AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i200_excinuclease_mthe_reg_300.orf -o200_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	RTH00601	195	M.thermo

Motif number 1

GTGGGATTATATTTCAGGGTCAACTTATAT	1	42	1	ATTTCAGGGT	    0.976131	-154
ATATATACCTTTGCCAGGATACATAAAGTT	1	68	1	TTGCCAGGAT	    0.982939	-128
AGTCTCATATCTGACAGGGTATCCCACGTG	1	106	1	CTGACAGGGT	    0.993994	-90
TGGGGGTATCATCACAGGATTATGGAACAC	1	133	0	ATCACAGGAT	    0.981812	-63
TTAAACATAAATCAGAGGATGGTAATGATA	1	174	1	ATCAGAGGAT	    0.972472	-22
          **********

Masking position 6
Map Score:   5.5611

Number of sites scoring better than the average of aligned sites = 345
Number in coding regions = 321
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 2

CCACAATAGAATGAGGTTCTTATTTTAAGT	1	16	0	ATGAGGTTCT	    0.976245	-180
TCATTCTATTGTGGGATTATATTTCAGGGT	1	32	1	GTGGGATTAT	    0.988385	-164
CCTGTCAGATATGAGACTCCAGACTCAACT	1	94	0	ATGAGACTCC	     0.96014	-102
TATGGAACACGTGGGATACCCTGTCAGATA	1	113	0	GTGGGATACC	    0.984468	-83
AACAAGTTCAGTGGGGGTATCATCACAGGA	1	144	0	GTGGGGGTAT	    0.981915	-52
          **********

Masking position 2
Map Score:   2.70592

Number of sites scoring better than the average of aligned sites = 532
Number in coding regions = 496
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

GAATGAGGTTCTTATTTTAAGTGATTT   	1	8	0	CTTATTTTAA	    0.842408	-188
CTATTGTGGGATTATATTTCAGGGTCAACT	1	37	1	ATTATATTTC	    0.947294	-159
TCAGGGTCAACTTATATATACCTTTGCCAG	1	55	1	CTTATATATA	    0.921341	-141
CAGACTCAACTTTATGTATCCTGGCAAAGG	1	75	0	TTTATGTATC	    0.974049	-121
TCATCACAGGATTATGGAACACGTGGGATA	1	125	0	ATTATGGAAC	     0.88828	-71
CATCCTCTGATTTATGTTTAAAACAAGTTC	1	165	0	TTTATGTTTA	    0.962048	-31
          **********

Masking position 5
Map Score:   1.9134

Number of sites scoring better than the average of aligned sites = 139
Number in coding regions = 100
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


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


Motif number 6

          **********

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