AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i231_protease_clp_aquae_reg_300.orf -o231_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	RAA00941	32	Aquifex_aeolicus
#2	RAA00271	19	Aquifex_aeolicus
#3	RAA01704	23	Aquifex_aeolicus
#4	RAA00300	18	Aquifex_aeolicus

Motif number 1

TCTCCTCCTTGTTTTTAAAATTATACCA  	1	9	0	GTTTTTAAAA	    0.801492	-24
  AGGCTTAAGTTTTTAAACC         	2	9	1	GTTTTTAAAC	    0.558011	-11
          ATCTTTAAAATATCTATT  	4	1	1	ATCTTTAAAA	    0.988872	-18
          **********

Masking position 7
Map Score:   5.67032

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 86
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

CTCCTTGTTTTTAAAATTATACCA      	1	5	0	TTAAAATTAT	    0.825556	-28
      AGGCTTAAGTTTTTAAACC     	2	5	1	TTAAGTTTTT	    0.981288	-15
    ATATAATTAACTATTTAGCGGGT   	3	7	1	TTAACTATTT	     0.98905	-17
         AATAGATATTTTAAAGAT   	4	8	0	ATAGATATTT	    0.948906	-11
          **********

Masking position 3
Map Score:   2.63344

Number of sites scoring better than the average of aligned sites = 405
Number in coding regions = 320
Number in noncoding regions = 85
Number of orfs with sites within 600 bp upstream = 95
Fraction of orfs with sites within 600 bp upstream = 0.0152586


Motif number 3

          **********

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 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