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motifsB.txt
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********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 5.1.1 (Release date: Wed Jan 29 15:00:42 2020 -0800)
For further information on how to interpret please access http://meme-suite.org/.
To get a copy of the MEME software please access http://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
********************************************************************************
DATAFILE= promotersB.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
mtlD 1.0000 100 uspA 1.0000 100
uspC 1.0000 100 uspD 1.0000 100
ddlA 1.0000 100 ddlB 1.0000 100
ligB 1.0000 100 abgR 1.0000 100
prfC 1.0000 100 iclR 1.0000 100
rimM 1.0000 100 putA 1.0000 100
rsmF 1.0000 100 rffD 1.0000 100
gdhA 1.0000 100 pphA 1.0000 100
pphB 1.0000 100 mdtG 1.0000 100
rhtA 1.0000 100 serA 1.0000 100
asnC 1.0000 100 ivy 1.0000 100
nac 1.0000 100 kdgR 1.0000 100
fklB 1.0000 100 allR 1.0000 100
ispA 1.0000 100 ispB 1.0000 100
greA 1.0000 100 ugd 1.0000 100
ldhA 1.0000 100 uxuB 1.0000 100
tdcD 1.0000 100 tdcA 1.0000 100
tdcR 1.0000 100 greB 1.0000 100
kduI 1.0000 100 rlmF 1.0000 100
queD 1.0000 100 codB 1.0000 100
wecH 1.0000 100 prlC 1.0000 100
sdiA 1.0000 100 rfaH 1.0000 100
feaR 1.0000 100 dld 1.0000 100
fkpA 1.0000 100 ackA 1.0000 100
eamA 1.0000 100 dcp 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 promotersB.fa -dna -oc . -nostatus -time 18000 -mod zoops -nmotifs 10 -minw 15 -maxw 15 -objfun classic -revcomp -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= 15 maxw= 15
nsites: minsites= 2 maxsites= 50 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= 5000 N= 50
sample: seed= 0 hsfrac= 0
searchsize= 5000 norand= no csites= 1000
Letter frequencies in dataset:
A 0.289 C 0.21 G 0.21 T 0.289
Background letter frequencies (from file dataset with add-one prior applied):
A 0.289 C 0.21 G 0.21 T 0.289
Background model order: 0
********************************************************************************
********************************************************************************
MOTIF ATATTGCCGCAATAT MEME-1 width = 15 sites = 28 llr = 342 E-value = 2.1e-040
********************************************************************************
--------------------------------------------------------------------------------
Motif ATATTGCCGCAATAT MEME-1 Description
--------------------------------------------------------------------------------
Simplified A 829:1::1::79:8:
pos.-specific C :::1:1991711:11
probability G 1:1:19::922::1:
matrix T 18:98:1::11:9:9
bits 2.2
2.0
1.8
1.6 ***
Relative 1.3 * **** ** *
Entropy 1.1 *** **** ** *
(17.6 bits) 0.9 ********* ** *
0.7 ********** ****
0.4 ***************
0.2 ***************
0.0 ---------------
Multilevel ATATTGCCGCAATAT
consensus G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ATATTGCCGCAATAT MEME-1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
