******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** 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 ******************************************************************************** PRIMARY SEQUENCES= upstream_all.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ "orf1ab" 1.0000 278 "S" 1.0000 100 "orf3" 1.0000 100 "orf4a" 1.0000 100 "orf4b" 1.0000 100 "orf5" 1.0000 100 "E" 1.0000 100 "M" 1.0000 100 "N" 1.0000 100 "orf8b" 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme upstream_all.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 10 -minw 6 -maxw 6 -objfun classic -minsites 3 -markov_order 0 model: mod= zoops nmotifs= 10 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 6 maxw= 6 nsites: minsites= 3 maxsites= 10 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 1178 N= 10 sample: seed= 0 hsfrac= 0 searchsize= 1178 norand= no csites= 1000 Letter frequencies in dataset: A 0.261 C 0.222 G 0.199 T 0.318 Background letter frequencies (from file dataset with add-one prior applied): A 0.261 C 0.222 G 0.199 T 0.318 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AACGAA MEME-1 width = 6 sites = 10 llr = 76 E-value = 4.4e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif AACGAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A a8::aa pos.-specific C :1a1:: probability G :1:9:: matrix T :::::: bits 2.3 2.1 * 1.9 * **** 1.6 * **** Relative 1.4 * **** Entropy 1.2 ****** (10.9 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel AACGAA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ "N" 79 2.05e-04 aattgatttt aacgaa tctcaatttc "M" 85 2.05e-04 gagtgggttt aacgaa ctccttcata "E" 93 2.05e-04 acatatggaa aacgaa ct "orf5" 93 2.05e-04 ccaggatttt aacgaa ct "orf4a" 91 2.05e-04 tcagttaatt aacgaa ctct "orf3" 89 2.05e-04 ttcactaatt aacgaa ctatta "S" 49 2.05e-04 gagtcaaatt aacgaa ctcgtaatat "orf1ab" 62 2.05e-04 ctttgatttt aacgaa cttaaataaa "orf4b" 74 3.61e-04 gacgcagctc agcgaa tcgcttggtt "orf8b" 46 1.13e-03 cactgggctt acccaa cacgggaaag -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "N" 0.00021 78_[+1]_16 "M" 0.00021 84_[+1]_10 "E" 0.00021 92_[+1]_2 "orf5" 0.00021 92_[+1]_2 "orf4a" 0.00021 90_[+1]_4 "orf3" 0.00021 88_[+1]_6 "S" 0.00021 48_[+1]_46 "orf1ab" 0.00021 61_[+1]_211 "orf4b" 0.00036 73_[+1]_21 "orf8b" 0.0011 45_[+1]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AACGAA width=6 seqs=10 "N" ( 79) AACGAA 1 "M" ( 85) AACGAA 1 "E" ( 93) AACGAA 1 "orf5" ( 93) AACGAA 1 "orf4a" ( 91) AACGAA 1 "orf3" ( 89) AACGAA 1 "S" ( 49) AACGAA 1 "orf1ab" ( 62) AACGAA 1 "orf4b" ( 74) AGCGAA 1 "orf8b" ( 46) ACCCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 1128 bayes= 6.80478 E= 4.4e-005 194 -997 -997 -997 162 -115 -99 -997 -997 217 -997 -997 -997 -115 218 -997 194 -997 -997 -997 194 -997 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 10 E= 4.4e-005 1.000000 0.000000 0.000000 0.000000 0.800000 0.100000 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.900000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACGAA MEME-1 regular expression -------------------------------------------------------------------------------- AACGAA -------------------------------------------------------------------------------- Time 0.23 secs. ******************************************************************************** ******************************************************************************** MOTIF CAGGGT MEME-2 width = 6 sites = 5 llr = 39 E-value = 6.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGGGT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :8::2: pos.-specific C a::::: probability G ::aa8: matrix T :2:::a bits 2.3 ** 2.1 * ** 1.9 * ** 1.6 * **** Relative 1.4 * **** Entropy 1.2 ****** (11.2 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel CAGGGT consensus T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGGT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ "orf8b" 85 1.45e-04 tccacctggg cagggt gtacctctta "orf5" 38 1.45e-04 gtcttccaat cagggt aataaacaaa "S" 76 1.45e-04 tctcctgtcg cagggt aagttactta "M" 45 5.13e-04 tgtaaaattc caggat agtaaacccc "orf1ab" 169 5.13e-04 atgctcaaca ctgggt ataattctaa -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGGT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "orf8b" 