AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i089_Sugar_Transport_1_pyro_reg_100.orf -o089_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	RPH00370	136	Pyrococcus_OT3

Motif number 1

AATAGTATAAAGTCGTATAATCTATCTAAG	1	22	0	AGTCGTATAA	    0.986878	-115
AATATATTTAAATAGTATAAAGTCGTATAA	1	32	0	AATAGTATAA	    0.988573	-105
ATTTTGCTATCTTAGTATCAAATATATTTA	1	52	0	CTTAGTATCA	    0.977954	-85
AGATAGCAAAATTTATATAATAGAACATTA	1	70	1	ATTTATATAA	    0.942887	-67
ATAATAGAACATTAGTATAAATCTTTAAGG	1	86	1	ATTAGTATAA	    0.995445	-51
          **********

Masking position 6
Map Score:   6.77743

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 29
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

    GCTGCTCCCTCCTTAGATAGATTATA	1	7	1	CCCTCCTTAG	    0.995135	-130
TTTATATAATAGAACATTAGTATAAATCTT	1	81	1	AGAACATTAG	    0.957801	-56
TATGGATGGGAGATCCTTAAAGATTTATAC	1	100	0	AGATCCTTAA	    0.982913	-37
TAAGGATCTCCCATCCATAGTCATGAGGTG	1	111	1	CCATCCATAG	    0.990575	-26
          **********

Masking position 8
Map Score:   2.17182

Number of sites scoring better than the average of aligned sites = 254
Number in coding regions = 246
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


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