AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i089_mjan_pyro_300.orf -o089_mjan_pyro_300.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	RPH00370	136	Pyrococcus_OT3

Motif number 1

AATAGTATAAAGTCGTATAATCTATCTAAG	1	22	0	AGTCGTATAA	    0.987727	-115
AATATATTTAAATAGTATAAAGTCGTATAA	1	32	0	AATAGTATAA	    0.989313	-105
ATTTTGCTATCTTAGTATCAAATATATTTA	1	52	0	CTTAGTATCA	    0.979368	-85
AGATAGCAAAATTTATATAATAGAACATTA	1	70	1	ATTTATATAA	    0.946397	-67
ATAATAGAACATTAGTATAAATCTTTAAGG	1	86	1	ATTAGTATAA	    0.995742	-51
          **********

Masking position 6
Map Score:   6.77743

Number of sites scoring better than the average of aligned sites = 90
Number in coding regions = 66
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

    GCTGCTCCCTCCTTAGATAGATTATA	1	7	1	CCCTCCTTAG	    0.995097	-130
TTTATATAATAGAACATTAGTATAAATCTT	1	81	1	AGAACATTAG	    0.957477	-56
TATGGATGGGAGATCCTTAAAGATTTATAC	1	100	0	AGATCCTTAA	    0.982778	-37
TAAGGATCTCCCATCCATAGTCATGAGGTG	1	111	1	CCATCCATAG	    0.990536	-26
          **********

Masking position 8
Map Score:   2.17182

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 83
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


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