AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i038_Galactose_Metabolism__pyro_reg_300.orf -o038_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00721	54	Pyrococcus_OT3
#2	RPH00717	92	Pyrococcus_OT3

Motif number 1

TTTGACTATTATAGTCAAAAC         	2	2	0	ATAGTCAAAA	    0.997623	-91
TTTGACTATAATAGTCAAAAACTTAATAAA	2	13	1	ATAGTCAAAA	    0.997623	-80
GCTCACTCACATTGTCGAAAATTTTATTAA	2	35	0	ATTGTCGAAA	    0.992876	-58
GTAATGTTGTAGAGTCTAAAAATCTTCAAG	2	64	0	AGAGTCTAAA	    0.992892	-29
          **********

Masking position 5
Map Score:   9.17926

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 18
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

CACCAACCTTAAAATTGTTTAGTTCAAAGTAT	1	28	0	AATTGTTTAG	    0.991952	-27
AAACAATTTTAAGGTTGGTGAGAGT       	1	40	1	AATTGGTGAG	    0.998112	-15
CATTGTCGAAAATTTTATTAAGTTTTTGACTA	2	24	0	AATTATTAAG	    0.982048	-69
AATTTTCGACAATGTGAGTGAGCTTGAAGATT	2	42	1	AATGAGTGAG	    0.990628	-51
AAAGATCAGTAATGTTGTAGAGTCTAAAAATC	2	70	0	AATTGTAGAG	    0.993327	-23
          **  ********

Masking position 5
Map Score:   6.12752

Number of sites scoring better than the average of aligned sites = 184
Number in coding regions = 177
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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:   2.15595e-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