AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i183_thiamin_biosynthesis_mthe_reg_100.orf -o183_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTH02079	84	M.thermo
#2	RTH01298	50	M.thermo

Motif number 1

TACTCCTACTTAAAATATACTCCATTAGAG	1	18	0	TAAAATATAC	    0.981223	-67
GTAGGAGTAATAAAATAATTTTTGATTAGT	1	39	1	TAAAATAATT	    0.987841	-46
ATCTCCAGGGAAAAATATATTT        	1	73	1	AAAAATATAT	    0.960216	-12
      TGAGTAAAATAATTCCGGGTCACG	2	5	1	TAAAATAATT	    0.987841	-46
          **********

Masking position 5
Map Score:   5.54383

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 15
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

          **********

No masking
Map Score:   1.09013e-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 3

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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