******************************************************************************** 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= NC_004703_promoter_regions.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ antisense_4|Start:20011| 1.0000 51 antisense_0|Start:981|St 1.0000 51 antisense_1|Start:11991| 1.0000 51 antisense_2|Start:12120| 1.0000 51 antisense_3|Start:16854| 1.0000 51 antisense_5|Start:25303| 1.0000 51 antisense_6|Start:30894| 1.0000 51 antisense_7|Start:32225| 1.0000 51 orphan_5|Start:4252|Stra 1.0000 51 orphan_8|Start:21681|Str 1.0000 51 orphan_9|Start:21734|Str 1.0000 51 orphan_2|Start:2720|Stra 1.0000 51 orphan_4|Start:4242|Stra 1.0000 51 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme NC_004703_promoter_regions.fasta -dna -nmotifs 5 -minw 5 -maxw 20 model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 5 maxw= 20 nsites: minsites= 2 maxsites= 13 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= 663 N= 13 sample: seed= 0 hsfrac= 0 searchsize= 663 norand= no csites= 1000 Letter frequencies in dataset: A 0.302 C 0.175 G 0.169 T 0.354 Background letter frequencies (from file dataset with add-one prior applied): A 0.301 C 0.175 G 0.169 T 0.354 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CSTTKTAT MEME-1 width = 8 sites = 11 llr = 75 E-value = 1.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif CSTTKTAT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::2:::8: pos.-specific C 94:::3:1 probability G 161:5::: matrix T ::7a5729 bits 2.6 2.3 2.0 * 1.8 * Relative 1.5 ** * Entropy 1.3 ** * (9.8 bits) 1.0 ** ***** 0.8 ** ***** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CGTTTTAT consensus C GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSTTKTAT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- antisense_7|Start:32225| 39 2.36e-05 GTCGGTATAA CGTTGTAT TCCTG antisense_1|Start:11991| 39 3.53e-05 GGCGTACCAC CGTTGCAT AACTA antisense_6|Start:30894| 14 1.09e-04 GCCATAAAAT CCTTGTAT AAACGAGATA antisense_2|Start:12120| 15 1.34e-04 TAGACATTTC CGTTTCAT AACTTTTCTG orphan_8|Start:21681|Str 4 1.97e-04 GAA CCTTTTAT TTTTTTGCCC antisense_3|Start:16854| 9 3.51e-04 TTCTCATA CGATTTAT TTTATTTGTT antisense_5|Start:25303| 12 3.95e-04 TGCCCTGTTC CCATGTAT CTCCGAACGG orphan_5|Start:4252|Stra 39 4.99e-04 CGATTGCCGC CGTTTTAC AAATG orphan_9|Start:21734|Str 18 6.65e-04 TTTTGAACAT CCTTGTTT GCAGATGAAA antisense_0|Start:981|St 38 7.47e-04 TCAAACGAAA CGTTTCTT TAAGGC antisense_4|Start:20011| 38 1.74e-03 TTGGCTAAAA GGGTTTAT TAAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSTTKTAT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- antisense_7|Start:32225| 2.4e-05 38_[+1]_5 antisense_1|Start:11991| 3.5e-05 38_[+1]_5 antisense_6|Start:30894| 0.00011 13_[+1]_30 antisense_2|Start:12120| 0.00013 14_[+1]_29 orphan_8|Start:21681|Str 0.0002 3_[+1]_40 antisense_3|Start:16854| 0.00035 8_[+1]_35 antisense_5|Start:25303| 0.0004 11_[+1]_32 orphan_5|Start:4252|Stra 0.0005 38_[+1]_5 orphan_9|Start:21734|Str 0.00066 17_[+1]_26 antisense_0|Start:981|St 0.00075 37_[+1]_6 antisense_4|Start:20011| 0.0017 37_[+1]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSTTKTAT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CSTTKTAT width=8 seqs=11 antisense_7|Start:32225| ( 39) CGTTGTAT 1 antisense_1|Start:11991| ( 39) CGTTGCAT 1 antisense_6|Start:30894| ( 14) CCTTGTAT 1 antisense_2|Start:12120| ( 15) CGTTTCAT 1 orphan_8|Start:21681|Str ( 4) CCTTTTAT 1 antisense_3|Start:16854| ( 9) CGATTTAT 1 antisense_5|Start:25303| ( 12) CCATGTAT 1 orphan_5|Start:4252|Stra ( 39) CGTTTTAC 1 orphan_9|Start:21734|Str ( 18) CCTTGTTT 1 antisense_0|Start:981|St ( 38) CGTTTCTT 1 antisense_4|Start:20011| ( 38) GGGTTTAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSTTKTAT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 572 bayes= 6.03368 E= 1.7e+000 -1010 237 -90 -1010 -1010 105 191 -1010 -73 -1010 -90 104 -1010 -1010 -1010 150 -1010 -1010 142 62 -1010 64 -1010 104 144 -1010 -1010 -96 -1010 -95 -1010 136 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSTTKTAT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 1.7e+000 0.000000 0.909091 0.090909 0.000000 0.000000 0.363636 0.636364 0.000000 0.181818 0.000000 0.090909 0.727273 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.454545 0.545455 0.000000 0.272727 0.000000 0.727273 0.818182 0.000000 0.000000 0.181818 0.000000 0.090909 0.000000 0.909091 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSTTKTAT MEME-1 regular expression -------------------------------------------------------------------------------- C[GC]TT[TG][TC]AT -------------------------------------------------------------------------------- Time 0.37 secs. ******************************************************************************** ******************************************************************************** MOTIF CCGGTTAAAGATMVMG MEME-2 width = 16 sites = 4 llr = 60 E-value = 1.