AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i135_mjan_pyro_100.orf -o135_mjan_pyro_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 =  	0.37
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00266	114	Pyrococcus_OT3

Motif number 1

AGTTGTCCCTCAATTCATATATCATTTCTG	1	18	1	CAATTCATAT	    0.976591	-97
ATTCATATATCATTTCTGGTCATTTCTGAT	1	30	1	CATTTCTGGT	    0.997793	-85
CATTTCTGGTCATTTCTGATCAGTTCGAGA	1	40	1	CATTTCTGAT	    0.996591	-75
ATCATATATCCAATTCCGGTGATTTT    	1	99	1	CAATTCCGGT	    0.997376	-16
          **********

Masking position 5
Map Score:   7.75494

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 12
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

ACCAGAAATGATATATGAATTGAGGGACAA	1	20	0	ATATATGAAT	    0.982914	-95
CGAAGCGCTTTTATATGAATGAATCATATA	1	77	1	TTATATGAAT	    0.992591	-38
CCGGAATTGGATATATGATTCATTCATATA	1	88	0	ATATATGATT	    0.992591	-27
          **********

Masking position 5
Map Score:   5.9917

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 12
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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