dcp + 4 1.72e-09 AAA ATATTGCCGCAATAT ATTTTCTTCT
ackA + 50 8.41e-09 CTGACGTTTT ATATTGCCGCAATAC ATTATAGGTA
feaR + 83 1.93e-08 TTTGTGTTGC ATATTGCCGCAATCT TGA
eamA + 44 5.21e-08 AATTTCATCT ATATTGTCGCAATAT CTTAGCTGAA
queD - 52 5.21e-08 AATTTCTCTA ATATTGCAGCAATAT GCCGTAGAGT
uspC + 16 5.21e-08 TTGGGATTGC ATACTGCCGCGATAT GGAGTAAAGC
rsmF + 52 9.57e-08 AAACTGCGCG ATATGGCCGCAATAC GTGGTACATG
gdhA - 57 1.31e-07 ATAGATATAA ATATTGCCGCACTCT ATACGATTGT
wecH + 66 1.44e-07 AACCTGCGAG ATATTCCCGGAATAT TGGTGGTGAT
codB + 60 1.44e-07 GGGTTTCAAA ATATTGCCGCTATGT ATTTCGTGTC
kduI + 84 2.08e-07 TGTTTCGTTT ATATTGCCGGAAGAT GA
ispB + 17 2.24e-07 TATTCCTAAC AAATTGCCGTAATAT GCCTTTGTTC
abgR + 75 2.89e-07 GTTATCGGTG ATATTGCCGAGATAT AGGTAAAAAT
rlmF + 9 5.74e-07 GGGGAATG ATGTTGCCGGCATAT TATTTACCCT
mdtG + 3 9.09e-07 TC ATACTGCCGCTATGT CATAGCAATC
asnC - 53 1.18e-06 TTCATTAAAA ATATTACCCCAATAT GAATGAATCA
pphB + 84 1.28e-06 AAAACCATGC AAATTGTCGCAATGT AA
rimM + 27 1.93e-06 TCATGACCAC TTATAGCCGGGATAT TGCTTTGTTT
mtlD + 41 2.98e-06 AGCCTCACCC TTATGGCCCGAATAT AAAACATTGA
kdgR + 59 3.48e-06 AAATCAGAAC ATGTTGCCACAATAC TTTCGCACCA
nac + 72 4.08e-06 ACTTACAACC GTGTTCCCGCGATAT TGCCAGTTCT
prfC + 14 4.08e-06 TTGATGGGTA AAATAGCCGCAATTT TTCGTTTTCA
ugd + 80 5.07e-06 CCTGATAAGA GTATTGGCGCGCTAT GCTACG
sdiA + 37 5.95e-06 CCGCAACGCC ATAGTGCCGCAAAAC CATTTATAAT
dld - 79 8.56e-06 AGTTGTT TTACTGCGGCAATGT TTCCACTCCT
serA + 6 1.07e-05 TCCAG GAATTTCCGCACTAT TTACCCAATC
fklB + 64 1.23e-05 TTTTATACCC ATATGGCCCGCCTAT GATGACCACC
greB - 38 1.32e-05 TCTGTTTGAT TAATTGCAGTAATAT TATAACGTGA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ATATTGCCGCAATAT MEME-1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
dcp 1.7e-09 3_[+1]_82
ackA 8.4e-09 49_[+1]_36
feaR 1.9e-08 82_[+1]_3
eamA 5.2e-08 43_[+1]_42
queD 5.2e-08 51_[-1]_34
uspC 5.2e-08 15_[+1]_70
rsmF 9.6e-08 51_[+1]_34
gdhA 1.3e-07 56_[-1]_29
wecH 1.4e-07 65_[+1]_20
codB 1.4e-07 59_[+1]_26
kduI 2.1e-07 83_[+1]_2
ispB 2.2e-07 16_[+1]_69
abgR 2.9e-07 74_[+1]_11
rlmF 5.7e-07 8_[+1]_77
mdtG 9.1e-07 2_[+1]_83
asnC 1.2e-06 52_[-1]_33
pphB 1.3e-06 83_[+1]_2
rimM 1.9e-06 26_[+1]_59
mtlD 3e-06 40_[+1]_45
kdgR 3.5e-06 58_[+1]_27
nac 4.1e-06 71_[+1]_14
prfC 4.1e-06 13_[+1]_72
ugd 5.1e-06 79_[+1]_6
sdiA 5.9e-06 36_[+1]_49
dld 8.6e-06 78_[-1]_7
serA 1.1e-05 5_[+1]_80
fklB 1.2e-05 63_[+1]_22
greB 1.3e-05 37_[-1]_48
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ATATTGCCGCAATAT MEME-1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF ATATTGCCGCAATAT width=15 seqs=28
dcp ( 4) ATATTGCCGCAATAT 1
ackA ( 50) ATATTGCCGCAATAC 1
feaR ( 83) ATATTGCCGCAATCT 1
eamA ( 44) ATATTGTCGCAATAT 1
queD ( 52) ATATTGCAGCAATAT 1
uspC ( 16) ATACTGCCGCGATAT 1
rsmF ( 52) ATATGGCCGCAATAC 1
gdhA ( 57) ATATTGCCGCACTCT 1
wecH ( 66) ATATTCCCGGAATAT 1
codB ( 60) ATATTGCCGCTATGT 1
kduI ( 84) ATATTGCCGGAAGAT 1
ispB ( 17) AAATTGCCGTAATAT 1
