AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00053_ctra_reg_100.orf -o00053_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 =  	0.41
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	ubiA	111	4-hydroxybenzoate octaphenyltransferase

Motif number 1

AAGTTCGTTTCAACGTACAGATAA      	1	5	0	CAACGTACAG	    0.968764	-107
CTGTACGTTGAAACGAACTTCAACGTACTT	1	15	1	AAACGAACTT	    0.993774	-97
AAACGAACTTCAACGTACTTTTTTCAGCAA	1	25	1	CAACGTACTT	    0.994258	-87
TTTCAGCAAGAAAAGCTCCTTCTGATTACA	1	46	1	AAAAGCTCCT	    0.955975	-66
TTATAGGTGTAAAAGATCTTGTATTGTAAT	1	70	0	AAAAGATCTT	    0.977163	-42
          **********

Masking position 3
Map Score:   5.41129

Number of sites scoring better than the average of aligned sites = 111
Number in coding regions = 110
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 2

TTCGTTTCAACGTACAGATAA         	1	2	0	CGTACAGATA	    0.986643	-110
CGAACTTCAACGTACTTTTTTCAGCAAGAA	1	28	1	CGTACTTTTT	    0.949775	-84
AAGAAAAGCTCCTTCTGATTACAATACAAG	1	53	1	CCTTCTGATT	    0.992377	-59
      AAACCCTTCGAATATTATGGGATT	1	98	0	CCTTCGAATA	    0.974224	-14
          **********

Masking position 3
Map Score:   0.526624

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 37
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 3

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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:   -1.17788e-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