AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i254_soj_mthe_reg_100.orf -o254_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	RTH01260	198	M.thermo

Motif number 1

TTTTTTAATCTGATAACTTATAACTTATCA	1	16	1	TGATAACTTA	    0.997201	-183
AAAGTATATGTGATAAGTTATAAGTTATCA	1	26	0	TGATAAGTTA	    0.992662	-173
AAGTTATAATTTATAACTTATAAAGTATAT	1	47	0	TTATAACTTA	    0.993813	-152
AAGTTATAAATTATAACTTAGATCCAGCAG	1	58	1	TTATAACTTA	    0.993813	-141
AAAGTGCTGCTGATAGATTAACGGCTGTTG	1	148	0	TGATAGATTA	    0.975193	-51
          **********

Masking position 5
Map Score:   11.7544

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 5
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

ATAAACCAGAAGGGTGGCTGTGGAAAGACA	1	117	1	AGGGTGGCTG	    0.996604	-82
TGATAGATTAACGGCTGTTGTTGTCTTTCC	1	138	0	ACGGCTGTTG	    0.994696	-61
CAAGGAGGAAAGTGCTGCTGATAGATTAAC	1	156	0	AGTGCTGCTG	    0.994917	-43
CCTTGACAGGAGGGTTCTTGTAATCGAC  	1	181	1	AGGGTTCTTG	    0.991819	-18
          **********

Masking position 9
Map Score:   4.57518

Number of sites scoring better than the average of aligned sites = 368
Number in coding regions = 352
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

GAAATTACCTCTCCCATCTCATCACCTGCT	1	83	0	CTCCCATCTC	    0.982874	-116
TTTCCACAGCCACCCTTCTGGTTTATGATT	1	113	0	CACCCTTCTG	    0.997245	-86
CTATCAGCAGCACTTTCCTCCTTGACAGGA	1	162	1	CACTTTCCTC	    0.972895	-37
CGATTACAAGAACCCTCCTGTCAAGGAGGA	1	177	0	AACCCTCCTG	    0.993036	-22
          **********

Masking position 9
Map Score:   2.60052

Number of sites scoring better than the average of aligned sites = 679
Number in coding regions = 644
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 4

          **********

No masking
Map Score:   -2.59896e-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:   -2.59896e-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 6

          **********

No masking
Map Score:   -2.59896e-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