AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i038_aful_mthe_100.orf -o038_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	RTH00414	143	M.thermo

Motif number 1

TTTGCATAGCTTTAATGGTCTGATTTCATATA	1	29	0	TTTATGGCTG	    0.997516	-115
GTGGGTAGGTCTTTGTGGTCTGCCTTTGCATA	1	53	0	CTTGTGGCTG	    0.998932	-91
GGTGGCCTGTTTTTGTGGGTAGGTCTTTGTGG	1	67	0	TTTGTGGTAG	    0.993746	-77
GTAAATAAGGTTTGGTGGCCTGTTTTTGTGGG	1	80	0	TTTGTGGCTG	    0.999374	-64
          *** **** ***

Masking position 6
Map Score:   7.82285

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 5
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 2

TAGCTTTAATGGTCTGATTTCATATATTAATC	1	23	0	GGTCTGTTCA	    0.989971	-121
AGGTCTTTGTGGTCTGCCTTTGCATAGCTTTA	1	47	0	GGTCTGTTTG	    0.999116	-97
TGTTTTTGTGGGTAGGTCTTTGTGGTCTGCCT	1	60	0	GGTAGGTTTG	    0.995639	-84
AAGGTTTGGTGGCCTGTTTTTGTGGGTAGGTC	1	74	0	GGCCTGTTTG	    0.998063	-70
TTATCACACAGATATGATTCTGTCTATATTTC	1	121	0	GATATGTCTG	    0.977683	-23
          ******  ****

Masking position 9
Map Score:   6.90825

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 86
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

          **********

No masking
Map Score:   -2.17836e-13

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:   -2.17836e-13

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:   -2.17836e-13

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