AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i118_aful_mthe_100.orf -o118_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	RTH01810	103	M.thermo

Motif number 1

          TCTATTTGACAGATGGGAGA	1	1	1	TCTATTTGAC	    0.924794	-103
AGGTGATCGTCTTGATTGACCGCATTTTAA	1	39	1	CTTGATTGAC	    0.980454	-65
CTATGAGTGGCCTGTATGACTTTAAAATGC	1	60	0	CCTGTATGAC	    0.997253	-44
GTTATGGCTGCTGGTATGGCTATGAGTGGC	1	79	0	CTGGTATGGC	    0.996355	-25
       TTACAGTTATGGCTGCTGGTATG	1	91	0	CAGTTATGGC	     0.97521	-13
          **********

Masking position 7
Map Score:   5.29615

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 273
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

GTTTCTCCCATCTGTCAAATAGA       	1	4	0	TCTGTCAAAT	    0.972162	-100
GATGGGAGAAACTTTAAAGGTGATCGTCTT	1	22	1	ACTTTAAAGG	    0.515105	-82
GGCCTGTATGACTTTAAAATGCGGTCAATC	1	52	0	ACTTTAAAAT	    0.537237	-52
          **********

Masking position 7
Map Score:   0.329093

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 37
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

          **********

No masking
Map Score:   -5.44113e-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 4

          **********

No masking
Map Score:   -5.44113e-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:   -5.44113e-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