AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_pyro_reg_300.orf -o047_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	RPH00713	51	Pyrococcus_OT3
#2	RPH00710	47	Pyrococcus_OT3

Motif number 1

TTCAGCTTAGCCCTTGTCTCTTCA      	1	5	0	CCCTTGTCTC	    0.998912	-47
CTGTTTCGAACTCTTCTTTCAGCTTAGCCC	1	22	0	CTCTTCTTTC	    0.995427	-30
   AGGCTCACCCCTGTTTCGAACTCTTCT	1	35	0	CCCCTGTTTC	    0.998912	-17
          **********

Masking position 5
Map Score:   5.3196

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 8
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

        TGAAGAGACAAGGGCTAAGCTG	1	3	1	AAGAGACAAG	    0.975405	-49
GACAAGGGCTAAGCTGAAAGAAGAGTTCGA	1	17	1	AAGCTGAAAG	    0.985903	-35
CAATGGATAAAAACTCCATGCTATTTATAT	2	15	1	AAACTCCATG	    0.986697	-33
        TTAACCACCAAGCATATAAATA	2	36	0	AACCACCAAG	    0.993694	-12
          **********

Masking position 8
Map Score:   1.2765

Number of sites scoring better than the average of aligned sites = 373
Number in coding regions = 341
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

GAAGAGACAAGGGCTAAGCTGAAAGAAGAG	1	12	1	GGGCTAAGCT	    0.986582	-40
GTTCGAAACAGGGGTGAGCCT         	1	41	1	GGGGTGAGCC	    0.981341	-11
          **********

Masking position 5
Map Score:   0.762967

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 9
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   -4.67335e-15

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:   -4.67335e-15

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 6

          **********

No masking
Map Score:   -4.67335e-15

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