AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00471_ctra_reg_100.orf -o00471_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	mraY	145	Muramoyl-Pentapeptide Transferase

Motif number 1

GTAAAAGATCAGAATTTCTTTTTAGAATAG	1	11	1	AGAATTTCTT	    0.993952	-135
AGTCGCTGTAAGATGCTCTTTTTAACTTGC	1	57	1	AGATGCTCTT	    0.991358	-89
TTTAAGATAGAGAATTTCTTATAGGAGCTT	1	103	1	AGAATTTCTT	    0.993952	-43
TTTTATTATGGGAAGCTCCTATAAGAAATT	1	115	0	GGAAGCTCCT	    0.942498	-31
          **********

Masking position 7
Map Score:   5.84474

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

AGCGACTTGAAAGTTAACTATTTCTATTCT	1	34	0	AAGTTAACTA	    0.800342	-112
TTCAAAAGGCAAGTTAAAAAGAGCATCTTA	1	65	0	AAGTTAAAAA	    0.983998	-81
TCTTAAACTTAAGCTTTCAAAAGGCAAGTT	1	80	0	AAGCTTTCAA	    0.959172	-66
TTGAAAGCTTAAGTTTAAGATAGAGAATTT	1	90	1	AAGTTTAAGA	    0.982077	-56
          **********

Masking position 5
Map Score:   2.16053

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 44
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:   2.43208e-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 4

          **********

No masking
Map Score:   2.43208e-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:   2.43208e-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