AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00450_tpal_reg_100.orf -o00450_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	TP0794	53	S-adenosylmethionine synthetase (metK)
#2	TP0798	32	methionyl-tRNA synthetase (metG)

Motif number 1

         CCTTTACTCCTAGGTTCAGTG	1	2	1	CTTTACTCCT	    0.999077	-52
        CACTGTACTCCTCGATTCAAAA	1	42	0	CTGTACTCCT	    0.998901	-12
       AGCGTTTCCTACTCTGATTTAAA	2	20	0	GTTTCCTACT	    0.994519	-13
          **********

Masking position 4
Map Score:   5.09101

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 11
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

CAGCTCACTGAACCTAGGAGTAAAGG    	1	7	0	AACCTAGGAG	    0.867773	-47
CGTAATTTTGAATCGAGGAGTACAGTG   	1	37	1	AATCGAGGAG	    0.996897	-17
TCTTGTTTAAATCAGAGTAGGAAACGCT  	2	15	1	ATCAGAGTAG	    0.991114	-18
          **********

Masking position 6
Map Score:   3.86952

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 56
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

          **********

No masking
Map Score:   -7.57276e-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:   -7.57276e-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:   -7.57276e-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