******************************************************************************** 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.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ORF1ab 1.0000 101 1 1.0000 101 2 1.0000 101 3 1.0000 101 4 1.0000 101 5 1.0000 101 6 1.0000 101 7 1.0000 101 8 1.0000 101 9 1.0000 101 10 1.0000 101 ******************************************************************************** ******************************************************************************** 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.fasta -dna -oc . -nostatus -time 14400 -mod zoops -nmotifs 3 -minw 6 -maxw 50 -objfun classic -markov_order 0 model: mod= zoops nmotifs= 3 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= 50 nsites: minsites= 2 maxsites= 11 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= 1111 N= 11 sample: seed= 0 hsfrac= 0 searchsize= 1111 norand= no csites= 1000 Letter frequencies in dataset: A 0.307 C 0.192 G 0.184 T 0.318 Background letter frequencies (from file dataset with add-one prior applied): A 0.307 C 0.192 G 0.184 T 0.318 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GTGWTRHWTYWSWTYACRYCTAAACGAAC MEME-1 width = 29 sites = 7 llr = 141 E-value = 7.6e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGWTRHWTYWSWTYACRYCTAAACGAAC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3334:34311413:17:611:aaa1:9a1 pos.-specific C :::1313113:41:6:7:671:::9:1:7 probability G 7:7::6::1:131:::34:::::::9::: matrix T :7:47:3666414a33::319::::1::1 bits 2.4 2.2 2.0 1.7 * ***** * Relative 1.5 * * * * ***** * Entropy 1.2 * * * * ******** (29.0 bits) 1.0 * * * * ** ********** 0.7 *** ** **************** 0.5 *** ** * * **************** 0.2 ************ **************** 0.0 ----------------------------- Multilevel GTGATGATTTACTTCACACCTAAACGAAC consensus AAATCACA CTGA TTGGT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGWTRHWTYWSWTYACRYCTAAACGAAC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- 9 65 3.63e-12 CATGACGTTC GTGTTGTTTTAGATTTCATCTAAACGAAC AAACTAAA 1 72 1.37e-11 GTTATTTCTA GTGATGTTCTTGTTAACAACTAAACGAAC A 2 71 9.09e-11 GTGCTCAAAG GAGTCAAATTACATTACACATAAACGAAC TT 8 73 1.33e-10 CTGCAAGATC ATAATGAAACTTGTCACGCCTAAACGAAC 4 29 1.46e-10 AATTCTTCTA GAGTTCCTGATCTTCTGGTCTAAACGAAC TAAATATTAT 10 55 3.36e-09 TCCATGAGCA GTGCTGACTCAACTCAGGCCTAAACTCAT GCAGACCACA 7 67 1.49e-08 AATAGTGTTT ATAACACTTTGCTTCACACTCAAAAGAAA GACAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGWTRHWTYWSWTYACRYCTAAACGAAC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9 3.6e-12 64_[+1]_8 1 1.4e-11 71_[+1]_1 2 9.1e-11 70_[+1]_2 8 1.3e-10 72_[+1] 4 1.5e-10 28_[+1]_44 10 3.4e-09 54_[+1]_18 7 1.5e-08 66_[+1]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGWTRHWTYWSWTYACRYCTAAACGAAC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTGWTRHWTYWSWTYACRYCTAAACGAAC width=29 seqs=7 9 ( 65) GTGTTGTTTTAGATTTCATCTAAACGAAC 1 1 ( 72) GTGATGTTCTTGTTAACAACTAAACGAAC 1 2 ( 71) GAGTCAAATTACATTACACATAAACGAAC 1 8 ( 73) ATAATGAAACTTGTCACGCCTAAACGAAC 1 4 ( 29) GAGTTCCTGATCTTCTGGTCTAAACGAAC 1 10 ( 55) GTGCTGACTCAACTCAGGCCTAAACTCAT 1 7 ( 67) ATAACACTTTGCTTCACACTCAAAAGAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGWTRHWTYWSWTYACRYCTAAACGAAC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 803 bayes= 7.43933 E= 7.6e-006 -10 -945 196 -945 -10 -945 -945 117 -10 -945 196 -945 48 -42 -945 43 -945 57 -945 117 -10 -42 164 -945 48 57 -945 -15 -10 -42 -945 85 -110 -42 -36 85 -110 57 -945 85 48 -945 -36 43 -110 116 64 -115 -10 -42 -36 43 -945 -945 -945 165 -110 157 -945 -15 122 -945 -945 -15 -945 190 64 -945 90 -945 122 -945 -110 157 -945 -15 -110 190 -945 -115 -945 -42 -945 143 170 -945 -945 -945 170 -945 -945 -945 170 -945 -945 -945 -110 216 -945 -945 -945 -945 222 -115 148 -42 -945 -945 170 -945 -945 -945 -110 190 -945 -115 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGWTRHWTYWSWTYACRYCTAAACGAAC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 7 E= 7.6e-006 0.285714 0.000000 0.714286 0.000000 0.285714 0.000000 0.000000 0.714286 0.285714 0.000000 0.714286 0.000000 0.428571 0.142857 0.000000 0.428571 0.000000 0.285714 0.000000 0.714286 0.285714 0.142857 0.571429 0.000000 0.428571 0.285714 0.000000 0.285714 0.285714 