0.00015 84_[+2]_10 "orf5" 0.00015 37_[+2]_57 "S" 0.00015 75_[+2]_19 "M" 0.00051 44_[+2]_50 "orf1ab" 0.00051 168_[+2]_104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGGT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAGGGT width=6 seqs=5 "orf8b" ( 85) CAGGGT 1 "orf5" ( 38) CAGGGT 1 "S" ( 76) CAGGGT 1 "M" ( 45) CAGGAT 1 "orf1ab" ( 169) CTGGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGGT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 1128 bayes= 7.59606 E= 6.4e+002 -897 217 -897 -897 162 -897 -897 -67 -897 -897 233 -897 -897 -897 233 -897 -38 -897 201 -897 -897 -897 -897 165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGGT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 5 E= 6.4e+002 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGGT MEME-2 regular expression -------------------------------------------------------------------------------- C[AT]GG[GA]T -------------------------------------------------------------------------------- Time 0.45 secs. ******************************************************************************** ******************************************************************************** MOTIF CGAGCT MEME-3 width = 6 sites = 4 llr = 33 E-value = 1.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGAGCT MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::a::: pos.-specific C a:::a3 probability G :a:a:: matrix T :::::8 bits 2.3 * * 2.1 ** ** 1.9 ***** 1.6 ***** Relative 1.4 ***** Entropy 1.2 ***** (11.9 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel CGAGCT consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ "orf8b" 4 1.62e-04 cca cgagct gcaccaaata "N" 39 1.62e-04 tgcattgctt cgagct taggctcttt "E" 6 1.62e-04 cgccc cgagct cgcttatcgt "orf3" 59 2.75e-04 aatacgacct cgagcc gcataaggtt -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "orf8b" 0.00016 3_[+3]_91 "N" 0.00016 38_[+3]_56 "E" 0.00016 5_[+3]_89 "orf3" 0.00028 58_[+3]_36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGAGCT width=6 seqs=4 "orf8b" ( 4) CGAGCT 1 "N" ( 39) CGAGCT 1 "E" ( 6) CGAGCT 1 "orf3" ( 59) CGAGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 1128 bayes= 8.45738 E= 1.0e+003 -865 217 -865 -865 -865 -865 233 -865 194 -865 -865 -865 -865 -865 233 -865 -865 217 -865 -865 -865 17 -865 123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 4 E= 1.0e+003 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGAGCT MEME-3 regular expression -------------------------------------------------------------------------------- CGAGC[TC] -------------------------------------------------------------------------------- Time 0.66 secs. ******************************************************************************** ******************************************************************************** MOTIF TGGMCR MEME-4 width = 6 sites = 5 llr = 37 E-value = 5.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGGMCR MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::6:6 pos.-specific C :::4a: probability G :aa::4 matrix T a::::: bits 2.3 ** 2.1 ** * 1.9 ** * 1.6 *** * Relative 1.4 *** * Entropy 1.2 ****** (10.7 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel TGGACA consensus C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGMCR MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ "E" 80 1.90e-04 agtctctctt tggaca tatggaaaac "orf1ab" 152 1.90e-04 atctaggcag tggaca tatgctcaac "M" 20 3.36e-04 tgtataatac tggacg ttcagtctat "orf4b" 53 4.98e-04 acaaaagctt tggcca aacaggacgc "orf5" 3 6.21e-04 tt tggccg tagatgttgt -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGMCR MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "E" 0.00019 79_[+4]_15 "orf1ab" 0.00019 151_[+4]_121 "M" 0.00034 19_[+4]_75 "orf4b" 0.0005 52_[+4]_42 "orf5" 0.00062 2_[+4]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGMCR MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGGMCR width=6 seqs=5 "E" ( 80) TGGACA 1 "orf1ab" ( 152) TGGACA 1 "M" ( 20) TGGACG 1 "orf4b" ( 53) TGGCCA 1 "orf5" ( 3) TGGCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGMCR MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 1128 bayes= 8.36966 E= 5.7e+003 -897 -897 -897 165 -897 -897 233 -897 -897 -897 233 -897 120 85 -897 -897 -897 217 -897 -897 120 -897 101 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGMCR MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 5 E= 5.7e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGGMCR MEME-4 regular expression -------------------------------------------------------------------------------- TGG[AC]C[AG] -------------------------------------------------------------------------------- Time 0.87 secs. ******************************************************************************** ******************************************************************************** MOTIF TSTCTC MEME-5 width = 6 sites = 5 llr = 37 E-value = 7.