AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i327_not_clear2_aquae_reg_100.orf -o327_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	RAA00391	54	Aquifex_aeolicus
#2	RAA00641	24	Aquifex_aeolicus
#3	RAA00643	18	Aquifex_aeolicus

Motif number 1

AGGTTATTTTAACATAAAATTTTAAGTCTGGA	1	11	0	AACATAATTT	    0.943294	-44
ATTTTATGTTAAAATAACCTCTCTCGTAAAAG	1	23	1	AAAATACTCT	    0.993265	-32
CACTAAGATTAAAATACCTTTTTT        	2	11	1	AAAATACTTT	    0.710895	-14
          AAAATATCTTTAATTATC    	3	1	1	AAAATACTTA	    0.709063	-18
          ****** * ***

Masking position 6
Map Score:   6.41847

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 44
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

TAACATAAAATTTTAAGTCTGGA       	1	4	0	TTTTAAGTCT	    0.977014	-51
GAGAGAGGTTATTTTAACATAAAATTTTAA	1	18	0	ATTTTAACAT	    0.760298	-37
 AAAAAAGGTATTTTAATCTTAGTG     	2	6	0	ATTTTAATCT	    0.962751	-19
   AAAATATCTTTAATTATC         	3	8	1	CTTTAATTAT	    0.964762	-11
          **********

Masking position 6
Map Score:   1.85172

Number of sites scoring better than the average of aligned sites = 246
Number in coding regions = 207
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 3

          **********

No masking
Map Score:   -6.15168e-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:   -6.15168e-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:   -6.15168e-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