AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i324_mixed9_pyro_reg_100.orf -o324_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	RPH00371	136	Pyrococcus_OT3

Motif number 1

CCTTAAAGATTTATACTAATGTTCTATTAT	1	42	1	TTATACTAAT	    0.995638	-95
TAATGTTCTATTATATAAATTTTGCTATCT	1	58	1	TTATATAAAT	    0.945159	-79
TAAATATATTTGATACTAAGATAGCAAAAT	1	76	0	TGATACTAAG	    0.978869	-61
TTATACGACTTTATACTATTTAAATATATT	1	96	0	TTATACTATT	    0.989053	-41
CTTAGATAGATTATACGACTTTATACTATT	1	106	0	TTATACGACT	    0.987428	-31
          **********

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

CACCTCATGACTATGGATGGGAGATCCTTA	1	17	1	CTATGGATGG	    0.990536	-120
GTATAAATCTTTAAGGATCTCCCATCCATA	1	28	0	TTAAGGATCT	    0.982778	-109
AAGATTTATACTAATGTTCTATTATATAAA	1	47	1	CTAATGTTCT	    0.957477	-90
TATAATCTATCTAAGGAGGGAGCAGC    	1	121	1	CTAAGGAGGG	    0.995097	-16
          **********

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