abgR ( 75) ATATTGCCGAGATAT 1
rlmF ( 9) ATGTTGCCGGCATAT 1
mdtG ( 3) ATACTGCCGCTATGT 1
asnC ( 53) ATATTACCCCAATAT 1
pphB ( 84) AAATTGTCGCAATGT 1
rimM ( 27) TTATAGCCGGGATAT 1
mtlD ( 41) TTATGGCCCGAATAT 1
kdgR ( 59) ATGTTGCCACAATAC 1
nac ( 72) GTGTTCCCGCGATAT 1
prfC ( 14) AAATAGCCGCAATTT 1
ugd ( 80) GTATTGGCGCGCTAT 1
sdiA ( 37) ATAGTGCCGCAAAAC 1
dld ( 79) TTACTGCGGCAATGT 1
serA ( 6) GAATTTCCGCACTAT 1
fklB ( 64) ATATGGCCCGCCTAT 1
greB ( 38) TAATTGCAGTAATAT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ATATTGCCGCAATAT MEME-1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4300 bayes= 8.92966 E= 2.1e-040
137 -1145 -97 -102
-70 -1145 -1145 150
162 -1145 -97 -1145
-1145 -97 -256 157
-202 -1145 -97 150
-302 -156 203 -302
-1145 208 -256 -202
-202 208 -256 -1145
-302 -97 203 -1145
-302 169 3 -202
123 -156 -24 -202
157 -56 -1145 -1145
-302 -1145 -256 168
137 -156 -56 -302
-1145 -56 -1145 157
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ATATTGCCGCAATAT MEME-1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 28 E= 2.1e-040
0.750000 0.000000 0.107143 0.142857
0.178571 0.000000 0.000000 0.821429
0.892857 0.000000 0.107143 0.000000
0.000000 0.107143 0.035714 0.857143
0.071429 0.000000 0.107143 0.821429
0.035714 0.071429 0.857143 0.035714
0.000000 0.892857 0.035714 0.071429
0.071429 0.892857 0.035714 0.000000
0.035714 0.107143 0.857143 0.000000
0.035714 0.678571 0.214286 0.071429
0.678571 0.071429 0.178571 0.071429
0.857143 0.142857 0.000000 0.000000
0.035714 0.000000 0.035714 0.928571
0.750000 0.071429 0.142857 0.035714
0.000000 0.142857 0.000000 0.857143
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ATATTGCCGCAATAT MEME-1 regular expression
--------------------------------------------------------------------------------
ATATTGCCG[CG]AATAT
--------------------------------------------------------------------------------
Time 0.49 secs.
********************************************************************************
********************************************************************************
MOTIF CGCGCHGYBYNSSWT MEME-2 width = 15 sites = 11 llr = 135 E-value = 6.0e+000
********************************************************************************
--------------------------------------------------------------------------------
Motif CGCGCHGYBYNSSWT MEME-2 Description
--------------------------------------------------------------------------------
Simplified A ::::34:1::41:4:
pos.-specific C a:9274:446245::
probability G :a18:19:3:255::
matrix T :::::2154431:6a
bits 2.2 **
2.0 **
1.8 *** * *
1.6 **** * *
Relative 1.3 ***** * * *
Entropy 1.1 ***** * * * *
(17.8 bits) 0.9 ***** * * ***
0.7 ***** ** * ***
0.4 ***** **** ****
0.2 ********** ****
0.0 ---------------
Multilevel CGCGCAGTCCAGCTT
consensus AC CTTTCGA
sequence G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCGCHGYBYNSSWT MEME-2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
