AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i231_protease_clp_aquae_reg_100.orf -o231_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	RAA00941	32	Aquifex_aeolicus
#2	RAA00271	19	Aquifex_aeolicus
#3	RAA01704	23	Aquifex_aeolicus
#4	RAA00300	18	Aquifex_aeolicus

Motif number 1

TTCTCCTCCTTGTTTTTAAAATTATACCA 	1	10	0	TGTTTTTAAA	    0.995294	-23
   AGGCTTAAGTTTTTAAACC        	2	8	1	AGTTTTTAAA	    0.997632	-12
     AATAGATATTTTAAAGAT       	4	4	0	ATATTTTAAA	    0.988939	-15
          **********

Masking position 8
Map Score:   5.67032

Number of sites scoring better than the average of aligned sites = 119
Number in coding regions = 109
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

      TGGTATAATTTTAAAAACAAGGAG	1	5	1	ATAATTTTAA	    0.824702	-28
     GGTTTAAAAACTTAAGCCT      	2	5	0	AAAAACTTAA	    0.981312	-15
   ACCCGCTAAATAGTTAATTATAT    	3	7	0	AAATAGTTAA	     0.98921	-17
   ATCTTTAAAATATCTATT         	4	8	1	AAATATCTAT	    0.949234	-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