AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i075_aful_mthe_300.orf -o075_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	RAG50348	150	Archaeoglobus_fulgidus

Motif number 1

TTGCGAAAGATTTAAAACTTTTCGGTAGGAG	1	18	0	TTTAAACTTT	    0.968176	-133
TTTTAAATCTTTCGCAATTTTATCTCAATTT	1	32	1	TTCGAATTTT	    0.992775	-119
TTTATCTCAATTTAAGATTTTGATTTGACAT	1	50	1	TTTAGATTTT	    0.968176	-101
TTTGACATACTTTGAAATTTATTTGAAAAAA	1	73	1	TTTGAATTTA	    0.976955	-78
TTACTATTTTTACGAAATTTTTTCAAATAAA	1	90	0	TACGAATTTT	    0.966133	-61
GGAATCCTCCTTTATAATTCTTACTATTTTT	1	110	0	TTTAAATTCT	    0.985192	-41
ACCACTCATATTTGGAATCCTCCTTTATAAT	1	123	0	TTTGAATCCT	    0.976896	-28
          **** ******

Masking position 7
Map Score:   9.64906

Number of sites scoring better than the average of aligned sites = 248
Number in coding regions = 172
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 92
Fraction of orfs with sites within 600 bp upstream = 0.0147767


Motif number 2

AATCAAAATCTTAAATTGAGATAAAATTGCGAA	1	42	0	TTATTGAATA	    0.996557	-109
ATTTAAGATTTTGATTTGACATACTTTGAAATT	1	59	1	TTATTGAATA	    0.996494	-92
TACTTTGAAATTTATTTGAAAAAATTTCGTAAA	1	80	1	TTATTGAAAA	    0.986085	-71
          ** * **** ***

Masking position 9
Map Score:   2.01256

Number of sites scoring better than the average of aligned sites = 4
Number in coding regions = 2
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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