AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i240_sensory_cassete6_bsub_reg_300.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

CAAAAGGCTCATGTTTTATTTTACAATAGA	1	47	1	ATGTTTTATT	    0.974237	-120
CTTGTGAAATATGTTTTCAGACGATTTTAA	1	84	1	ATGTTTTCAG	    0.983593	-83
TTGCGGCTGACTGTTTTTTTAAAATCGTCT	1	102	0	CTGTTTTTTT	    0.976091	-65
TCATTCTAGCATGTTTTCGTTTTGCGGCTG	1	123	0	ATGTTTTCGT	    0.991366	-44
CCTGTTCTTTCCGTTTTCATTCTAGCATGT	1	139	0	CCGTTTTCAT	    0.985849	-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	    0.992626	-114
TCTGAAAACATATTTCACAAGGCTTTTATC	1	75	0	TATTTCACAA	    0.991342	-92
GTTTTCAGACGATTTTAAAAAAACAGTCAG	1	96	1	GATTTTAAAA	    0.977639	-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

GAGCCTTTTGGCAGAAAGATTTGAATCTGA	1	27	0	GCAGAAAGAT	     0.99315	-140
ACAGTCAGCCGCAAAACGAAAACATGCTAG	1	118	1	GCAAAACGAA	    0.987465	-49
TAGAATGAAAACGGAAAGAACAGGTGACAT	1	145	1	ACGGAAAGAA	    0.987465	-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