AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i077_Lipopolysaccharide_Biosynthesis_2__pyro_reg_100.orf -o077_pyro_100.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	RPH00655	109	Pyrococcus_OT3

Motif number 1

CAAAAACTTCTTAATATCCTC         	1	2	0	TTAATATCCT	    0.924531	-108
CGCTTTTAAGTCAAAAACTTCTTAATATCC	1	13	0	TCAAAAACTT	    0.993917	-97
AGTTTTTGACTTAAAAGCGTTAGTACTAAG	1	24	1	TTAAAAGCGT	    0.975609	-86
TACAGCAATTTTAAAAAGCTAAGTATTTCA	1	65	1	TTAAAAAGCT	    0.978907	-45
AAAAATTTGATGAAATACTTAGCTTTTTAA	1	75	0	TGAAATACTT	     0.95634	-35
TGCACCTCGCTCAAAAATTTGATGAAATAC	1	87	0	TCAAAAATTT	    0.969049	-23
          **********

Masking position 4
Map Score:   5.50712

Number of sites scoring better than the average of aligned sites = 562
Number in coding regions = 448
Number in noncoding regions = 114
Number of orfs with sites within 600 bp upstream = 133
Fraction of orfs with sites within 600 bp upstream = 0.021362


Motif number 2

CTAACGCTTTTAAGTCAAAAACTTCTTAAT	1	17	0	TAAGTCAAAA	      0.9594	-93
GCGTTAGTACTAAGAGAGCAGATAATACAG	1	40	1	TAAGAGAGCA	    0.989642	-70
AGAGAGCAGATAATACAGCAATTTTAAAAA	1	52	1	TAATACAGCA	    0.993811	-58
AAAAGCTAAGTATTTCATCAAATTTTTGAG	1	78	1	TATTTCATCA	    0.958101	-32
          **********

Masking position 7
Map Score:   1.89005

Number of sites scoring better than the average of aligned sites = 168
Number in coding regions = 152
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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:   1.16119e-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