AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ifhlA_hinf_opreg_100.orf -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0536	102	urease accessory protein (ureG)

Motif number 1

TTTTACTTGTAGGGGCAAATCACATTTGCC	1	33	1	AGGGGCAAAT	    0.999512	-70
ACGAATGTTCAAGGGCAAATGTGATTTGCC	1	46	0	AAGGGCAAAT	    0.998829	-57
GTTGATATATAGGGGCAAATGTAACTTGCC	1	74	1	AGGGGCAAAT	    0.999512	-29
    GGGTGTAGGGGCAAGTTACATTTGCC	1	87	0	AGGGGCAAGT	     0.99935	-16
          **********

Masking position 7
Map Score:   18.3364

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 7
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

AATGTGATTTGCCCCTACAAGTAAAATCTC	1	29	0	GCCCCTACAA	    0.998991	-74
AATCACATTTGCCCTTGAACATTCGTTGAT	1	50	1	GCCCTTGAAC	    0.993121	-53
AGTTACATTTGCCCCTATATATCAACGAAT	1	70	0	GCCCCTATAT	    0.997253	-33
AATGTAACTTGCCCCTACACCC        	1	91	1	GCCCCTACAC	    0.999626	-12
          **********

Masking position 6
Map Score:   10.3702

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 15
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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:   -1.9652e-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