AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i346_weak7_aquae_reg_100.orf -o346_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -x5 -e 
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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAA01493	138	Aquifex_aeolicus

Motif number 1

TCGACTCCGCCCTGGGCCACCA        	1	3	0	CCTGGGCCAC	    0.994005	-136
CGGGGTGTCGGCGGTTCGACTCCGCCCTGG	1	18	0	GCGGTTCGAC	    0.978634	-121
CGGCTGAAAACCGGGGTGTCGGCGGTTCGA	1	29	0	CCGGGGTGTC	    0.996813	-110
CGGTTTTCAGCCGGGTGCTCTACCACCTGA	1	46	1	CCGGGTGCTC	    0.998748	-93
GTCGTAAGGCCCGGTAGCTCAGGTGGTAGA	1	64	0	CCGGTAGCTC	    0.994816	-75
          **********

Masking position 4
Map Score:   7.26061

Number of sites scoring better than the average of aligned sites = 99
Number in coding regions = 82
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

GGTGCTCTACCACCTGAGCTACCGGGCCTT	1	59	1	CACCTGAGCT	    0.998407	-80
TAAATTATGACACTTGAACTCAAAGGGAAT	1	114	0	CACTTGAACT	    0.996655	-25
          **********

Masking position 5
Map Score:   0.769067

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 6
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

          **********

No masking
Map Score:   -9.70439e-14

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:   -9.70439e-14

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:   -9.70439e-14

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