AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -itorR_ecoli_opreg_100.orf -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	torR_torC	129	torR: response transcriptional regulator for torA (sensor TorS), torC: trimethylamine N-oxide reductase, cytochrome c-type subunit

Motif number 1

TAATGAGCAAATATGAACAGCGGCACTGGT	1	49	1	ATATGAACAG	    0.998974	-81
GCACTGGTCAGGATGAACGGCTTACGGCAG	1	71	1	GGATGAACGG	    0.995163	-59
TTACGGCAGAATATGAACAGATATGAACAG	1	92	1	ATATGAACAG	    0.998974	-38
ATATGAACAGATATGAACAGAATGAGTAAA	1	102	1	ATATGAACAG	    0.998974	-28
          **********

Masking position 6
Map Score:   12.7472

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 9
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

GCTGTTCATATTTGCTCATTAAGATCGCTT	1	40	0	TTTGCTCATT	    0.995029	-90
TCTGTTCATATCTGTTCATATTCTGCCGTA	1	93	0	TCTGTTCATA	    0.964766	-37
  CAGAGGGTTTTACTCATTCTGTTCATAT	1	112	0	TTTACTCATT	    0.990728	-18
          **********

Masking position 8
Map Score:   2.32876

Number of sites scoring better than the average of aligned sites = 57
Number in coding regions = 46
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

          **********

No masking
Map Score:   1.58751e-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:   1.58751e-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:   1.58751e-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