prlC + 22 1.96e-08 ATTCGTCATT CGCGCAGTCCTGGTT AAAGAGGTTA
uxuB + 18 1.96e-08 GGCATGGCTG CGCGCCGTGCCGGTT CCTTCTTCCT
ispA + 85 1.38e-07 AGAATTTGTA CGCGCTGTTCGGCTT G
rsmF - 37 3.02e-07 GCGGCCATAT CGCGCAGTTTAGCAT AAACGCTCCG
prfC - 38 5.78e-07 TAAGCGGCAT CGCGCCGCGCTTGTT GAAAACGAAA
allR - 42 7.03e-07 CCTGGCCTGC CGCGCCGTCTAACTT CCGTCATACC
ivy - 21 8.42e-07 TTCTATGTCG CGCGAAGCTCACGAT AATTTGCAAA
ispB - 47 4.02e-06 CCGGGCTTTT CGCCCCGATTACCTT ACTGTGAACA
dcp + 35 4.27e-06 TTCTCCTGAA CGCGAGGTGTTCCAT AGCGTAGGCT
ddlA - 70 4.79e-06 TTCAGAAGGC CGCGAATCCCCCGTT TTGTCGTGGA
greA + 77 7.60e-06 CCCGGCTGTT CGGCCTGCCCGGCAT AACTCCTCA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCGCHGYBYNSSWT MEME-2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
prlC 2e-08 21_[+2]_64
uxuB 2e-08 17_[+2]_68
ispA 1.4e-07 84_[+2]_1
rsmF 3e-07 36_[-2]_49
prfC 5.8e-07 37_[-2]_48
allR 7e-07 41_[-2]_44
ivy 8.4e-07 20_[-2]_65
ispB 4e-06 46_[-2]_39
dcp 4.3e-06 34_[+2]_51
ddlA 4.8e-06 69_[-2]_16
greA 7.6e-06 76_[+2]_9
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCGCHGYBYNSSWT MEME-2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF CGCGCHGYBYNSSWT width=15 seqs=11
prlC ( 22) CGCGCAGTCCTGGTT 1
uxuB ( 18) CGCGCCGTGCCGGTT 1
ispA ( 85) CGCGCTGTTCGGCTT 1
rsmF ( 37) CGCGCAGTTTAGCAT 1
prfC ( 38) CGCGCCGCGCTTGTT 1
allR ( 42) CGCGCCGTCTAACTT 1
ivy ( 21) CGCGAAGCTCACGAT 1
ispB ( 47) CGCCCCGATTACCTT 1
dcp ( 35) CGCGAGGTGTTCCAT 1
ddlA ( 70) CGCGAATCCCCCGTT 1
greA ( 77) CGGCCTGCCCGGCAT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCGCHGYBYNSSWT MEME-2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4300 bayes= 9.63535 E= 6.0e+000
-1010 225 -1010 -1010
-1010 -1010 225 -1010
-1010 211 -121 -1010
-1010 -21 196 -1010
-9 179 -1010 -1010
33 79 -121 -67
-1010 -1010 211 -167
-167 79 -1010 91
-1010 79 37 33
-1010 160 -1010 33
33 -21 -21 -9
-167 79 111 -167
-1010 137 111 -1010
33 -1010 -1010 114
-1010 -1010 -1010 179
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCGCHGYBYNSSWT MEME-2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 11 E= 6.0e+000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.909091 0.090909 0.000000
0.000000 0.181818 0.818182 0.000000
0.272727 0.727273 0.000000 0.000000
0.363636 0.363636 0.090909 0.181818
0.000000 0.000000 0.909091 0.090909
0.090909 0.363636 0.000000 0.545455
0.000000 0.363636 0.272727 0.363636
0.000000 0.636364 0.000000 0.363636
0.363636 0.181818 0.181818 0.272727
0.090909 0.363636 0.454545 0.090909
0.000000 0.545455 0.454545 0.000000
0.363636 0.000000 0.000000 0.636364
0.000000 0.000000 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CGCGCHGYBYNSSWT MEME-2 regular expression
--------------------------------------------------------------------------------
CGCG[CA][AC]G[TC][CTG][CT][AT][GC][CG][TA]T
--------------------------------------------------------------------------------
Time 0.95 secs.
