AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i316_mixed3_mthe_reg_300.orf -o316_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	RTH01836	222	M.thermo

Motif number 1

CTGTTCCCATTACCGGTAATATGATCTGATAGGT	1	33	1	TACCGAATGA	    0.992863	-190
CACCGTGAACTCCATGTGAGAAGAAACCTATCAG	1	58	0	TCCAGAAAGA	    0.995588	-165
CACATGGAGTTCACGGTGACATGAACATTTCACA	1	74	1	TCACGAATGA	    0.996964	-149
CGCTGTGAACTCCATGTGAAATGTTCATGTCACC	1	88	0	TCCAGAATGT	    0.990809	-135
CACATGGAGTTCACAGCGATATGAACACCATATG	1	104	1	TCACGAATGA	    0.996964	-119
TATATATCTTTCACCGGCATATCACATTCTGAGG	1	143	0	TCACGAATCA	    0.990051	-80
TTAAATGTAATCCAAGTTAAAAGAGTAGCTTCCC	1	194	1	TCCAGAAAGA	    0.995588	-29
          **** *  * ****

Masking position 9
Map Score:   15.6831

Number of sites scoring better than the average of aligned sites = 157
Number in coding regions = 144
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

TCATGTCACCGTGAACTCCATGTGAGAAGA	1	68	0	GTGAACTCCA	    0.997742	-155
TCATATCGCTGTGAACTCCATGTGAAATGT	1	98	0	GTGAACTCCA	    0.997742	-125
TCACAGCGATATGAACACCATATGATGAAC	1	114	1	ATGAACACCA	    0.993921	-109
ACACCATATGATGAACCTCAGAATGTGATA	1	128	1	ATGAACCTCA	    0.978968	-95
ATATATACTCATGTACTGAAGATTAAATGT	1	172	1	ATGTACTGAA	     0.92699	-51
TGAAGATTAAATGTAATCCAAGTTAAAAGA	1	188	1	ATGTAATCCA	    0.978114	-35
          **********

Masking position 5
Map Score:   10.7148

Number of sites scoring better than the average of aligned sites = 204
Number in coding regions = 187
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

          **********

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 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