AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i240_bsub_mtub_100.orf -o240_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	lytS	166	two-component sensor histidine kinase

Motif number 1

CAAAAGGCTCATGTTTTATTTTACAATAGA	1	47	1	ATGTTTTATT	    0.972173	-120
CTTGTGAAATATGTTTTCAGACGATTTTAA	1	84	1	ATGTTTTCAG	    0.982554	-83
TTGCGGCTGACTGTTTTTTTAAAATCGTCT	1	102	0	CTGTTTTTTT	    0.974172	-65
TCATTCTAGCATGTTTTCGTTTTGCGGCTG	1	123	0	ATGTTTTCGT	    0.990784	-44
CCTGTTCTTTCCGTTTTCATTCTAGCATGT	1	139	0	CCGTTTTCAT	    0.984803	-28
          **********

Masking position 5
Map Score:   5.83853

Number of sites scoring better than the average of aligned sites = 662
Number in coding regions = 582
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 2

CTTTTATCTATTGTAAAATAAAACATGAGC	1	53	0	TTGTAAAATA	    0.992251	-114
GATAAAAGCCTTGTGAAATATGTTTTCAGA	1	75	1	TTGTGAAATA	    0.990891	-92
CTGACTGTTTTTTTAAAATCGTCTGAAAAC	1	96	0	TTTTAAAATC	    0.976395	-71
          **********

Masking position 6
Map Score:   2.25503

Number of sites scoring better than the average of aligned sites = 105
Number in coding regions = 78
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 3

AGCCTTTTGGCAGAAAGATTTGAATCTGAA	1	26	0	CAGAAAGATT	    0.986733	-141
ATCTTTCTGCCAAAAGGCTCATGTTTTATT	1	37	1	CAAAAGGCTC	    0.990187	-130
AAACATATTTCACAAGGCTTTTATCTATTG	1	70	0	CACAAGGCTT	    0.989763	-97
AGAATGAAAACGGAAAGAACAGGTGACATG	1	146	1	CGGAAAGAAC	    0.963913	-21
          **********

Masking position 5
Map Score:   1.07803

Number of sites scoring better than the average of aligned sites = 543
Number in coding regions = 506
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 4

          **********

No masking
Map Score:   -2.8889e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   -2.8889e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   -2.8889e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0