AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i263_hypothetical_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	HI0033	53	conserved hypothetical protein
#2	HI0034	124	conserved hypothetical protein

Motif number 1

GTTATTTTTTACCGCACTTTACTAAAAT  	1	9	0	ACCGCACTTT	     0.99875	-45
GTAAAAAATAACCGCACTTTTTAGATAAGG	1	27	1	ACCGCACTTT	     0.99875	-27
CGCGAAATTAACCGCGCTTTTTATGTCTAA	2	27	0	ACCGCGCTTT	    0.995775	-98
CGCGGTTAATTTCGCGCTTATTTTTTGCGT	2	41	1	TTCGCGCTTA	    0.990796	-84
ATGATAGAATTCCGCACCTTTATTGCTAAG	2	95	1	TCCGCACCTT	    0.996778	-30
      TTTGTTCTCACTTAGCAATAAAGG	2	111	0	TTCTCACTTA	    0.960089	-14
          **********

Masking position 9
Map Score:   17.7562

Number of sites scoring better than the average of aligned sites = 1773
Number in coding regions = 1231
Number in noncoding regions = 542
Number of orfs with sites within 600 bp upstream = 335
Fraction of orfs with sites within 600 bp upstream = 0.0538066


Motif number 2

CGGTTATTTTTTACCGCACTTTACTAAAAT	1	11	0	TTACCGCACT	    0.996039	-43
CGGTAAAAAATAACCGCACTTTTTAGATAA	1	25	1	TAACCGCACT	    0.996039	-29
AGCGCGAAATTAACCGCGCTTTTTATGTCT	2	29	0	TAACCGCGCT	     0.99749	-96
AGCGCGGTTAATTTCGCGCTTATTTTTTGC	2	39	1	ATTTCGCGCT	    0.983934	-86
TCTTGCGCAAAATCCACGCAAAAAATAAGC	2	56	0	AATCCACGCA	    0.949245	-69
CAATGATAGAATTCCGCACCTTTATTGCTA	2	93	1	ATTCCGCACC	    0.991225	-32
          **********

Masking position 5
Map Score:   12.1017

Number of sites scoring better than the average of aligned sites = 684
Number in coding regions = 419
Number in noncoding regions = 265
Number of orfs with sites within 600 bp upstream = 183
Fraction of orfs with sites within 600 bp upstream = 0.0293929


Motif number 3

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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:   -1.75204e-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