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TSTCTC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::: pos.-specific C :4:a:a probability G :6:::: matrix T a:a:a: bits 2.3 2.1 * * 1.9 * * 1.6 * **** Relative 1.4 ****** Entropy 1.2 ****** (10.6 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel TGTCTC consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTCTC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ "orf8b" 24 3.15e-04 caaataacac tgtctc ttggtacact "orf5" 16 3.15e-04 ccgtagatgt tgtctc catacggtct "orf1ab" 214 3.15e-04 tagagcgtcg tgtctc ttgtacgtct "E" 72 6.67e-04 aatccattag tctctc tttggacata "S" 64 6.67e-04 actcgtaata tctctc ctgtcgcagg -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTCTC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "orf8b" 0.00032 23_[+5]_71 "orf5" 0.00032 15_[+5]_79 "orf1ab" 0.00032 213_[+5]_59 "E" 0.00067 71_[+5]_23 "S" 0.00067 63_[+5]_31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTCTC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TSTCTC width=6 seqs=5 "orf8b" ( 24) TGTCTC 1 "orf5" ( 16) TGTCTC 1 "orf1ab" ( 214) TGTCTC 1 "E" ( 72) TCTCTC 1 "S" ( 64) TCTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTCTC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 1128 bayes= 8.36966 E= 7.2e+003 -897 -897 -897 165 -897 85 159 -897 -897 -897 -897 165 -897 217 -897 -897 -897 -897 -897 165 -897 217 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTCTC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 5 E= 7.2e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTCTC MEME-5 regular expression -------------------------------------------------------------------------------- T[GC]TCTC -------------------------------------------------------------------------------- Time 1.07 secs. ******************************************************************************** ******************************************************************************** MOTIF CTGWCG MEME-6 width = 6 sites = 3 llr = 24 E-value = 1.1e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTGWCG MEME-6 Description -------------------------------------------------------------------------------- Simplified A :::3:: pos.-specific C a:::a: probability G ::a::a matrix T :a:7:: bits 2.3 * * 2.1 * * ** 1.9 * * ** 1.6 *** ** Relative 1.4 *** ** Entropy 1.2 *** ** (11.5 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel CTGTCG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGWCG MEME-6 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ "orf4a" 1 1.97e-04 . ctgtcg atcttgagtc "S" 70 1.97e-04 aatatctctc ctgtcg cagggtaagt "M" 70 3.59e-04 cctctaccac ctgacg agtgggttta -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGWCG MEME-6 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "orf4a" 0.0002 [+6]_94 "S" 0.0002 69_[+6]_25 "M" 0.00036 69_[+6]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGWCG MEME-6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTGWCG width=6 seqs=3 "orf4a" ( 1) CTGTCG 1 "S" ( 70) CTGTCG 1 "M" ( 70) CTGACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGWCG MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 1128 bayes= 8.55075 E= 1.1e+004 -823 216 -823 -823 -823 -823 -823 165 -823 -823 233 -823 35 -823 -823 106 -823 216 -823 -823 -823 -823 233 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGWCG MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 3 E= 1.1e+004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTGWCG MEME-6 regular expression -------------------------------------------------------------------------------- CTG[TA]CG -------------------------------------------------------------------------------- Time 1.28 secs. ******************************************************************************** ******************************************************************************** MOTIF AVGCAG MEME-7 width = 6 sites = 4 llr = 29 E-value = 2.5e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif AVGCAG MEME-7 Description -------------------------------------------------------------------------------- Simplified A a5::a: pos.