AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i183_thiamin_biosynthesis_aquae_reg_100.orf -o183_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	RAA01395	37	Aquifex_aeolicus
#2	RAA01396	163	Aquifex_aeolicus
#3	RAA01090	65	Aquifex_aeolicus

Motif number 1

TAATATACTCAGCCGGCGTAGCTCAGCGGT	2	81	1	AGCCGGCGTA	    0.996058	-83
AGGCTTACGAAGCCCGCGCTCTACCGCTGA	2	103	0	AGCCCGCGCT	    0.626027	-61
GGGCTTCGTAAGCCTGAGGTCGTGGGTTCG	2	118	1	AGCCTGAGGT	    0.991168	-46
GGTGTTTGAGAGCCGGCGGTGGGATTCGAA	2	144	0	AGCCGGCGGT	    0.996455	-20
          **********

Masking position 1
Map Score:   7.65587

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 10
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

GAAATTTTTCAGTGATTTAAATATA     	1	6	0	AGTGATTTAA	    0.980844	-32
          AATAATTTAATACTTTAAAT	2	1	1	AATAATTTAA	    0.990355	-163
AAATTCGGGAAATAATTTAAAGTATTAAAT	2	15	0	AATAATTTAA	    0.990355	-149
GGCTGAGTATATTAATTTAAACATTCATAA	2	65	0	ATTAATTTAA	    0.981766	-99
          **********

Masking position 5
Map Score:   6.37245

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 10
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

AATATACTCAGCCGGCGTAGCTCAGCGGTA	2	82	1	GCCGGCGTAG	      0.9949	-82
GGCTTACGAAGCCCGCGCTCTACCGCTGAG	2	102	0	GCCCGCGCTC	    0.882727	-62
GGCTTCGTAAGCCTGAGGTCGTGGGTTCGA	2	119	1	GCCTGAGGTC	    0.985835	-45
GTGTTTGAGAGCCGGCGGTGGGATTCGAAC	2	143	0	GCCGGCGGTG	    0.992608	-21
          **********

Masking position 5
Map Score:   5.50746

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 11
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

TACCTCCAGAAATTTTTCAGTGATTTAAAT	1	14	0	AATTTTTCAG	    0.995923	-24
TTATTTCCCGAATTTTTCAGGTGTTGAAAA	2	30	1	AATTTTTCAG	    0.995923	-134
      ACCTTATTTTCCAGTTCTTATAAG	3	52	0	TATTTTCCAG	    0.991486	-14
          **********

Masking position 2
Map Score:   4.2241

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 23
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

CCTCCAGAAATTTTTCAGTGATTTAAATAT	1	12	0	TTTTTCAGTG	     0.99222	-26
ATTTCCCGAATTTTTCAGGTGTTGAAAAGG	2	32	1	TTTTTCAGGT	     0.99222	-132
    ACCTTATTTTCCAGTTCTTATAAGAG	3	50	0	TTTTCCAGTT	     0.99222	-16
          **********

Masking position 7
Map Score:   2.21567

Number of sites scoring better than the average of aligned sites = 82
Number in coding regions = 70
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 6

          **********

No masking
Map Score:   5.92755e-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 7

          **********

No masking
Map Score:   5.92755e-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 8

          **********

No masking
Map Score:   5.92755e-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