********************************************************************************
********************************************************************************
MOTIF ACRGGCGSAGSCTGT MEME-3 width = 15 sites = 2 llr = 40 E-value = 1.6e+005
********************************************************************************
--------------------------------------------------------------------------------
Motif ACRGGCGSAGSCTGT MEME-3 Description
--------------------------------------------------------------------------------
Simplified A a:5:::::a::::::
pos.-specific C :a:::a:5::5a:::
probability G ::5aa:a5:a5::a:
matrix T ::::::::::::a:a
bits 2.2 * **** * * *
2.0 * **** * * *
1.8 ** **** ** ****
1.6 ** **** ** ****
Relative 1.3 ** ************
Entropy 1.1 ***************
(28.7 bits) 0.9 ***************
0.7 ***************
0.4 ***************
0.2 ***************
0.0 ---------------
Multilevel ACAGGCGCAGCCTGT
consensus G G G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ACRGGCGSAGSCTGT MEME-3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
pphA + 1 9.91e-10 . ACGGGCGCAGGCTGT TTCATCAATA
allR + 67 2.36e-09 GCAGGCCAGG ACAGGCGGAGCCTGT GGCACAGAAG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ACRGGCGSAGSCTGT MEME-3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
pphA 9.9e-10 [+3]_85
allR 2.4e-09 66_[+3]_19
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ACRGGCGSAGSCTGT MEME-3 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF ACRGGCGSAGSCTGT width=15 seqs=2
pphA ( 1) ACGGGCGCAGGCTGT 1
allR ( 67) ACAGGCGGAGCCTGT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ACRGGCGSAGSCTGT MEME-3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4300 bayes= 11.0694 E= 1.6e+005
178 -765 -765 -765
-765 224 -765 -765
79 -765 124 -765
-765 -765 224 -765
-765 -765 224 -765
-765 224 -765 -765
-765 -765 224 -765
-765 124 124 -765
178 -765 -765 -765
-765 -765 224 -765
-765 124 124 -765
-765 224 -765 -765
-765 -765 -765 178
-765 -765 224 -765
-765 -765 -765 178
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ACRGGCGSAGSCTGT MEME-3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 2 E= 1.6e+005
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.500000 0.000000 0.500000 0.000000
0.000000 0.000000 1.000000 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 0.500000 0.500000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.500000 0.500000 0.000000
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 0.000000 1.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif ACRGGCGSAGSCTGT MEME-3 regular expression
--------------------------------------------------------------------------------
AC[AG]GGCG[CG]AG[CG]CTGT
--------------------------------------------------------------------------------
Time 1.40 secs.
********************************************************************************
********************************************************************************
MOTIF CRGCGCAGSMACGCS MEME-4 width = 15 sites = 2 llr = 39 E-value = 1.7e+005
********************************************************************************
--------------------------------------------------------------------------------
Motif CRGCGCAGSMACGCS MEME-4 Description
--------------------------------------------------------------------------------
Simplified A :5::::a::5a::::
pos.-specific C a::a:a::55:a:a5
probability G :5a:a::a5:::a:5
matrix T :::::::::::::::
bits 2.2 * **** * ***
2.0 * **** * ***
1.8 * ****** ****
1.6 * ****** ****
Relative 1.3 * ******* *****
Entropy 1.1 ***************
(28.3 bits) 0.9 ***************
0.7 ***************
0.4 ***************
0.2 ***************
0.0 ---------------
Multilevel CAGCGCAGCAACGCC
consensus G GC G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CRGCGCAGSMACGCS MEME-4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
rsmF - 14 5.20e-10 ATAAACGCTC CGGCGCAGGCACGCC GGAGCAGTGG
rimM + 63 2.95e-09 CTTCTTTGAT CAGCGCAGCAACGCG ATCAGAAATA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CRGCGCAGSMACGCS MEME-4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
rsmF 5.2e-10 13_[-4]_72
rimM 2.9e-09 62_[+4]_23
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CRGCGCAGSMACGCS MEME-4 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF CRGCGCAGSMACGCS width=15 seqs=2
rsmF ( 14) CGGCGCAGGCACGCC 1
rimM ( 63) CAGCGCAGCAACGCG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CRGCGCAGSMACGCS MEME-4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4300 bayes= 11.0694 E= 1.7e+005
-765 224 -765 -765
79 -765 124 -765
-765 -765 224 -765
-765 224 -765 -765
-765 -765 224 -765
-765 224 -765 -765
178 -765 -765 -765
-765 -765 224 -765
-765 124 124 -765
79 124 -765 -765
178 -765 -765 -765
-765 224 -765 -765
-765 -765 224 -765
-765 224 -765 -765
-765 124 124 -765
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CRGCGCAGSMACGCS MEME-4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 2 E= 1.7e+005
0.000000 1.000000 0.000000 0.000000
0.500000 0.000000 0.500000 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 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.500000 0.500000 0.000000
0.500000 0.500000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.500000 0.500000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif CRGCGCAGSMACGCS MEME-4 regular expression
--------------------------------------------------------------------------------
C[AG]GCGCAG[CG][AC]ACGC[CG]
--------------------------------------------------------------------------------
Time 1.84 secs.
