AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i299_mixed14_mthe_reg_100.orf -o299_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	RTH02082	137	M.thermo

Motif number 1

TCTCTTATATGGACCTATATATAAAGGACC	1	33	1	GGACCTATAT	     0.98026	-105
TATATATAAAGGACCCCCATATAATTAATT	1	48	1	GGACCCCCAT	    0.999176	-90
CGCTACAGCGGGACCTCCAGTGGCTGACTG	1	109	1	GGACCTCCAG	    0.999176	-29
        TGAGTCCCCCAGTCAGCCACTG	1	126	0	AGTCCCCCAG	    0.994676	-12
          **********

Masking position 9
Map Score:   7.50713

Number of sites scoring better than the average of aligned sites = 364
Number in coding regions = 347
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

TTAATTATATGGGGGTCCTTTATATATAGG	1	46	0	GGGGGTCCTT	    0.990451	-92
GTCAGCCACTGGAGGTCCCGCTGTAGCGAT	1	107	0	GGAGGTCCCG	    0.958186	-31
GTGGCTGACTGGGGGACTCA          	1	128	1	GGGGGACTCA	    0.955511	-10
          **********

Masking position 5
Map Score:   2.38361

Number of sites scoring better than the average of aligned sites = 189
Number in coding regions = 175
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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 5

          **********

No masking
Map Score:   2.15595e-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