AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i240_bsub_mtub_300.orf -o240_bsub_mtub_300.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	    0.974074	-120
CTTGTGAAATATGTTTTCAGACGATTTTAA	1	84	1	ATGTTTTCAG	    0.983512	-83
TTGCGGCTGACTGTTTTTTTAAAATCGTCT	1	102	0	CTGTTTTTTT	    0.975939	-65
TCATTCTAGCATGTTTTCGTTTTGCGGCTG	1	123	0	ATGTTTTCGT	     0.99132	-44
CCTGTTCTTTCCGTTTTCATTCTAGCATGT	1	139	0	CCGTTTTCAT	    0.985767	-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

GCTCATGTTTTATTTTACAATAGATAAAAG	1	53	1	TATTTTACAA	    0.991929	-114
TCTGAAAACATATTTCACAAGGCTTTTATC	1	75	0	TATTTCACAA	    0.990504	-92
GTTTTCAGACGATTTTAAAAAAACAGTCAG	1	96	1	GATTTTAAAA	     0.97533	-71
          **********

Masking position 7
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

TCAGATTCAAATCTTTCTGCCAAAAGGCTC	1	27	1	ATCTTTCTGC	    0.992867	-140
CTAGCATGTTTTCGTTTTGCGGCTGACTGT	1	118	0	TTCGTTTTGC	    0.986952	-49
ATGTCACCTGTTCTTTCCGTTTTCATTCTA	1	145	0	TTCTTTCCGT	    0.986952	-22
          **********

Masking position 5
Map Score:   0.290996

Number of sites scoring better than the average of aligned sites = 362
Number in coding regions = 329
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


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