-specific C :3:8:: probability G :3a3:a matrix T :::::: bits 2.3 * * 2.1 * * 1.9 * * ** 1.6 * * ** Relative 1.4 * **** Entropy 1.2 * **** (10.5 bits) 0.9 * **** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel AAGCAG consensus C G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVGCAG MEME-7 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ "E" 24 1.56e-04 cttatcgttt aagcag ctctgcgcta "orf1ab" 146 2.75e-04 ctgctcatct aggcag tggacatatg "orf4b" 65 4.08e-04 gccaaacagg acgcag ctcagcgaat "S" 34 5.49e-04 tcttcaatta aaggag agtcaaatta -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVGCAG MEME-7 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "E" 0.00016 23_[+7]_71 "orf1ab" 0.00028 145_[+7]_127 "orf4b" 0.00041 64_[+7]_30 "S" 0.00055 33_[+7]_61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVGCAG MEME-7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AVGCAG width=6 seqs=4 "E" ( 24) AAGCAG 1 "orf1ab" ( 146) AGGCAG 1 "orf4b" ( 65) ACGCAG 1 "S" ( 34) AAGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVGCAG MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 1128 bayes= 8.45738 E= 2.5e+004 194 -865 -865 -865 94 17 33 -865 -865 -865 233 -865 -865 175 33 -865 194 -865 -865 -865 -865 -865 233 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVGCAG MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 4 E= 2.5e+004 1.000000 0.000000 0.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVGCAG MEME-7 regular expression -------------------------------------------------------------------------------- A[ACG]G[CG]AG -------------------------------------------------------------------------------- Time 1.48 secs. ******************************************************************************** ******************************************************************************** MOTIF SGWACA MEME-8 width = 6 sites = 3 llr = 22 E-value = 6.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif SGWACA MEME-8 Description -------------------------------------------------------------------------------- Simplified A ::7a:a pos.-specific C 3:::a: probability G 7a:::: matrix T ::3::: bits 2.3 * 2.1 * * 1.9 * *** 1.6 * *** Relative 1.4 ** *** Entropy 1.2 ** *** (10.7 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel GGAACA consensus C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGWACA MEME-8 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ "S" 13 1.56e-04 aaaattaaaa ggaaca ccagttcttc "orf4a" 41 3.31e-04 atggtcctac cgaaca tgttactagt "orf8b" 32 5.21e-04 actgtctctt ggtaca ctgggcttac -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGWACA MEME-8 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "S" 0.00016 12_[+8]_82 "orf4a" 0.00033 40_[+8]_54 "orf8b" 0.00052 31_[+8]_63 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGWACA MEME-8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SGWACA width=6 seqs=3 "S" ( 13) GGAACA 1 "orf4a" ( 41) CGAACA 1 "orf8b" ( 32) GGTACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGWACA MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 1128 bayes= 8.55075 E= 6.4e+004 -823 58 174 -823 -823 -823 233 -823 135 -823 -823 7 194 -823 -823 -823 -823 216 -823 -823 194 -823 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGWACA MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 3 E= 6.4e+004 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SGWACA MEME-8 regular expression -------------------------------------------------------------------------------- [GC]G[AT]ACA -------------------------------------------------------------------------------- Time 1.69 secs. ******************************************************************************** ******************************************************************************** MOTIF RTGGGW MEME-9 width = 6 sites = 3 llr = 22 E-value = 4.6e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif RTGGGW MEME-9 Description -------------------------------------------------------------------------------- Simplified A 7::::3 pos.