AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i203_dna_repair_aquae_reg_300.orf -o203_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAA01396	163	Aquifex_aeolicus
#2	RAA00145	17	Aquifex_aeolicus

Motif number 1

TAATATACTCAGCCGGCGTAGCTCAGCGGT	1	81	1	AGCCGGCGTA	    0.997103	-83
AGGCTTACGAAGCCCGCGCTCTACCGCTGA	1	103	0	AGCCCGCGCT	    0.594844	-61
GGGCTTCGTAAGCCTGAGGTCGTGGGTTCG	1	118	1	AGCCTGAGGT	    0.991636	-46
GGTGTTTGAGAGCCGGCGGTGGGATTCGAA	1	144	0	AGCCGGCGGT	    0.995303	-20
          **********

Masking position 1
Map Score:   9.26468

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 10
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

AATATACTCAGCCGGCGTAGCTCAGCGGTA	1	82	1	GCCGGCGTAG	    0.996411	-82
GGCTTACGAAGCCCGCGCTCTACCGCTGAG	1	102	0	GCCCGCGCTC	    0.840878	-62
GGCTTCGTAAGCCTGAGGTCGTGGGTTCGA	1	119	1	GCCTGAGGTC	    0.984912	-45
GTGTTTGAGAGCCGGCGGTGGGATTCGAAC	1	143	0	GCCGGCGGTG	    0.989304	-21
          **********

Masking position 5
Map Score:   7.11628

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 11
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

          AATAATTTAATACTTTAAAT	1	1	1	AATAATTTAA	    0.991068	-163
AAATTCGGGAAATAATTTAAAGTATTAAAT	1	15	0	AATAATTTAA	    0.991068	-149
GGCTGAGTATATTAATTTAAACATTCATAA	1	65	0	ATTAATTTAA	    0.973964	-99
    AATAGTATTAATATATG         	2	7	1	ATTAATATAT	    0.935907	-11
          **********

Masking position 5
Map Score:   7.05434

Number of sites scoring better than the average of aligned sites = 30
Number in coding regions = 17
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

          **********

No masking
Map Score:   -3.95472e-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:   -3.95472e-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 6

          **********

No masking
Map Score:   -3.95472e-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