AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_Mannose_Metabolism_mthe_reg_100.orf -o039_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	RTH00811	112	M.thermo

Motif number 1

          CTTTATTCATTGAGGTAATG	1	1	1	CTTTATTCAT	    0.979074	-112
CCGTATGAATTTTTAATCACATTACCTCAA	1	20	0	TTTTAATCAC	     0.98877	-93
GAAGGTCTGACTTTATCCATATTGGTGATT	1	53	1	CTTTATCCAT	    0.980573	-60
ATATTTGAATTGTTAATCACCAATATGGAT	1	67	0	TGTTAATCAC	    0.975417	-46
ACAATTCAAATATTATCCAGTGAATGGGGC	1	84	1	TATTATCCAG	    0.966546	-29
          TTTTTAACAGCCCCATTCAC	1	103	0	TTTTTAACAG	    0.894999	-10
          **********

Masking position 4
Map Score:   6.35146

Number of sites scoring better than the average of aligned sites = 161
Number in coding regions = 109
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 2

TTTATTCATTGAGGTAATGTGATTAAAAAT	1	12	1	GAGGTAATGT	    0.991876	-101
AATTCATACGGAGTGAAGGTCTGACTTTAT	1	39	1	GAGTGAAGGT	    0.997002	-74
AAATATTATCCAGTGAATGGGGCTGTTAAA	1	91	1	CAGTGAATGG	    0.994233	-22
          **********

Masking position 6
Map Score:   1.6458

Number of sites scoring better than the average of aligned sites = 70
Number in coding regions = 64
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

ATCACATTACCTCAATGAATAAAG      	1	5	0	CTCAATGAAT	    0.986697	-108
GACCTTCACTCCGTATGAATTTTTAATCAC	1	30	0	CCGTATGAAT	    0.989103	-83
TGTTAATCACCAATATGGATAAAGTCAGAC	1	57	0	CAATATGGAT	    0.946895	-56
TCACTGGATAATATTTGAATTGTTAATCAC	1	77	0	ATATTTGAAT	    0.874271	-36
TCAAATATTATCCAGTGAATGGGGCTGTTA	1	89	1	TCCAGTGAAT	    0.945096	-24
          **********

Masking position 6
Map Score:   0.55827

Number of sites scoring better than the average of aligned sites = 429
Number in coding regions = 391
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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 6

          **********

No masking
Map Score:   1.3033e-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