AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i008_aful_mthe_300.orf -o008_aful_mthe_300.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

          TGGGGGTAGACCTGTGAGGACAGC	1	1	1	TGGGGTGCTG	    0.999163	-99
ACAGGGTTCTGGCGGATCTTGCTGTCCTCACAGG	1	21	0	GGGGATTCTG	    0.999099	-79
CTGTCTGTGGTGAGGGGAGTGGTGTAAACAGGGT	1	48	0	TGGGGGGGTG	    0.997316	-52
CCCCCTCGCAGGCGGATCTTTCTGTCTGTGGTGA	1	69	0	GGGGATTCTG	    0.999099	-31
ATCCGCCTGCGAGGGGGGTGCCTG          	1	86	1	GAGGGGTCTG	    0.997943	-14
          ** **** *  ***

Masking position 13
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

AGGACAGCAAGATCCGCCAGAACCCTGTTT	1	27	1	GATCCGCCAG	    0.996071	-73
CTGTTTACACCACTCCCCTCACCACAGACA	1	51	1	CACTCCCCTC	    0.996399	-49
CAGACAGAAAGATCCGCCTGCGAGGGGGGT	1	75	1	GATCCGCCTG	    0.985029	-25
      CAGGCACCCCCCTCGCAGGCGGAT	1	86	0	CACCCCCCTC	     0.99861	-14
          **********

Masking position 2
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

GGGTAGACCTGTGAGGACAGCAAGATCCGC	1	14	1	GTGAGGACAG	    0.996541	-86
TGTAAACAGGGTTCTGGCGGATCTTGCTGT	1	30	0	GTTCTGGCGG	    0.984993	-70
TCTGTCTGTGGTGAGGGGAGTGGTGTAAAC	1	53	0	GTGAGGGGAG	    0.999123	-47
AGATCCGCCTGCGAGGGGGGTGCCTG    	1	84	1	GCGAGGGGGG	    0.999036	-16
          **********

Masking position 6
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