AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i008_Uracil_Utilization_mthe_reg_100.orf -o008_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	RTH01017	99	M.thermo

Motif number 1

GCTGTCCTCACAGGTCTACCCCCA          	1	1	0	CAGCACCCCA	    0.999087	-99
CCTGTGAGGACAGCAAGATCCGCCAGAACCCTGT	1	21	1	CAGAATCCCC	    0.999017	-79
ACCCTGTTTACACCACTCCCCTCACCACAGACAG	1	48	1	CACCCCCCCA	    0.997066	-52
TCACCACAGACAGAAAGATCCGCCTGCGAGGGGG	1	69	1	CAGAATCCCC	    0.999017	-31
          CAGGCACCCCCCTCGCAGGCGGAT	1	86	0	CAGACCCCTC	    0.997778	-14
          ***  * **** **

Masking position 2
Map Score:   10.0542

Number of sites scoring better than the average of aligned sites = 207
Number in coding regions = 195
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

AAACAGGGTTCTGGCGGATCTTGCTGTCCT	1	27	0	CTGGCGGATC	    0.995861	-73
TGTCTGTGGTGAGGGGAGTGGTGTAAACAG	1	51	0	GAGGGGAGTG	    0.996148	-49
ACCCCCCTCGCAGGCGGATCTTTCTGTCTG	1	75	0	CAGGCGGATC	      0.9862	-25
ATCCGCCTGCGAGGGGGGTGCCTG      	1	86	1	GAGGGGGGTG	    0.998593	-14
          **********

Masking position 9
Map Score:   8.21157

Number of sites scoring better than the average of aligned sites = 179
Number in coding regions = 168
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

GGGTAGACCTGTGAGGACAGCAAGATCCGC	1	14	1	GTGAGGACAG	     0.99658	-86
TGTAAACAGGGTTCTGGCGGATCTTGCTGT	1	30	0	GTTCTGGCGG	    0.985157	-70
TCTGTCTGTGGTGAGGGGAGTGGTGTAAAC	1	53	0	GTGAGGGGAG	    0.999133	-47
AGATCCGCCTGCGAGGGGGGTGCCTG    	1	84	1	GCGAGGGGGG	    0.999047	-16
          **********

Masking position 6
Map Score:   7.06334

Number of sites scoring better than the average of aligned sites = 265
Number in coding regions = 258
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

          **********

No masking
Map Score:   1.66429e-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:   1.66429e-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:   1.66429e-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