AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i324_mjan_pyro_100.orf -o324_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	RPH00371	136	Pyrococcus_OT3

Motif number 1

ATAATAGAACATTAGTATAAATCTTTAAGG	1	42	0	ATTAGTATAA	    0.995006	-95
AGATAGCAAAATTTATATAATAGAACATTA	1	58	0	ATTTATATAA	    0.937732	-79
ATTTTGCTATCTTAGTATCAAATATATTTA	1	76	1	CTTAGTATCA	    0.975867	-61
AATATATTTAAATAGTATAAAGTCGTATAA	1	96	1	AATAGTATAA	    0.987479	-41
AATAGTATAAAGTCGTATAATCTATCTAAG	1	106	1	AGTCGTATAA	    0.985624	-31
          **********

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

TAAGGATCTCCCATCCATAGTCATGAGGTG	1	17	0	CCATCCATAG	      0.9903	-120
TATGGATGGGAGATCCTTAAAGATTTATAC	1	28	1	AGATCCTTAA	    0.981959	-109
TTTATATAATAGAACATTAGTATAAATCTT	1	47	0	AGAACATTAG	     0.95552	-90
    GCTGCTCCCTCCTTAGATAGATTATA	1	121	0	CCCTCCTTAG	    0.994867	-16
          **********

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