60 102 -897 40 40 -897 -897 98 140 -897 -897 -60 -897 161 2 -60 98 -897 -897 40 140 -897 -897 -60 98 2 -897 -60 140 2 -897 -897 -60 161 -897 -60 40 2 -897 40 98 -897 2 -60 -897 102 -897 98 98 -897 -897 40 40 -897 -897 98 -897 202 2 -897 40 2 -897 40 140 2 -897 -897 -897 161 102 -897 98 -897 2 -60 -60 -897 202 -897 -60 -897 -897 140 -897 -897 -897 172 -897 -897 -897 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 38 nsites= 5 E= 2.3e-001 0.800000 0.000000 0.200000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.600000 0.000000 0.400000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.200000 0.000000 0.800000 0.000000 0.400000 0.000000 0.000000 0.600000 0.200000 0.000000 0.800000 0.000000 0.200000 0.200000 0.200000 0.400000 0.000000 0.000000 0.200000 0.800000 0.600000 0.000000 0.400000 0.000000 0.600000 0.200000 0.200000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.400000 0.000000 0.400000 0.400000 0.000000 0.000000 0.600000 0.800000 0.000000 0.000000 0.200000 0.000000 0.600000 0.200000 0.200000 0.600000 0.000000 0.000000 0.400000 0.800000 0.000000 0.000000 0.200000 0.600000 0.200000 0.000000 0.200000 0.800000 0.200000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.400000 0.200000 0.000000 0.400000 0.600000 0.000000 0.200000 0.200000 0.000000 0.400000 0.000000 0.600000 0.600000 0.000000 0.000000 0.400000 0.400000 0.000000 0.000000 0.600000 0.000000 0.800000 0.200000 0.000000 0.400000 0.200000 0.000000 0.400000 0.800000 0.200000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.600000 0.000000 0.200000 0.200000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AG][CG][CT]A[GA][GA][TA][GA][TACGA][TG][AG][ACG][AC]GG[CTA][TA][AT][CGT][AT][AT][ACT][AC][CAT][ATC][AGT][TC][AT][TA][CG][ATC][AC][CG][AGT][GA][TA]TT -------------------------------------------------------------------------------- Time 0.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 8 sites = 5 llr = 41 E-value = 1.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::4:8a:: pos.-specific C :::::::: probability G ::2:2::: matrix T aa4a::aa bits 2.3 2.1 1.9 1.6 ** * *** Relative 1.4 ** * *** Entropy 1.2 ** ***** (11.8 bits) 0.9 ** ***** 0.7 ** ***** 0.5 ** ***** 0.2 ******** 0.0 -------- Multilevel TTATAATT consensus T G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------- "N" - 11 1.42e-04 CCTGGTACTA TTATAATT TTATTGCAGC "M" - 4 1.42e-04 CCTGGTACTA TTATAATT TTA "E" - 13 1.42e-04 AATTTGCCAC TTTTAATT AAACTTAAAA "S" - 91 1.42e-04 GA TTTTAATT TAGAGTTCTT upstream_region_"ORF1ab" + 140 3.11e-04 CAAGGTTGGC TTGTGATT CACATAGGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "N" 0.00014 10_[-3]_89 "M" 0.00014 3_[-3]_89 "E" 0.00014 12_[-3]_65 "S" 0.00014 90_[-3]_2 upstream_region_"ORF1ab" 0.00031 139_[+3]_191 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=8 seqs=5 "N" ( 11) TTATAATT 1 "M" ( 4) TTATAATT 1 "E" ( 13) TTTTAATT 1 "S" ( 91) TTTTAATT 1 upstream_region_"ORF1ab" ( 140) TTGTGATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 695 bayes= 7.10852 E= 1.6e+004 -897 -897 -897 172 -897 -897 -897 172 40 -897 2 40 -897 -897 -897 172 140 -897 2 -897 172 -897 -897 -897 -897 -897 -897 172 -897 -897 -897 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 1.6e+004 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.400000 0.000000 0.200000 0.400000 0.000000 0.000000 0.000000 1.000000 0.800000 0.000000 0.200000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TT[ATG]T[AG]ATT -------------------------------------------------------------------------------- Time 0.87 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- upstream_region_"ORF1ab" 3.30e-20 77_[-2(1.01e-11)]_162_[+1(3.44e-17)]_22 "S" 3.34e-09 [+2(7.60e-12)]_62 "E" 6.28e-10 33_[+2(2.79e-12)]_14 "M" 3.76e-37 15_[+2(5.35e-20)]_5_[+1(3.96e-24)]_3 "N" 4.96e-37 22_[+2(5.35e-20)]_5_[+1(3.96e-24)]_3 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo ********************************************************************************