AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i089_Sugar_Transport_1_pyro_reg_300.orf -o089_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	RPH00370	136	Pyrococcus_OT3

Motif number 1

CTTAGATAGATTATACGACTTTATACTATT	1	22	1	TTATACGACT	     0.98803	-115
TTATACGACTTTATACTATTTAAATATATT	1	32	1	TTATACTATT	    0.989578	-105
TAAATATATTTGATACTAAGATAGCAAAAT	1	52	1	TGATACTAAG	    0.979873	-85
TAATGTTCTATTATATAAATTTTGCTATCT	1	70	0	TTATATAAAT	    0.947655	-67
CCTTAAAGATTTATACTAATGTTCTATTAT	1	86	0	TTATACTAAT	    0.995848	-51
          **********

Masking position 5
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

TATAATCTATCTAAGGAGGGAGCAGC    	1	7	0	CTAAGGAGGG	    0.995307	-130
AAGATTTATACTAATGTTCTATTATATAAA	1	81	0	CTAATGTTCT	     0.95927	-56
GTATAAATCTTTAAGGATCTCCCATCCATA	1	100	1	TTAAGGATCT	    0.983527	-37
CACCTCATGACTATGGATGGGAGATCCTTA	1	111	0	CTATGGATGG	    0.990743	-26
          **********

Masking position 3
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