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCGGTTAAAGATMVMG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 33::3:aaa:8:5353 pos.-specific C 88:3:3:::333535: probability G ::a8:3:::8:3:5:8 matrix T ::::85:::::5:::: bits 2.6 * 2.3 * 2.0 * 1.8 ** **** Relative 1.5 **** **** * Entropy 1.3 **** **** * (21.8 bits) 1.0 **** ***** * ** 0.8 ***** ***** **** 0.5 **************** 0.3 **************** 0.0 ---------------- Multilevel CCGGTTAAAGATAGAG consensus AA CAC CCCCACA sequence G G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGTTAAAGATMVMG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- antisense_1|Start:11991| 14 9.86e-09 AGCAATTTTT CCGGTGAAAGCTCCAG GCGTACCACC antisense_7|Start:32225| 1 1.78e-08 . CAGGTTAAAGACCGAG TAATATTTAT antisense_3|Start:16854| 36 6.86e-08 TCACGATAAT ACGGTCAAACAGAGCG antisense_4|Start:20011| 7 4.23e-07 TTACGA CCGCATAAAGATAACA ATTTGTTGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGTTAAAGATMVMG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- antisense_1|Start:11991| 9.9e-09 13_[+2]_22 antisense_7|Start:32225| 1.8e-08 [+2]_35 antisense_3|Start:16854| 6.9e-08 35_[+2] antisense_4|Start:20011| 4.2e-07 6_[+2]_29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGTTAAAGATMVMG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCGGTTAAAGATMVMG width=16 seqs=4 antisense_1|Start:11991| ( 14) CCGGTGAAAGCTCCAG 1 antisense_7|Start:32225| ( 1) CAGGTTAAAGACCGAG 1 antisense_3|Start:16854| ( 36) ACGGTCAAACAGAGCG 1 antisense_4|Start:20011| ( 7) CCGCATAAAGATAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGTTAAAGATMVMG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 468 bayes= 7.59991 E= 1.4e+001 -27 209 -865 -865 -27 209 -865 -865 -865 -865 256 -865 -865 51 214 -865 -27 -865 -865 108 -865 51 56 50 173 -865 -865 -865 173 -865 -865 -865 173 -865 -865 -865 -865 51 214 -865 131 51 -865 -865 -865 51 56 50 73 151 -865 -865 -27 51 156 -865 73 151 -865 -865 -27 -865 214 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGTTAAAGATMVMG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 4 E= 1.4e+001 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.250000 0.250000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.500000 0.500000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.500000 0.500000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGGTTAAAGATMVMG MEME-2 regular expression -------------------------------------------------------------------------------- [CA][CA]G[GC][TA][TCG]AAA[GC][AC][TCG][AC][GAC][AC][GA] -------------------------------------------------------------------------------- Time 0.80 secs. ******************************************************************************** ******************************************************************************** MOTIF CGGAAS MEME-3 width = 6 sites = 3 llr = 26 E-value = 6.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGGAAS MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::aa: pos.-specific C a::::7 probability G :aa::3 matrix T :::::: bits 2.6 *** 2.3 *** 2.0 *** 1.8 ***** Relative 1.5 ****** Entropy 1.3 ****** (12.7 bits) 1.0 ****** 0.8 ****** 0.5 ****** 0.3 ****** 0.0 ------ Multilevel CGGAAC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAS MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ orphan_5|Start:4252|Stra 24 7.92e-05 ATAAGGTGAT CGGAAC GATTGCCGCC antisense_5|Start:25303| 27 7.92e-05 TATCTCCGAA CGGAAC ATAAATTGTT orphan_2|Start:2720|Stra 28 1.56e-04 TGGTTAAATC CGGAAG ATTTTCTATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAS MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- orphan_5|Start:4252|Stra 7.9e-05 23_[+3]_22 antisense_5|Start:25303| 7.9e-05 26_[+3]_19 orphan_2|Start:2720|Stra 0.00016 27_[+3]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAS MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGGAAS width=6 seqs=3 orphan_5|Start:4252|Stra ( 24) CGGAAC 1 antisense_5|Start:25303| ( 27) CGGAAC 1 orphan_2|Start:2720|Stra ( 28) CGGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 598 bayes= 7.28881 E= 6.0e+001 -823 251 -823 -823 -823 -823 256 -823 -823 -823 256 -823 173 -823 -823 -823 173 -823 -823 -823 -823 192 97 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 3 E= 6.0e+001 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAS MEME-3 regular expression -------------------------------------------------------------------------------- CGGAA[CG] -------------------------------------------------------------------------------- Time 1.04 secs. ******************************************************************************** ******************************************************************************** MOTIF CCGMCC MEME-4 width = 6 sites = 2 llr = 19 E-value = 3.