-specific C :::::: probability G 3:aaa: matrix T :a:::7 bits 2.3 *** 2.1 *** 1.9 *** 1.6 **** Relative 1.4 **** Entropy 1.2 ***** (10.6 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel ATGGGT consensus G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGGGW MEME-9 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ "E" 42 2.08e-04 ctgcgctact atgggt cccgtgtaga "M" 77 3.67e-04 cacctgacga gtgggt ttaacgaact "orf3" 6 5.37e-04 actgt atggga aaacttaagt -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGGGW MEME-9 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "E" 0.00021 41_[+9]_53 "M" 0.00037 76_[+9]_18 "orf3" 0.00054 5_[+9]_89 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGGGW MEME-9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RTGGGW width=6 seqs=3 "E" ( 42) ATGGGT 1 "M" ( 77) GTGGGT 1 "orf3" ( 6) ATGGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGGGW MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 1128 bayes= 7.69967 E= 4.6e+004 135 -823 75 -823 -823 -823 -823 165 -823 -823 233 -823 -823 -823 233 -823 -823 -823 233 -823 35 -823 -823 106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGGGW MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 3 E= 4.6e+004 0.666667 0.000000 0.333333 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 1.000000 0.000000 0.333333 0.000000 0.000000 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGGGW MEME-9 regular expression -------------------------------------------------------------------------------- [AG]TGGG[TA] -------------------------------------------------------------------------------- Time 1.89 secs. ******************************************************************************** ******************************************************************************** MOTIF TGVTGG MEME-10 width = 6 sites = 4 llr = 28 E-value = 7.9e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGVTGG MEME-10 Description -------------------------------------------------------------------------------- Simplified A ::5:3: pos.-specific C ::3::: probability G :a3:8a matrix T a::a:: bits 2.3 * * 2.1 * * 1.9 * * 1.6 ** * * Relative 1.4 ** *** Entropy 1.2 ** *** (10.0 bits) 0.9 ** *** 0.7 ****** 0.5 ****** 0.2 ****** 0.0 ------ Multilevel TGATGG consensus C A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGVTGG MEME-10 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ "orf4a" 29 2.08e-04 cttcaactca tgatgg tcctaccgaa "orf1ab" 111 3.67e-04 tgcacttgtc tggtgg gattgtggca "orf4b" 12 5.43e-04 agctatcctt tgctgg ttatactgaa "orf3" 35 8.16e-04 atcgttgttg tgatag atacgaggaa -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGVTGG MEME-10 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "orf4a" 0.00021 28_[+10]_66 "orf1ab" 0.00037 110_[+10]_162 "orf4b" 0.00054 11_[+10]_83 "orf3" 0.00082 34_[+10]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGVTGG MEME-10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGVTGG width=6 seqs=4 "orf4a" ( 29) TGATGG 1 "orf1ab" ( 111) TGGTGG 1 "orf4b" ( 12) TGCTGG 1 "orf3" ( 35) TGATAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGVTGG MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 1128 bayes= 8.45738 E= 7.9e+004 -865 -865 -865 165 -865 -865 233 -865 94 17 33 -865 -865 -865 -865 165 -6 -865 191 -865 -865 -865 233 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGVTGG MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 4 E= 7.9e+004 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGVTGG MEME-10 regular expression -------------------------------------------------------------------------------- TG[ACG]T[GA]G -------------------------------------------------------------------------------- Time 2.09 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- "orf1ab" 5.42e-03 278 "S" 4.53e-04 100 "orf3" 5.39e-02 100 "orf4a" 7.59e-03 100 "orf4b" 6.57e-02 100 "orf5" 1.04e-02 100 "E" 1.57e-04 100 "M" 5.17e-03 100 "N" 5.44e-01 100 "orf8b" 9.94e-04 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************