AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i152_Xanthine_Dehydrogenase_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	Rv0375c	75	hypothetical protein Rv0375c
#2	Rv0376c	48	hypothetical protein Rv0376c

Motif number 1

GCCCTTTTCGCGGGCGGCCGACACTGGGGCG	1	12	1	CGGCGGCCGA	    0.928572	-64
CAGGTACTTGCATGCGCCCCAGTGTCGGCCG	1	26	0	CAGCGCCCCA	     0.99809	-50
CGTTCGTATTCGAAAGGCCCAGGTACTTGCA	1	45	0	CGAAGGCCCA	    0.991288	-31
CTTTCGAATACGAACGTGCCACCAGC     	1	60	1	CGACGTGCCA	    0.997922	-16
GCACTTCACGCACGCTTCCCAAAGTAGGCTT	2	17	0	CAGCTTCCCA	    0.996505	-32
GCGTGCGTGAAGTGCTTGCCGAGCTG     	2	33	1	AGGCTTGCCG	    0.963163	-16
          ** ********

Masking position 9
Map Score:   9.94124

Number of sites scoring better than the average of aligned sites = 5480
Number in coding regions = 5075
Number in noncoding regions = 405
Number of orfs with sites within 600 bp upstream = 330
Fraction of orfs with sites within 600 bp upstream = 0.0530035


Motif number 2

 CGCCCTTTTCGCGGGCGGCCGACACTGGG	1	10	1	CGCGGGCGGC	    0.995314	-66
CCCAGGTACTTGCATGCGCCCCAGTGTCGG	1	29	0	TGCATGCGCC	    0.982803	-47
CTTTCGAATACGAACGTGCCACCAGC    	1	60	1	CGAACGTGCC	    0.811584	-16
CGCTTCCCAAAGTAGGCTTCAGTGC     	2	6	0	AGTAGGCTTC	    0.964253	-43
AAGCACTTCACGCACGCTTCCCAAAGTAGG	2	20	0	CGCACGCTTC	    0.995102	-29
          **********

Masking position 6
Map Score:   4.64367

Number of sites scoring better than the average of aligned sites = 7212
Number in coding regions = 6767
Number in noncoding regions = 445
Number of orfs with sites within 600 bp upstream = 384
Fraction of orfs with sites within 600 bp upstream = 0.0616768


Motif number 3

CGGCCGCCCGCGAAAAGGGCG         	1	2	0	CGAAAAGGGC	    0.997976	-74
CGTTCGTATTCGAAAGGCCCAGGTACTTGC	1	46	0	CGAAAGGCCC	    0.995572	-30
GGGAAGCGTGCGTGAAGTGCTTGCCGAGCT	2	28	1	CGTGAAGTGC	    0.993734	-21
          **********

Masking position 5
Map Score:   1.40771

Number of sites scoring better than the average of aligned sites = 118
Number in coding regions = 99
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


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


Motif number 6

          **********

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