AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i339_weak10_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -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	HI1010	158	3-hydroxyisobutyrate dehydrogenase, putative

Motif number 1

AAACGTTATGAGCTCATAATCTGATTTGAA	1	18	0	AGCTCATAAT	    0.988847	-141
TGAGATCTAGATCACAGAATGATAAAAAAT	1	74	0	ATCACAGAAT	    0.988087	-85
TGTGATCTAGATCTCAGATTTAATTTATTG	1	88	1	ATCTCAGATT	    0.984756	-71
AATTTATTGTATCGGCTAATATACAGATAA	1	109	1	ATCGGCTAAT	    0.967929	-50
     TTTTAATCTCCTAATAGATCTTAAC	1	144	0	ATCTCCTAAT	    0.994905	-15
          **********

Masking position 8
Map Score:   6.33802

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 77
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

TATTTTTTGTTAATTTTAGTGATAAAACGT	1	42	0	TAATTTTAGT	    0.981791	-117
TAAAAAATGTTATTTTTTGTTAATTTTAGT	1	52	0	TATTTTTTGT	    0.991048	-107
CAAAAAATAACATTTTTTATCATTCTGTGA	1	63	1	CATTTTTTAT	     0.92562	-96
TCTCAGATTTAATTTATTGTATCGGCTAAT	1	99	1	AATTTATTGT	    0.929875	-60
AATATACAGATAAATTTAGTTAAGATCTAT	1	126	1	TAAATTTAGT	     0.94246	-33
          **********

Masking position 5
Map Score:   3.80746

Number of sites scoring better than the average of aligned sites = 436
Number in coding regions = 356
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 3

AAAACGTTATGAGCTCATAATCTGATTTGA	1	19	0	GAGCTCATAA	    0.989675	-140
AATTAAATCTGAGATCTAGATCACAGAATG	1	83	0	GAGATCTAGA	    0.989675	-76
AATCTCCTAATAGATCTTAACTAAATTTAT	1	135	0	TAGATCTTAA	    0.976257	-24
GATCTATTAGGAGATTAAAA          	1	149	1	GAGATTAAAA	    0.976264	-10
          **********

Masking position 5
Map Score:   2.67835

Number of sites scoring better than the average of aligned sites = 40
Number in coding regions = 29
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

          **********

No masking
Map Score:   1.72962e-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:   1.72962e-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 6

          **********

No masking
Map Score:   1.72962e-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