AlignACE version 2.2  July 7, 1998
alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jtorR.reg -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 = 	182

Input sequences:
#1	torR_torC 129 bp torR 230 1-693 CDS
 torC 390 1-1173 CDS

Motif number 1

ATATGAACAGATATGAACAGAATGAGTAAA	1	19	0	ATATGAACAG	    0.998974	-111
TTACGGCAGAATATGAACAGATATGAACAG	1	29	0	ATATGAACAG	    0.998974	-101
GCACTGGTCAGGATGAACGGCTTACGGCAG	1	50	0	GGATGAACGG	    0.995163	-80
TAATGAGCAAATATGAACAGCGGCACTGGT	1	72	0	ATATGAACAG	    0.998974	-58
          **********

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

  CAGAGGGTTTTACTCATTCTGTTCATAT	1	9	1	TTTACTCATT	    0.990189	-121
TCTGTTCATATCTGTTCATATTCTGCCGTA	1	28	1	TCTGTTCATA	     0.96455	-102
GCTGTTCATATTTGCTCATTAAGATCGCTT	1	81	1	TTTGCTCATT	    0.994917	-49
          **********

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