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCGMCC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::5:: pos.-specific C aa:5aa probability G ::a::: matrix T :::::: bits 2.6 *** ** 2.3 *** ** 2.0 *** ** 1.8 *** ** Relative 1.5 *** ** Entropy 1.3 *** ** (13.7 bits) 1.0 ****** 0.8 ****** 0.5 ****** 0.3 ****** 0.0 ------ Multilevel CCGACC consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGMCC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ orphan_4|Start:4242|Stra 21 2.77e-05 CAAATGTACA CCGCCC CCCAAAAAAG orphan_2|Start:2720|Stra 8 7.54e-05 AAAGATC CCGACC TGTTTGGTTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGMCC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- orphan_4|Start:4242|Stra 2.8e-05 20_[+4]_25 orphan_2|Start:2720|Stra 7.5e-05 7_[+4]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGMCC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCGMCC width=6 seqs=2 orphan_4|Start:4242|Stra ( 21) CCGCCC 1 orphan_2|Start:2720|Stra ( 8) CCGACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGMCC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 598 bayes= 8.21917 E= 3.3e+002 -765 251 -765 -765 -765 251 -765 -765 -765 -765 256 -765 73 151 -765 -765 -765 251 -765 -765 -765 251 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGMCC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 2 E= 3.3e+002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGMCC MEME-4 regular expression -------------------------------------------------------------------------------- CCG[AC]CC -------------------------------------------------------------------------------- Time 1.28 secs. ******************************************************************************** ******************************************************************************** MOTIF TGCCC MEME-5 width = 5 sites = 2 llr = 16 E-value = 6.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCCC MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::: pos.-specific C ::aaa probability G :a::: matrix T a:::: bits 2.6 **** 2.3 **** 2.0 **** 1.8 **** Relative 1.5 ***** Entropy 1.3 ***** (11.6 bits) 1.0 ***** 0.8 ***** 0.5 ***** 0.3 ***** 0.0 ----- Multilevel TGCCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----- orphan_8|Start:21681|Str 17 3.21e-04 TTTATTTTTT TGCCC TATTATCTTA antisense_5|Start:25303| 2 3.21e-04 T TGCCC TGTTCCCATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- orphan_8|Start:21681|Str 0.00032 16_[+5]_30 antisense_5|Start:25303| 0.00032 1_[+5]_45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGCCC width=5 seqs=2 orphan_8|Start:21681|Str ( 17) TGCCC 1 antisense_5|Start:25303| ( 2) TGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 5 n= 611 bayes= 8.2503 E= 6.2e+002 -765 -765 -765 149 -765 -765 256 -765 -765 251 -765 -765 -765 251 -765 -765 -765 251 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 5 nsites= 2 E= 6.2e+002 0.000000 0.000000 0.000000 1.000000 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 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCC MEME-5 regular expression -------------------------------------------------------------------------------- TGCCC -------------------------------------------------------------------------------- Time 1.49 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- antisense_4|Start:20011| 2.22e-04 6_[+2(4.23e-07)]_29 antisense_0|Start:981|St 2.37e-01 51 antisense_1|Start:11991| 7.35e-07 13_[+2(9.86e-09)]_9_[+1(3.53e-05)]_\ 5 antisense_2|Start:12120| 3.08e-01 51 antisense_3|Start:16854| 5.37e-05 35_[+2(6.86e-08)] antisense_5|Start:25303| 1.92e-04 26_[+3(7.92e-05)]_19 antisense_6|Start:30894| 1.41e-01 51 antisense_7|Start:32225| 8.03e-07 [+2(1.78e-08)]_22_[+1(2.36e-05)]_5 orphan_5|Start:4252|Stra 1.30e-03 23_[+3(7.92e-05)]_22 orphan_8|Start:21681|Str 2.05e-02 51 orphan_9|Start:21734|Str 5.52e-01 51 orphan_2|Start:2720|Stra 2.65e-03 7_[+4(7.54e-05)]_38 orphan_4|Start:4242|Stra 1.79e-02 20_[+4(2.77e-05)]_25 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: d66a10486638 ********************************************************************************