********************************************************************************
********************************************************************************
MOTIF TTCCTCCSGHGYTTA MEME-5 width = 15 sites = 5 llr = 76 E-value = 1.5e+005
********************************************************************************
--------------------------------------------------------------------------------
Motif TTCCTCCSGHGYTTA MEME-5 Description
--------------------------------------------------------------------------------
Simplified A ::2::::::4:::28
pos.-specific C ::8a:aa422:6:::
probability G :2::2::68:8:::2
matrix T a8::8::::424a8:
bits 2.2 * **
2.0 * **
1.8 * * ** *
1.6 * * ** * *
Relative 1.3 * ** **** * *
Entropy 1.1 ********* *****
(22.0 bits) 0.9 ********* *****
0.7 ********* *****
0.4 ***************
0.2 ***************
0.0 ---------------
Multilevel TTCCTCCGGAGCTTA
consensus GA G CCTTT AG
sequence C
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TTCCTCCSGHGYTTA MEME-5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
ivy - 66 3.08e-09 TTAAACATCA TTCCTCCCGAGCTTA TCCTGCCCAT
ddlB - 58 2.88e-08 CATGTTGTTC TTCCTCCGGAGTTTG CGGCTTCAGT
pphA + 28 4.67e-08 CATCAATATT TTCCTCCCGCGCTAA AGATCACATA
nac + 23 1.57e-07 AAGTTCATGT TGCCTCCGGTTTTTA AGAGTCGGCC
rlmF + 53 2.61e-07 TGCGGGTATC TTACGCCGCTGCTTA AAGGAAAATG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TTCCTCCSGHGYTTA MEME-5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
ivy 3.1e-09 65_[-5]_20
ddlB 2.9e-08 57_[-5]_28
pphA 4.7e-08 27_[+5]_58
nac 1.6e-07 22_[+5]_63
rlmF 2.6e-07 52_[+5]_33
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TTCCTCCSGHGYTTA MEME-5 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF TTCCTCCSGHGYTTA width=15 seqs=5
ivy ( 66) TTCCTCCCGAGCTTA 1
ddlB ( 58) TTCCTCCGGAGTTTG 1
pphA ( 28) TTCCTCCCGCGCTAA 1
nac ( 23) TGCCTCCGGTTTTTA 1
rlmF ( 53) TTACGCCGCTGCTTA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TTCCTCCSGHGYTTA MEME-5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4300 bayes= 10.6907 E= 1.5e+005
-897 -897 -897 179
-897 -897 -7 146
-53 192 -897 -897
-897 225 -897 -897
-897 -897 -7 146
-897 225 -897 -897
-897 225 -897 -897
-897 92 151 -897
-897 -7 192 -897
47 -7 -897 47
-897 -897 192 -53
-897 151 -897 47
-897 -897 -897 179
-53 -897 -897 146
146 -897 -7 -897
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TTCCTCCSGHGYTTA MEME-5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 5 E= 1.5e+005
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.200000 0.800000
0.200000 0.800000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.200000 0.800000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.400000 0.600000 0.000000
0.000000 0.200000 0.800000 0.000000
0.400000 0.200000 0.000000 0.400000
0.000000 0.000000 0.800000 0.200000
0.000000 0.600000 0.000000 0.400000
0.000000 0.000000 0.000000 1.000000
0.200000 0.000000 0.000000 0.800000
0.800000 0.000000 0.200000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif TTCCTCCSGHGYTTA MEME-5 regular expression
--------------------------------------------------------------------------------
T[TG][CA]C[TG]CC[GC][GC][ATC][GT][CT]T[TA][AG]
--------------------------------------------------------------------------------
Time 2.27 secs.
