AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i177_cobalamin_biosynthesis_2_mthe_reg_100.orf -o177_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	RTH01626	132	M.thermo

Motif number 1

GGCCGACAGAAGATGATGGAGTTTAGAGAC	1	15	0	AGATGATGGA	    0.997852	-118
TATCTTACGGGGCTGATGCATTCCATCAGC	1	51	1	GGCTGATGCA	    0.997538	-82
AAATGACCGGAGCTGATGGAATGCATCAGC	1	62	0	AGCTGATGGA	    0.998596	-71
          GTATGATGGTCAGCGCTCAA	1	123	0	GTATGATGGT	    0.986227	-10
          **********

Masking position 6
Map Score:   7.93426

Number of sites scoring better than the average of aligned sites = 192
Number in coding regions = 179
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

TCATCTTCTGTCGGCCGCAGGGTATCTTAC	1	29	1	TCGGCCGCAG	    0.992766	-104
CAGGGTATCTTACGGGGCTGATGCATTCCA	1	46	1	TACGGGGCTG	    0.994712	-87
GAGAAAAATGACCGGAGCTGATGGAATGCA	1	67	0	ACCGGAGCTG	    0.992846	-66
TTTAAATAAATTGAGCGCTGACCATCATAC	1	113	1	TTGAGCGCTG	    0.987229	-20
          **********

Masking position 7
Map Score:   1.8176

Number of sites scoring better than the average of aligned sites = 227
Number in coding regions = 207
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

          **********

No masking
Map Score:   5.21701e-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:   5.21701e-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:   5.21701e-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