0.142857 0.000000 0.571429 0.142857 0.142857 0.142857 0.571429 0.142857 0.285714 0.000000 0.571429 0.428571 0.000000 0.142857 0.428571 0.142857 0.428571 0.285714 0.142857 0.285714 0.142857 0.142857 0.428571 0.000000 0.000000 0.000000 1.000000 0.142857 0.571429 0.000000 0.285714 0.714286 0.000000 0.000000 0.285714 0.000000 0.714286 0.285714 0.000000 0.571429 0.000000 0.428571 0.000000 0.142857 0.571429 0.000000 0.285714 0.142857 0.714286 0.000000 0.142857 0.000000 0.142857 0.000000 0.857143 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.857143 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.714286 0.000000 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGWTRHWTYWSWTYACRYCTAAACGAAC MEME-1 regular expression -------------------------------------------------------------------------------- [GA][TA][GA][AT][TC][GA][ACT][TA]T[TC][AT][CG][TA]T[CT][AT][CG][AG][CT]CTAAACGAAC -------------------------------------------------------------------------------- Time 0.54 secs. ******************************************************************************** ******************************************************************************** MOTIF CMGKRWTGSMRMCDATHWWYDRHRMAYMKASSWYKMSWVYDRSHGTGMC MEME-2 width = 49 sites = 3 llr = 129 E-value = 2.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CMGKRWTGSMRMCDATHWWYDRHRMAYMKASSWYKMSWVYDRSHGTGMC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :7::73:::773:3a:377:37373a:3:a::7::3:33:33:3:::7: pos.-specific C a3::::::33:7a:::3::3::3:7:77::73:3:77:37::33:::3a probability G ::a33::a7:3::3::::::33:3::::7:37::3:3:3:377:a:a:: matrix T :::7:7a::::::3:a33373:3:::3:3:::377::7:33::3:a::: bits 2.4 * * * * * * * 2.2 * * * * * * * 2.0 * * * * * * * 1.7 * * ** * ** * * *** * Relative 1.5 * * *** * ** * *** * * *** * Entropy 1.2 * * *** ** ** ******** ** * ** *** * (62.0 bits) 1.0 ***** ******* ** * * ********* **** * ** ***** 0.7 ************* ** *** * *************** * ** ***** 0.5 ************* ** *** * ***************** ** ***** 0.2 ************************************************* 0.0 ------------------------------------------------- Multilevel CAGTATTGGAACCAATAAATAAAACACCGACGATTCCTACAGGAGTGAC consensus C GGA CCGA G CTTCGGCGA TAT GCTCGAGACTGACC C sequence T T T T G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMGKRWTGSMRMCDATHWWYDRHRMAYMKASSWYKMSWVYDRSHGTGMC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------------- ORF1ab 42 2.34e-20 ACGGTTTCGT CCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGAC CGAAAGGTAA 3 22 3.33e-20 GTTGTTAATC CAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCC TTTGTAAGCA 5 19 8.00e-20 ACAGTCGCTA CAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGAC AATATTGCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMGKRWTGSMRMCDATHWWYDRHRMAYMKASSWYKMSWVYDRSHGTGMC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ORF1ab 2.3e-20 41_[+2]_11 3 3.3e-20 21_[+2]_31 5 8e-20 18_[+2]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMGKRWTGSMRMCDATHWWYDRHRMAYMKASSWYKMSWVYDRSHGTGMC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CMGKRWTGSMRMCDATHWWYDRHRMAYMKASSWYKMSWVYDRSHGTGMC width=49 seqs=3 ORF1ab ( 42) CCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGAC 1 3 ( 22) CAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCC 1 5 ( 19) CAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMGKRWTGSMRMCDATHWWYDRHRMAYMKASSWYKMSWVYDRSHGTGMC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 49 n= 583 bayes= 8.04439 E= 2.6e+001 -823 238 -823 -823 112 80 -823 -823 -823 -823 244 -823 -823 -823 86 107 112 -823 86 -823 12 -823 -823 107 -823 -823 -823 165 -823 -823 244 -823 -823 80 186 -823 112 80 -823 -823 112 -823 86 -823 12 179 -823 -823 -823 238 -823 -823 12 -823 86 7 170 -823 -823 -823 -823 -823 -823 165 12 80 -823 7 112 -823 -823 7 112 -823 -823 7 -823 80 -823 107 12 -823 86 7 112 -823 86 -823 12 80 -823 7 112 -823 86 -823 12 179 -823 -823 170 -823 -823 -823 -823 179 -823 7 12 179 -823 -823 -823 -823 186 7 170 -823 -823 -823 -823 179 86 -823 -823 80 186 -823 112 -823 -823 7 -823 80 -823 107 -823 -823 86 107 12 179 -823 -823 -823 179 86 -823 12 -823 -823 107 12 80 86 -823 -823 179 -823 7 12 -823 86 7 12 -823 186 -823 -823 80 186 -823 12 80 -823 7 -823 -823 244 -823 -823 -823 -823 165 -823 -823 244 -823 112 80 -823 -823 -823 238 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMGKRWTGSMRMCDATHWWYDRHRMAYMKASSWYKMSWVYDRSHGTGMC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 49 nsites= 3 E= 2.6e+001 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.666667 0.000000 0.333333 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.666667 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.333333 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.333333 0.333333 0.666667 0.000000 0.333333 0.000000 0.333333 0.333333 0.000000 0.333333 0.666667 0.000000 0.333333 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.333333 0.666667 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.666667 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.333333 0.666667 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.333333 0.000000 0.000000 0.666667 0.333333 0.333333 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.333333 0.000000 0.333333 0.333333 0.333333 0.000000 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.333333 0.333333 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CMGKRWTGSMRMCDATHWWYDRHRMAYMKASSWYKMSWVYDRSHGTGMC MEME-2 regular expression -------------------------------------------------------------------------------- C[AC]G[TG][AG][TA]TG[GC][AC][AG][CA]C[AGT]AT[ACT][AT][AT][TC][AGT][AG][ACT][AG][CA]A[CT][CA][GT]A[CG][GC][AT][TC][TG][CA][CG][TA][ACG][CT][AGT][GA][GC][ACT]GTG[AC]C -------------------------------------------------------------------------------- Time 1.03 secs. ******************************************************************************** ******************************************************************************** MOTIF TGCTGCA MEME-3 width = 7 sites = 5 llr = 46 E-value = 3.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCTGCA MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::::a pos.-specific C ::a::a: probability G :8:2a:: matrix T a2:8::: bits 2.4 * ** 2.2 * ** 2.0 * ** 1.7 * * *** Relative 1.5 *** *** Entropy 1.2 *** *** (13.2 bits) 1.0 ******* 0.7 ******* 0.5 ******* 0.2 ******* 0.0 ------- Multilevel TGCTGCA consensus T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGCA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------- 10 5 3.87e-05 TTCC TGCTGCA GATTTGGATG 5 1 3.87e-05 . TGCTGCA TACAGTCGCT 2 28 3.87e-05 TTGTGGATCC TGCTGCA AATTTGATGA 7 51 6.12e-05 TTCTTATTGT TGCGGCA ATAGTGTTTA ORF1ab 17 1.28e-04 CTCGTCTATC TTCTGCA GGCTGCTTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGCA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10 3.9e-05 4_[+3]_90 5 3.9e-05 [+3]_94 2 3.9e-05 27_[+3]_67 7 6.1e-05 50_[+3]_44 ORF1ab 0.00013 16_[+3]_78 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGCA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGCTGCA width=7 seqs=5 10 ( 5) TGCTGCA 1 5 ( 1) TGCTGCA 1 2 ( 28) TGCTGCA 1 7 ( 51) TGCGGCA 1 ORF1ab ( 17) TTCTGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGCA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 1045 bayes= 7.95309 E= 3.4e+001 -897 -897 -897 165 -897 -897 212 -67 -897 238 -897 -897 -897 -897 12 133 -897 -897 244 -897 -897 238 -897 -897 170 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGCA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 5 E= 3.4e+001 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTGCA MEME-3 regular expression -------------------------------------------------------------------------------- T[GT]C[TG]GCA -------------------------------------------------------------------------------- Time 1.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ORF1ab 1.28e-17 41_[+2(2.34e-20)]_11 1 7.83e-08 71_[+1(1.37e-11)]_1 2 4.17e-09 27_[+3(3.87e-05)]_36_[+1(9.09e-11)]_\ 2 3 4.12e-16 21_[+2(3.33e-20)]_31 4 1.66e-06 28_[+1(1.46e-10)]_44 5 5.20e-18 [+3(3.87e-05)]_11_[+2(8.00e-20)]_34 6 4.10e-01 101 7 6.45e-07 50_[+3(6.12e-05)]_9_[+1(1.49e-08)]_\ 6 8 3.34e-07 72_[+1(1.33e-10)] 9 6.21e-08 64_[+1(3.63e-12)]_8 10 3.95e-08 4_[+3(3.87e-05)]_43_[+1(3.36e-09)]_\ 18 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: noble-meme.grid.gs.washington.edu ********************************************************************************