AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i240_sensory_cassete6_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

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

Motif number 1

TCTATTGTAAAATAAAACATGAGCCTTTTG	1	47	0	AATAAAACAT	    0.975456	-120
TTAAAATCGTCTGAAAACATATTTCACAAG	1	84	0	CTGAAAACAT	    0.984194	-83
AGACGATTTTAAAAAAACAGTCAGCCGCAA	1	102	1	AAAAAAACAG	    0.977225	-65
CAGCCGCAAAACGAAAACATGCTAGAATGA	1	123	1	ACGAAAACAT	    0.991704	-44
ACATGCTAGAATGAAAACGGAAAGAACAGG	1	139	1	ATGAAAACGG	    0.986462	-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	    0.992251	-114
TCTGAAAACATATTTCACAAGGCTTTTATC	1	75	0	TATTTCACAA	    0.990891	-92
GTTTTCAGACGATTTTAAAAAAACAGTCAG	1	96	1	GATTTTAAAA	    0.976395	-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

          **********

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 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