AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i264_hypothetical1_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	HI1150	35	conserved hypothetical protein
#2	HI1151	88	conserved hypothetical protein

Motif number 1

CAAAGTGCGGATGAAAATTTCAATGTTT  	1	9	0	ATGAAAATTT	    0.952999	-27
AATTTTTAATAGGAAAAAATA         	2	2	0	AGGAAAAAAT	    0.992762	-87
ATTTTTTCCTATTAAAAATTTTCAACATTT	2	12	1	ATTAAAAATT	    0.962254	-77
CTTTAAAAATAAGATAAAATGTTGAAAATT	2	28	0	AAGATAAAAT	    0.983488	-61
TTTAAAGTTTATGGTAAAATGCACGCCAAT	2	51	1	ATGGTAAAAT	    0.965178	-38
TTTTATCCTTTATAAAAATTGGCGTGCATT	2	68	0	TATAAAAATT	    0.794077	-21
ATTTTTATAAAGGATAAAAA          	2	79	1	AGGATAAAAA	     0.95628	-10
          **********

Masking position 6
Map Score:   8.5039

Number of sites scoring better than the average of aligned sites = 1307
Number in coding regions = 1007
Number in noncoding regions = 300
Number of orfs with sites within 600 bp upstream = 253
Fraction of orfs with sites within 600 bp upstream = 0.040636


Motif number 2

          AAACATTGAAATTTTCATCCG	1	1	1	AAACTTGAAA	    0.996913	-35
AAATAAGATAAAATGTTGAAAATTTTTAATA	2	21	0	AAATTTGAAA	    0.991671	-68
ATTTTACCATAAACTTTAAAAATAAGATAAA	2	40	0	AAACTTAAAA	     0.99526	-49
CAATTTTTATAAAGGATAAAAA         	2	77	1	AAAGATAAAA	    0.978335	-12
          **** ******

Masking position 7
Map Score:   5.57604

Number of sites scoring better than the average of aligned sites = 124
Number in coding regions = 96
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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