AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i135_Transmembrane_Transport_9_pyro_reg_300.orf -o135_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	RPH00266	114	Pyrococcus_OT3

Motif number 1

AGTTGTCCCTCAATTCATATATCATTTCTG	1	18	1	CAATTCATAT	     0.97735	-97
ATTCATATATCATTTCTGGTCATTTCTGAT	1	30	1	CATTTCTGGT	    0.997866	-85
CATTTCTGGTCATTTCTGATCAGTTCGAGA	1	40	1	CATTTCTGAT	    0.996704	-75
ATCATATATCCAATTCCGGTGATTTT    	1	99	1	CAATTCCGGT	    0.997463	-16
          **********

Masking position 5
Map Score:   7.75494

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 23
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

ACCAGAAATGATATATGAATTGAGGGACAA	1	20	0	ATATATGAAT	    0.981931	-95
CGAAGCGCTTTTATATGAATGAATCATATA	1	77	1	TTATATGAAT	    0.993002	-38
CCGGAATTGGATATATGATTCATTCATATA	1	88	0	ATATATGATT	    0.993002	-27
          **********

Masking position 5
Map Score:   5.9917

Number of sites scoring better than the average of aligned sites = 8
Number in coding regions = 7
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


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