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

Motif number 1

  AAACATTGAAATTTTCATCCGCACTTTG	1	9	1	AAATTTTCAT	    0.952091	-27
         TATTTTTTCCTATTAAAAATT	2	2	1	ATTTTTTCCT	    0.992616	-87
AAATGTTGAAAATTTTTAATAGGAAAAAAT	2	12	0	AATTTTTAAT	    0.961579	-77
AATTTTCAACATTTTATCTTATTTTTAAAG	2	28	1	ATTTTATCTT	     0.98324	-61
ATTGGCGTGCATTTTACCATAAACTTTAAA	2	51	0	ATTTTACCAT	    0.964599	-38
AATGCACGCCAATTTTTATAAAGGATAAAA	2	68	1	AATTTTTATA	    0.790778	-21
          TTTTTATCCTTTATAAAAAT	2	79	0	TTTTTATCCT	    0.955434	-10
          **********

Masking position 5
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

CGGATGAAAATTTCAATGTTT          	1	1	0	TTTCAAGTTT	    0.996913	-35
TATTAAAAATTTTCAACATTTTATCTTATTT	2	21	1	TTTCAAATTT	    0.991671	-68
TTTATCTTATTTTTAAAGTTTATGGTAAAAT	2	40	1	TTTTAAGTTT	     0.99526	-49
         TTTTTATCCTTTATAAAAATTG	2	77	0	TTTTATCTTT	    0.978335	-12
          ****** ****

Masking position 5
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