********************************************************************************
********************************************************************************
MOTIF MTTTTMTTHWTCWGW MEME-6 width = 15 sites = 18 llr = 177 E-value = 1.6e+005
********************************************************************************
--------------------------------------------------------------------------------
Motif MTTTTMTTHWTCWGW MEME-6 Description
--------------------------------------------------------------------------------
Simplified A 4::::3::24113:6
pos.-specific C 422226:13:27:::
probability G 112::1::1112:a:
matrix T 176881a9457:7:4
bits 2.2 *
2.0 *
1.8 * *
1.6 * *
Relative 1.3 ** *
Entropy 1.1 ** ** * *
(14.2 bits) 0.9 * ** ** ****
0.7 **** ** ****
0.4 ******** ******
0.2 ***************
0.0 ---------------
Multilevel CTTTTCTTTTTCTGA
consensus ACC A CA GA T
sequence A
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif MTTTTMTTHWTCWGW MEME-6 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
dcp + 19 2.09e-07 GCCGCAATAT ATTTTCTTCTCCTGA ACGCGAGGTG
codB - 21 2.48e-06 AATCCGCCGC ATTCTATTCATCTGA AGATAAAAAG
mdtG - 54 2.48e-06 GTGTGCTTAT CTTTTCTTCTTATGT TCACCGCGCC
asnC + 24 4.06e-06 TTTCCATAGG ATTTTCTTATGCAGA TTGATGATTC
tdcD + 23 5.05e-06 TCATTCATCT CTTTTCTCATCCTGA GTTACGGATT
pphB - 19 5.05e-06 GGGTGTTTTT ATTTTATTCGTCAGT TGTCGTTAAT
eamA + 73 7.04e-06 GCTGAATTTA CTTTTCTTTAACAGT TGATTCGTTA
sdiA - 76 7.04e-06 TTATATATAA ATCTTATTTATGTGA TAGTTTGAAT
ddlB + 27 7.04e-06 GAAAAATTGC CCGTTCTTTAGCTGA AATCAAACTG
abgR - 51 9.59e-06 TCACCGATAA CCGTTATTTATCAGA CCAAAGAAAC
greB - 58 1.54e-05 CATCTCGTTG ATTCCCTTTGTCTGT TTGATTAATT
gdhA - 28 1.69e-05 GATTGTGCTT ATGTTGTTTATGTGA TGTGCTTTTG
prfC - 62 1.84e-05 GCCAATAAAT TCTTTCTTCTTGAGT AAGCGGCATC
rfaH + 26 2.01e-05 TGCATAATGA CTCTTATCCTTGTGT GGCAATTTCA
wecH + 1 3.27e-05 . CTTTTTTTAACCAGA TACAGAGACA
putA + 28 3.27e-05 CATGCCATTA CTCCTGTTGTTCTGA AAGGTGCAAC
iclR + 25 3.27e-05 GACCATGACA GCCTCCTTTTTCTGT ATCGTGGAAA
uspC - 61 6.15e-05 GCTCATAACC TGTTCCTTATTCTGT GAACTTCAGG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif MTTTTMTTHWTCWGW MEME-6 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
dcp 2.1e-07 18_[+6]_67
codB 2.5e-06 20_[-6]_65
mdtG 2.5e-06 53_[-6]_32
asnC 4.1e-06 23_[+6]_62
tdcD 5.1e-06 22_[+6]_63
pphB 5.1e-06 18_[-6]_67
eamA 7e-06 72_[+6]_13
sdiA 7e-06 75_[-6]_10
ddlB 7e-06 26_[+6]_59
abgR 9.6e-06 50_[-6]_35
greB 1.5e-05 57_[-6]_28
gdhA 1.7e-05 27_[-6]_58
prfC 1.8e-05 61_[-6]_24
rfaH 2e-05 25_[+6]_60
wecH 3.3e-05 [+6]_85
putA 3.3e-05 27_[+6]_58
iclR 3.3e-05 24_[+6]_61
uspC 6.1e-05 60_[-6]_25
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif MTTTTMTTHWTCWGW MEME-6 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF MTTTTMTTHWTCWGW width=15 seqs=18
dcp ( 19) ATTTTCTTCTCCTGA 1
codB ( 21) ATTCTATTCATCTGA 1
mdtG ( 54) CTTTTCTTCTTATGT 1
asnC ( 24) ATTTTCTTATGCAGA 1
tdcD ( 23) CTTTTCTCATCCTGA 1
pphB ( 19) ATTTTATTCGTCAGT 1
eamA ( 73) CTTTTCTTTAACAGT 1
sdiA ( 76) ATCTTATTTATGTGA 1
ddlB ( 27) CCGTTCTTTAGCTGA 1
abgR ( 51) CCGTTATTTATCAGA 1
greB ( 58) ATTCCCTTTGTCTGT 1
gdhA ( 28) ATGTTGTTTATGTGA 1
prfC ( 62) TCTTTCTTCTTGAGT 1
rfaH ( 26) CTCTTATCCTTGTGT 1
wecH ( 1) CTTTTTTTAACCAGA 1
putA ( 28) CTCCTGTTGTTCTGA 1
iclR ( 25) GCCTCCTTTTTCTGT 1
uspC ( 61) TGTTCCTTATTCTGT 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif MTTTTMTTHWTCWGW MEME-6 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4300 bayes= 8.02898 E= 1.6e+005
