AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_aquae_reg_300.orf -o012_aquae_300.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	RAA01502	110	Aquifex_aeolicus

Motif number 1

GGGACAGAAGCCGCCTGTGTAAGCAGTTTT	1	39	0	CCGCCTGTGT	    0.993833	-72
CGGCTTCTGTCCCCGTATCATAGATACGCG	1	56	1	CCCCGTATCA	    0.995258	-55
CGGGCTAAAACCGCGTATCTATGATACGGG	1	67	0	CCGCGTATCT	    0.999297	-44
CGGTTTTAGCCCGCGGATTTACTATAAAAT	1	84	1	CCGCGGATTT	    0.996739	-27
          **********

Masking position 8
Map Score:   6.43443

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 45
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

GCCGCCTGTGTAAGCAGTTTTTTAAAATGA	1	30	0	TAAGCAGTTT	    0.982207	-81
ACTGCTTACACAGGCGGCTTCTGTCCCCGT	1	42	1	CAGGCGGCTT	    0.990085	-69
GTATCATAGATACGCGGTTTTAGCCCGCGG	1	70	1	TACGCGGTTT	    0.995788	-41
TTATAGTAAATCCGCGGGCTAAAACCGCGT	1	81	0	TCCGCGGGCT	    0.994236	-30
          **********

Masking position 10
Map Score:   3.59632

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 84
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

          **********

No masking
Map Score:   -1.46782e-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:   -1.46782e-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:   -1.46782e-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