AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i158_CYD_operon_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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	cydD	122	ATP-binding component of cytochrome-related transport, Zn sensitive

Motif number 1

ACAAAAGTAAAGAAGGCGACACCATGCGAC	1	26	1	AGAAGGCGAC	    0.998796	-97
AGAAGGCGACACCATGCGACTATGGGTCGC	1	36	1	ACCATGCGAC	    0.994332	-87
GGGGAAAAAATAAAGGCGACCCATAGTCGC	1	51	0	TAAAGGCGAC	    0.991761	-72
 TGCACGCTTAGCAGGTGAGTTATCAGAAT	1	104	0	AGCAGGTGAG	    0.991738	-19
          **********

Masking position 4
Map Score:   5.32015

Number of sites scoring better than the average of aligned sites = 454
Number in coding regions = 428
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

          **********

No masking
Map Score:   1.23224e-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 3

          **********

No masking
Map Score:   1.23224e-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:   1.23224e-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