AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i018_non-Oxidative_glucose_Metabolism_mthe_reg_300.orf -o018_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	RTH00146	60	M.thermo
#2	RTH01779	194	M.thermo

Motif number 1

CAGTCCAGTCCAGTCCAGTCCATCCTATCC	2	103	0	CAGTCCAGTC	    0.999327	-92
CAGTCCAGTCCAGTCCAGTCCAGTCCAGTC	2	118	0	CAGTCCAGTC	    0.999327	-77
GATCTTTTATCAGTCCAGTCCAGTCCAGTC	2	128	0	CAGTCCAGTC	    0.999327	-67
TCTGCATTCACTGTCTACTCCAGGATCTTT	2	151	0	CTGTCTACTC	    0.987024	-44
          **********

Masking position 4
Map Score:   12.8363

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 6
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

GATAGGATGGACTGGACTGGACTGGACTGG	2	104	1	ACTGGACTGG	    0.998632	-91
ACTGGACTGGACTGGACTGGACTGGACTGG	2	114	1	ACTGGACTGG	    0.998632	-81
ACTGGACTGGACTGGACTGGACTGATAAAA	2	124	1	ACTGGACTGG	    0.998632	-71
GATAAAAGATCCTGGAGTAGACAGTGAATG	2	147	1	CCTGGAGTAG	    0.990209	-48
          **********

Masking position 6
Map Score:   12.8363

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 11
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

TGAGTTAATCCCTATGAGGAATGCCGGGAC	1	22	0	CCTATGAGGA	     0.99317	-39
AATCATCCTTTCTCTGATGAGTTAATCCCT	1	39	0	TCTCTGATGA	    0.980299	-22
TTAAACTTTTCGTATGATGATGTGGGGTGC	2	36	1	CGTATGATGA	    0.989543	-159
CATCTCTCCATGTTCGAGGATCTGCATTCA	2	171	0	TGTTCGAGGA	    0.960735	-24
          **********

Masking position 7
Map Score:   1.7399

Number of sites scoring better than the average of aligned sites = 172
Number in coding regions = 161
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

GCATTCCTCATAGGGATTAACTCATCAGAG	1	28	1	TAGGGATTAA	    0.897315	-33
CTCATCAGAGAAAGGATGATTGA       	1	48	1	AAAGGATGAT	    0.979858	-13
TAAACTTTTCGTATGATGATGTGGGGTGCG	2	37	1	GTATGATGAT	    0.843591	-158
CTGTAGGTTTAAGGGAGGAATAGGATAGGA	2	81	1	AAGGGAGGAA	    0.981198	-114
GAGGAATAGGATAGGATGGACTGGACTGGA	2	95	1	ATAGGATGGA	    0.946774	-100
CTCGAACATGGAGAGATGAAAA        	2	183	1	GAGAGATGAA	    0.967239	-12
          **********

Masking position 6
Map Score:   1.00165

Number of sites scoring better than the average of aligned sites = 1121
Number in coding regions = 1043
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 5

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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 7

          **********

No masking
Map Score:   -2.39152e-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