AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i257_aful_mthe_100.orf -o257_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	RTH01549	140	M.thermo

Motif number 1

CACGCCACCATCTCCAGTCAATTATTTATT	1	14	1	TCTCCAGTCA	    0.994416	-127
CAATTATTTATTTCCAGGAAGAGGAATCCA	1	32	1	TTTCCAGGAA	    0.971877	-109
ATCTGCAACTCTTCCAGTAAGTCTGCAGAA	1	61	1	CTTCCAGTAA	    0.986681	-80
TTCCAGTAAGTCTGCAGAAACCAGAAACCC	1	72	1	TCTGCAGAAA	     0.98573	-69
CACAGGATCTTCTACACAAATTATTTATAG	1	101	1	TCTACACAAA	    0.966664	-40
          **********

Masking position 6
Map Score:   5.888

Number of sites scoring better than the average of aligned sites = 350
Number in coding regions = 313
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

TAATTGACTGGAGATGGTGGCGTGTGG   	1	8	0	GAGATGGTGG	    0.982279	-133
CTTACTGGAAGAGTTGCAGATGGATTCCTC	1	52	0	GAGTTGCAGA	    0.984934	-89
GGTTTCTGCAGACTTACTGGAAGAGTTGCA	1	64	0	GACTTACTGG	    0.980733	-77
AAGATCCTGTGGGTTTCTGGTTTCTGCAGA	1	82	0	GGGTTTCTGG	    0.997077	-59
  TTATCCATGGGTTTAAGGTTCTATAAAT	1	123	0	GGGTTTAAGG	    0.983587	-18
          **********

Masking position 5
Map Score:   5.31214

Number of sites scoring better than the average of aligned sites = 758
Number in coding regions = 722
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 3

CTTCCTGGAAATAAATAATTGACTGGAGAT	1	23	0	ATAAATAATT	    0.992034	-118
TTAAGGTTCTATAAATAATTTGTGTAGAAG	1	109	0	ATAAATAATT	    0.992034	-32
          **********

Masking position 5
Map Score:   2.04472

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 4

          **********

No masking
Map Score:   7.34864e-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:   7.34864e-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:   7.34864e-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