AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00520_ctra_reg_100.orf -o00520_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	glgX	117	Glycogen Hydrolase (debranching)

Motif number 1

TCATACAACAAAAGGAAGAGGGTCTCTCTT	1	22	1	AAAGGAAGAG	    0.999449	-96
CTTAAACACAAAAGGAAGAGAGACCCTCTT	1	37	0	AAAGGAAGAG	    0.999449	-81
CTAACCGAAGAAATGAAGAGAAGAGAGGGG	1	67	0	AAATGAAGAG	    0.998498	-51
          **********

Masking position 6
Map Score:   9.96121

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 19
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 2

TGCTATCATACAACAAAAGGAAGAGGGTCT	1	17	1	CAACAAAAGG	    0.975309	-101
AGGGGCTTAAACACAAAAGGAAGAGAGACC	1	42	0	ACACAAAAGG	    0.990013	-76
AGAAATGAAGAGAAGAGAGGGGCTTAAACA	1	59	0	AGAAGAGAGG	    0.989501	-59
AAAATCTAACCGAAGAAATGAAGAGAAGAG	1	72	0	CGAAGAAATG	    0.977421	-46
AAAAACTAGAACAAGTAAGTTTAATAAAAA	1	98	0	ACAAGTAAGT	    0.924148	-20
          **********

Masking position 3
Map Score:   2.46168

Number of sites scoring better than the average of aligned sites = 315
Number in coding regions = 315
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

AACAAAAGGAAGAGGGTCTCTCTTCCTTTT	1	28	1	AGAGGGTCTC	    0.998596	-90
TGAAGAGAAGAGAGGGGCTTAAACACAAAA	1	54	0	AGAGGGGCTT	    0.998587	-64
          **********

Masking position 3
Map Score:   1.54483

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 11
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:   -2.59896e-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:   -2.59896e-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 6

          **********

No masking
Map Score:   -2.59896e-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