AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i254_aful_mthe_100.orf -o254_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	RTH01260	198	M.thermo

Motif number 1

TTTTTTAATCTGATAACTTATAACTTATCA	1	16	1	TGATAACTTA	    0.997187	-183
AAAGTATATGTGATAAGTTATAAGTTATCA	1	26	0	TGATAAGTTA	    0.992623	-173
AAGTTATAATTTATAACTTATAAAGTATAT	1	47	0	TTATAACTTA	     0.99378	-152
AAGTTATAAATTATAACTTAGATCCAGCAG	1	58	1	TTATAACTTA	     0.99378	-141
AAAGTGCTGCTGATAGATTAACGGCTGTTG	1	148	0	TGATAGATTA	    0.975075	-51
          **********

Masking position 5
Map Score:   11.7544

Number of sites scoring better than the average of aligned sites = 3
Number in coding regions = 3
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

ATAAACCAGAAGGGTGGCTGTGGAAAGACA	1	117	1	AGGGTGGCTG	    0.996659	-82
TGATAGATTAACGGCTGTTGTTGTCTTTCC	1	138	0	ACGGCTGTTG	    0.994783	-61
CAAGGAGGAAAGTGCTGCTGATAGATTAAC	1	156	0	AGTGCTGCTG	       0.995	-43
CCTTGACAGGAGGGTTCTTGTAATCGAC  	1	181	1	AGGGTTCTTG	    0.991952	-18
          **********

Masking position 9
Map Score:   4.57518

Number of sites scoring better than the average of aligned sites = 296
Number in coding regions = 279
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

AGCAGGTGATGAGATGGGAGAGGTAATTTC	1	83	1	GAGATGGGAG	    0.982599	-116
AATCATAAACCAGAAGGGTGGCTGTGGAAA	1	113	1	CAGAAGGGTG	    0.997201	-86
TCCTGTCAAGGAGGAAAGTGCTGCTGATAG	1	162	0	GAGGAAAGTG	    0.972465	-37
TCCTCCTTGACAGGAGGGTTCTTGTAATCG	1	177	1	CAGGAGGGTT	    0.992923	-22
          **********

Masking position 2
Map Score:   2.60052

Number of sites scoring better than the average of aligned sites = 702
Number in coding regions = 670
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

          **********

No masking
Map Score:   -2.59896e-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:   -2.59896e-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:   -2.59896e-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