AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i325_not_clear_mthe_reg_300.orf -o325_mthe_300.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	RTH00986	172	M.thermo
#2	RTH01119	67	M.thermo

Motif number 1

TCCGGTGCTATCCATAAATGAACTGATTAC	1	21	1	TCCATAAATG	    0.956934	-152
TGATTACTGGTATATGGATGTTCATTTAAA	1	44	1	TATATGGATG	    0.953022	-129
GAACTCAAAATATTTAAATGAACATCCATA	1	56	0	TATTTAAATG	    0.936834	-117
TGCTTATGATTCTTTTGATGTCACACTGAA	1	107	0	TCTTTTGATG	    0.965872	-66
TCTTATTAATTCTGTAGGTGGGTGCTTATG	1	129	0	TCTGTAGGTG	    0.978393	-44
ATCACGATCATATATATATGGAGGAGGCCA	2	18	0	TATATATATG	    0.919093	-50
GATAAATAGATCTTTAAGTGTAATGGTGGT	2	45	1	TCTTTAAGTG	    0.979535	-23
          **********

Masking position 5
Map Score:   7.40012

Number of sites scoring better than the average of aligned sites = 110
Number in coding regions = 85
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

TTAAATATTTTGAGTTCACAGAACCACTGC	1	69	1	TGAGTTCACA	     0.98308	-104
ATGTCACACTGAAGTTCACATGCAGTGGTT	1	90	0	GAAGTTCACA	    0.985938	-83
ATGATTCTTTTGATGTCACACTGAAGTTCA	1	102	0	TGATGTCACA	    0.982719	-71
TATATATGGAGGAGGCCAAAGGATT     	2	6	0	GGAGGCCAAA	    0.981026	-62
          **********

Masking position 3
Map Score:   2.64003

Number of sites scoring better than the average of aligned sites = 267
Number in coding regions = 256
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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:   -1.75204e-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