AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i196_mixed_replication_rec__aquae_reg_100.orf -o196_aquae_100.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	RAA01468	39	Aquifex_aeolicus
#2	RAA00012	74	Aquifex_aeolicus

Motif number 1

AATTCTAAAGCTATAAAATTTTGAGT     	1	6	0	CTATAAATTT	    0.993711	-34
AATTTTATAGCTTTAGAATTTATTATCCAGA	1	17	1	CTTTAAATTT	    0.997508	-23
ATTAAGGAATTTTTATATTTTAATTCACAAA	2	33	0	TTTTAATTTT	    0.975542	-42
ATAAAAATTCCTTAATAATTTTACAAGGGTC	2	48	1	CTTAAAATTT	    0.993729	-27
          ***** *****

Masking position 5
Map Score:   6.27368

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 62
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 2

ATTCTAAAGCTATAAAATTTTGAGT     	1	6	0	TATAAAATTT	    0.923438	-34
      AATCTGGATAATAAATTCTAAAGC	1	26	0	TGGATAATAA	    0.965561	-14
GAAAAGAGTTTGTGAATTAAAATATAAAAA	2	25	1	TGTGAATTAA	    0.965637	-50
AATAGACCCTTGTAAAATTATTAAGGAATT	2	53	0	TGTAAAATTA	    0.991782	-22
          **********

Masking position 6
Map Score:   0.705723

Number of sites scoring better than the average of aligned sites = 158
Number in coding regions = 119
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 3

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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:   -1.17788e-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