AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ideoR_hinf_opreg_300.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	HI1116	110	deoxyribose-phosphate aldolase (deoC)

Motif number 1

CAAGATAAGGAATAAATAAA          	1	1	0	AATAAATAAA	    0.993576	-110
AAACCATAGTCAAAAATAAAGAATTTTTGC	1	55	1	CAAAAATAAA	    0.989654	-56
TTTTTGCTACAATAGGTAAAACATAAATAA	1	78	1	AATAGGTAAA	    0.981682	-33
ATAGGTAAAACATAAATAAAAGGAGGAAAA	1	89	1	CATAAATAAA	    0.995814	-22
          **********

Masking position 4
Map Score:   7.10566

Number of sites scoring better than the average of aligned sites = 105
Number in coding regions = 69
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 2

TCATCTCAACAAGATAAGGAATAAATAAA 	1	10	0	AAGATAAGGA	    0.996135	-101
ACCATAGTCAAAAATAAAGAATTTTTGCTA	1	57	1	AAAATAAAGA	    0.984557	-54
GTAAAACATAAATAAAAGGAGGAAAATA  	1	93	1	AATAAAAGGA	    0.989965	-18
          **********

Masking position 6
Map Score:   3.06241

Number of sites scoring better than the average of aligned sites = 61
Number in coding regions = 39
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

          **********

No masking
Map Score:   -1.46782e-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:   -1.46782e-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:   -1.46782e-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