AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i334_1_aquae_reg_300.orf -o334_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	RAA01050	20	Aquifex_aeolicus
#2	RAA01696	145	Aquifex_aeolicus
#3	RAA01698	50	Aquifex_aeolicus

Motif number 1

CTCCACCCCCACCACCCAACC         	2	2	0	ACCACCCAAC	    0.875452	-144
GAGGGTTCGACTCCCTCCACCCCCACCACC	2	16	0	CTCCCTCCAC	    0.930607	-130
CTGGGCGAAAAGCCCGTGAGGGTTCGACTC	2	33	0	AGCCCGTGAG	    0.954687	-113
GGGACTTAAAATCCCCTGGGCGAAAAGCCC	2	48	0	ATCCCCTGGG	    0.978165	-98
GGGGATTTTAAGTCCCCCGCGTCTGCCAAT	2	62	1	AGTCCCCCGC	     0.98923	-84
GCGTCTGCCAATTCCGCCACACCCCCTAAC	2	80	1	ATTCCGCCAC	    0.967346	-66
ATTCCGCCACACCCCCTAACTAAAGAAATA	2	90	1	ACCCCCTAAC	    0.980399	-56
         GATTTCTTGAGAAAAGTTCTT	2	135	0	ATTTCTTGAG	    0.693607	-11
TTATTATAAAAGTTCTTCGCTT        	3	3	0	AGTTCTTCGC	    0.915692	-48
    TTACCTACCTCCTCGCAAGATAAAAA	3	35	0	ACCTCCTCGC	    0.984874	-16
          **********

Masking position 5
Map Score:   8.02389

Number of sites scoring better than the average of aligned sites = 1770
Number in coding regions = 1597
Number in noncoding regions = 173
Number of orfs with sites within 600 bp upstream = 104
Fraction of orfs with sites within 600 bp upstream = 0.0167041


Motif number 2

  GATTTCTTGAGAAAAGTTCTTTCTATAA	2	128	0	GAGAAAAGTT	    0.991593	-18
AAAAAGTTATTATAAAAGTTCTTCGCTT  	3	9	0	TATAAAAGTT	    0.989549	-42
CCTCGCAAGATAAAAAAGTTATTATAAAAG	3	21	0	TAAAAAAGTT	    0.989549	-30
          **********

Masking position 5
Map Score:   2.69003

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 30
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

          **********

No masking
Map Score:   8.05918e-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:   8.05918e-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:   8.05918e-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