AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i038_Galactose_Metabolism__pyro_reg_100.orf -o038_pyro_100.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

         GTTTTGACTATAATAGTCAAA	2	2	1	TTTTGACTAT	    0.997676	-91
TTTATTAAGTTTTTGACTATTATAGTCAAA	2	13	0	TTTTGACTAT	    0.997676	-80
TTAATAAAATTTTCGACAATGTGAGTGAGC	2	35	1	TTTCGACAAT	    0.993032	-58
CTTGAAGATTTTTAGACTCTACAACATTAC	2	64	1	TTTAGACTCT	    0.993049	-29
          **********

Masking position 6
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

ATACTTTGAACTAAACAATTTTAAGGTTGGTG	1	28	1	CTAAACAATT	    0.991757	-27
       ACTCTCACCAACCTTAAAATTGTTT	1	40	0	CTCACCAATT	    0.998066	-15
TAGTCAAAAACTTAATAAAATTTTCGACAATG	2	24	1	CTTAATAATT	    0.981616	-69
AATCTTCAAGCTCACTCACATTGTCGAAAATT	2	42	0	CTCACTCATT	      0.9904	-51
GATTTTTAGACTCTACAACATTACTGATCTTT	2	70	1	CTCTACAATT	    0.993164	-23
          ********  **

Masking position 8
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