AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i014_Glycolysis_1_mthe_reg_100.orf -o014_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	RTH01963	195	M.thermo

Motif number 1

AATTTAATTTTTCACTGGTTTAACATCATC	1	23	1	TTCACTGGTT	    0.945252	-173
CCCCACATAGTGAAGGTGTTAAATGCAGAA	1	61	0	TGAAGGTGTT	    0.969736	-135
TATGTGGGGATGCGCTGGATATTACAGGCA	1	82	1	TGCGCTGGAT	    0.983249	-114
CGGGAGTTGTTGAAGGGGTTCATGAATGAA	1	114	0	TGAAGGGGTT	    0.995195	-82
GTGACATCCGTGCGGGAGTTGTTGAAGGGG	1	126	0	TGCGGGAGTT	    0.979048	-70
ATAGTATGGTTGAGGTGTATTATAAAATAT	1	159	0	TGAGGTGTAT	    0.923453	-37
        GATTAATGGGATATCTCATAGT	1	184	0	TTAATGGGAT	    0.892645	-12
          **********

Masking position 1
Map Score:   6.44541

Number of sites scoring better than the average of aligned sites = 2029
Number in coding regions = 1889
Number in noncoding regions = 140
Number of orfs with sites within 600 bp upstream = 125
Fraction of orfs with sites within 600 bp upstream = 0.0200771


Motif number 2

ATAGTGAAGGTGTTAAATGCAGAAAGCTGT	1	55	0	TGTTAAATGC	    0.959328	-141
TGAATTTGCCTGTAATATCCAGCGCATCCC	1	88	0	TGTAATATCC	    0.993075	-108
TAAAATATGCTGTGACATCCGTGCGGGAGT	1	137	0	TGTGACATCC	     0.99283	-59
AGGTGTATTATAAAATATGCTGTGACATCC	1	147	0	TAAAATATGC	    0.933585	-49
AACCATACTATGAGATATCCCATTAATC  	1	178	1	TGAGATATCC	    0.986583	-18
          **********

Masking position 5
Map Score:   5.6949

Number of sites scoring better than the average of aligned sites = 147
Number in coding regions = 130
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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:   -3.30951e-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