AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i277_hypothetical21_pyro_reg_300.orf -o277_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	RPH00744	36	Pyrococcus_OT3
#2	RPH00015	89	Pyrococcus_OT3

Motif number 1

    CGGGAAATTGTATAAGGGAGAGAATAT	1	7	1	ATTTATAAGG	    0.998185	-30
TAAGGGAGAGAATATATAAGGTTG       	1	23	1	AATTATAAGG	    0.995426	-14
TATTCAAAAAATTTTATAATGTTCCCAAAGA	2	24	0	ATTTATAATG	    0.992809	-66
AGAAATCCCTATTACATAGGGATTTTAAACT	2	59	0	ATTCATAGGG	    0.994745	-31
          *** *******

Masking position 6
Map Score:   7.02481

Number of sites scoring better than the average of aligned sites = 52
Number in coding regions = 43
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

AAAATAGTTTAAAATCCCTATGTAATAGGG	2	54	1	AAAATCCCTA	    0.997559	-36
CTGTCACCTAGAAATCCCTATTACATAGGG	2	69	0	GAAATCCCTA	    0.998345	-21
          **********

Masking position 5
Map Score:   2.21925

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 5
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

          **********

No masking
Map Score:   -1.82309e-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:   -1.82309e-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:   -1.82309e-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