AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i257_hsp60_hsp10_mthe_reg_100.orf -o257_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	RTH01549	140	M.thermo

Motif number 1

AATAAATAATTGACTGGAGATGGTGGCGTG	1	14	0	TGACTGGAGA	    0.994068	-127
TGGATTCCTCTTCCTGGAAATAAATAATTG	1	32	0	TTCCTGGAAA	    0.972769	-109
TTCTGCAGACTTACTGGAAGAGTTGCAGAT	1	61	0	TTACTGGAAG	    0.985961	-80
GGGTTTCTGGTTTCTGCAGACTTACTGGAA	1	72	0	TTTCTGCAGA	    0.985786	-69
CTATAAATAATTTGTGTAGAAGATCCTGTG	1	101	0	TTTGTGTAGA	    0.964543	-40
          **********

Masking position 5
Map Score:   5.888

Number of sites scoring better than the average of aligned sites = 256
Number in coding regions = 212
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 2

TAATTGACTGGAGATGGTGGCGTGTGG   	1	8	0	GAGATGGTGG	    0.984134	-133
CTTACTGGAAGAGTTGCAGATGGATTCCTC	1	52	0	GAGTTGCAGA	    0.986516	-89
GGTTTCTGCAGACTTACTGGAAGAGTTGCA	1	64	0	GACTTACTGG	    0.982748	-77
AAGATCCTGTGGGTTTCTGGTTTCTGCAGA	1	82	0	GGGTTTCTGG	    0.997388	-59
  TTATCCATGGGTTTAAGGTTCTATAAAT	1	123	0	GGGTTTAAGG	    0.985308	-18
          **********

Masking position 5
Map Score:   5.31214

Number of sites scoring better than the average of aligned sites = 646
Number in coding regions = 611
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 3

ATCTCCAGTCAATTATTTATTTCCAGGAAG	1	23	1	AATTATTTAT	    0.992695	-118
CTTCTACACAAATTATTTATAGAACCTTAA	1	109	1	AATTATTTAT	    0.992695	-32
          **********

Masking position 5
Map Score:   2.04472

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:   7.34864e-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:   7.34864e-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 6

          **********

No masking
Map Score:   7.34864e-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