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_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	HI1116	110	deoxyribose-phosphate aldolase (deoC)

Motif number 1

          TTTATTTATTCCTTATCTTG	1	1	1	TTTATTTATT	    0.994369	-110
GCAAAAATTCTTTATTTTTGACTATGGTTT	1	55	0	TTTATTTTTG	    0.990955	-56
TTATTTATGTTTTACCTATTGTAGCAAAAA	1	78	0	TTTACCTATT	    0.983953	-33
TTTTCCTCCTTTTATTTATGTTTTACCTAT	1	89	0	TTTATTTATG	    0.996325	-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

TCAACAAGATAAGGAATAAATAAA      	1	5	0	AAGGAATAAA	    0.976595	-106
CGTAAAACCATAGTCAAAAATAAAGAATTT	1	51	1	TAGTCAAAAA	    0.950544	-60
TTTACCTATTGTAGCAAAAATTCTTTATTT	1	68	0	GTAGCAAAAA	    0.965647	-43
TACAATAGGTAAAACATAAATAAAAGGAGG	1	85	1	AAAACATAAA	    0.913059	-26
TAAATAAAAGGAGGAAAATA          	1	101	1	GAGGAAAATA	    0.965647	-10
          **********

Masking position 6
Map Score:   1.00513

Number of sites scoring better than the average of aligned sites = 1431
Number in coding regions = 1212
Number in noncoding regions = 219
Number of orfs with sites within 600 bp upstream = 187
Fraction of orfs with sites within 600 bp upstream = 0.0300353


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