AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i339_weak10_hinf_reg_100.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

TTCAAATCAGATTATGAGCTCATAACGTTT	1	18	1	ATTATGAGCT	    0.989497	-141
ATTTTTTATCATTCTGTGATCTAGATCTCA	1	74	1	ATTCTGTGAT	    0.988761	-85
CAATAAATTAAATCTGAGATCTAGATCACA	1	88	0	AATCTGAGAT	    0.985641	-71
TTATCTGTATATTAGCCGATACAATAAATT	1	109	0	ATTAGCCGAT	    0.969212	-50
GTTAAGATCTATTAGGAGATTAAAA     	1	144	1	ATTAGGAGAT	    0.995154	-15
          **********

Masking position 3
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

ACGTTTTATCACTAAAATTAACAAAAAATA	1	42	1	ACTAAAATTA	    0.980247	-117
ACTAAAATTAACAAAAAATAACATTTTTTA	1	52	1	ACAAAAAATA	    0.990281	-107
TCACAGAATGATAAAAAATGTTATTTTTTG	1	63	0	ATAAAAAATG	    0.919702	-96
ATTAGCCGATACAATAAATTAAATCTGAGA	1	99	0	ACAATAAATT	    0.924313	-60
ATAGATCTTAACTAAATTTATCTGTATATT	1	126	0	ACTAAATTTA	    0.937797	-33
          **********

Masking position 6
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	    0.989108	-140
AATTAAATCTGAGATCTAGATCACAGAATG	1	83	0	GAGATCTAGA	    0.989108	-76
AATCTCCTAATAGATCTTAACTAAATTTAT	1	135	0	TAGATCTTAA	    0.974972	-24
GATCTATTAGGAGATTAAAA          	1	149	1	GAGATTAAAA	    0.974979	-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