43 108 -192 -138
-1081 8 -192 132
-1081 8 -34 108
-1081 -34 -1081 152
-1081 -34 -1081 152
-6 140 -92 -238
-1081 -1081 -1081 179
-1081 -92 -1081 162
-38 66 -192 43
43 -1081 -92 79
-238 -34 -92 120
-238 178 8 -1081
20 -1081 -1081 120
-1081 -1081 225 -1081
94 -1081 -1081 62
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif MTTTTMTTHWTCWGW MEME-6 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 18 E= 1.6e+005
0.388889 0.444444 0.055556 0.111111
0.000000 0.222222 0.055556 0.722222
0.000000 0.222222 0.166667 0.611111
0.000000 0.166667 0.000000 0.833333
0.000000 0.166667 0.000000 0.833333
0.277778 0.555556 0.111111 0.055556
0.000000 0.000000 0.000000 1.000000
0.000000 0.111111 0.000000 0.888889
0.222222 0.333333 0.055556 0.388889
0.388889 0.000000 0.111111 0.500000
0.055556 0.166667 0.111111 0.666667
0.055556 0.722222 0.222222 0.000000
0.333333 0.000000 0.000000 0.666667
0.000000 0.000000 1.000000 0.000000
0.555556 0.000000 0.000000 0.444444
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif MTTTTMTTHWTCWGW MEME-6 regular expression
--------------------------------------------------------------------------------
[CA][TC][TC]TT[CA]TT[TCA][TA]T[CG][TA]G[AT]
--------------------------------------------------------------------------------
Time 2.68 secs.
********************************************************************************
********************************************************************************
MOTIF GRGTGACGGAAAGGC MEME-7 width = 15 sites = 4 llr = 65 E-value = 2.6e+005
********************************************************************************
--------------------------------------------------------------------------------
Motif GRGTGACGGAAAGGC MEME-7 Description
--------------------------------------------------------------------------------
Simplified A :5::38:::8a83:3
pos.-specific C :::::38::3:3::8
probability G a5a:8:3a8:::8a:
matrix T :::a::::3::::::
bits 2.2 * * * *
2.0 * * * *
1.8 * ** * * *
1.6 * ** * * *
Relative 1.3 * *** *** * ***
Entropy 1.1 ***************
(23.6 bits) 0.9 ***************
0.7 ***************
0.4 ***************
0.2 ***************
0.0 ---------------
Multilevel GAGTGACGGAAAGGC
consensus G ACG TC CA A
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GRGTGACGGAAAGGC MEME-7 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ---------------
uspA + 12 1.51e-08 CGCAGGACGC GGGTGACGTAACGGC ACAAGAAACG
queD - 31 2.27e-08 ATATGCCGTA GAGTACCGGAAAGGC TGTTTTTTCG
uxuB - 39 2.27e-08 CGTCTTCAGA GAGTGACGGCAAGGA AGAAGGAACC
mtlD + 19 2.27e-08 GAGAGGGTTT GGGTGAGGGAAAAGC CTCACCCTTA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GRGTGACGGAAAGGC MEME-7 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
uspA 1.5e-08 11_[+7]_74
queD 2.3e-08 30_[-7]_55
uxuB 2.3e-08 38_[-7]_47
mtlD 2.3e-08 18_[+7]_67
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GRGTGACGGAAAGGC MEME-7 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF GRGTGACGGAAAGGC width=15 seqs=4
uspA ( 12) GGGTGACGTAACGGC 1
queD ( 31) GAGTACCGGAAAGGC 1
uxuB ( 39) GAGTGACGGCAAGGA 1
mtlD ( 19) GGGTGAGGGAAAAGC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif GRGTGACGGAAAGGC MEME-7 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 4300 bayes= 10.0688 E= 2.6e+005
-865 -865 225 -865
79 -865 125 -865
-865 -865 225 -865
-865 -865 -865 179
-21 -865 183 -865
137 25 -865 -865