AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i008_aful_mthe_100.orf -o008_aful_mthe_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTH01017	99	M.thermo

Motif number 1

GCTGTCCTCACAGGTCTACCCCCA          	1	1	0	CAGCACCCCA	    0.999154	-99
CCTGTGAGGACAGCAAGATCCGCCAGAACCCTGT	1	21	1	CAGAATCCCC	    0.999089	-79
ACCCTGTTTACACCACTCCCCTCACCACAGACAG	1	48	1	CACCCCCCCA	    0.997285	-52
TCACCACAGACAGAAAGATCCGCCTGCGAGGGGG	1	69	1	CAGAATCCCC	    0.999089	-31
          CAGGCACCCCCCTCGCAGGCGGAT	1	86	0	CAGACCCCTC	    0.997922	-14
          ***  * **** **

Masking position 2
Map Score:   10.0542

Number of sites scoring better than the average of aligned sites = 128
Number in coding regions = 123
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

AAACAGGGTTCTGGCGGATCTTGCTGTCCT	1	27	0	CTGGCGGATC	    0.996049	-73
TGTCTGTGGTGAGGGGAGTGGTGTAAACAG	1	51	0	GAGGGGAGTG	    0.996372	-49
ACCCCCCTCGCAGGCGGATCTTTCTGTCTG	1	75	0	CAGGCGGATC	    0.985169	-25
ATCCGCCTGCGAGGGGGGTGCCTG      	1	86	1	GAGGGGGGTG	    0.998609	-14
          **********

Masking position 9
Map Score:   8.21157

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 80
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

GCGGATCTTGCTGTCCTCACAGGTCTACCC	1	14	0	CTGTCCTCAC	    0.997124	-86
ACAGCAAGATCCGCCAGAACCCTGTTTACA	1	30	1	CCGCCAGAAC	    0.987484	-70
GTTTACACCACTCCCCTCACCACAGACAGA	1	53	1	CTCCCCTCAC	    0.999269	-47
    CAGGCACCCCCCTCGCAGGCGGATCT	1	84	0	CCCCCCTCGC	    0.999198	-16
          **********

Masking position 5
Map Score:   7.06334

Number of sites scoring better than the average of aligned sites = 258
Number in coding regions = 250
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


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