AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i030_Glycerol_Uptake_aquae_reg_300.orf -o030_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	RAA01298	139	Aquifex_aeolicus

Motif number 1

CTCTGAGCTACGCCCGCTTTTTATTATTAA	1	41	0	CGCCCGCTTT	    0.998266	-99
AGAGGTAGAGCACCTGCTTCCCAAGCAGGA	1	67	1	CACCTGCTTC	    0.996229	-73
AACCGGCGACCTCCTGCTTGGGAAGCAGGT	1	78	0	CTCCTGCTTG	    0.996226	-62
AGCAGGAGGTCGCCGGTTCGAGTCCCGTCG	1	90	1	CGCCGGTTCG	    0.994326	-50
CGAGTCCCGTCGCCCGCTCCAAATTTTTGT	1	108	1	CGCCCGCTCC	    0.999202	-32
          **********

Masking position 8
Map Score:   11.6008

Number of sites scoring better than the average of aligned sites = 72
Number in coding regions = 55
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

TGGTGTTTTAAGGAGGTTGAT         	1	2	0	AGGAGGTTGA	    0.967668	-138
TAATAAAAAGCGGGCGTAGCTCAGAGGTAG	1	45	1	CGGGCGTAGC	    0.997519	-95
GGGCGTAGCTCAGAGGTAGAGCACCTGCTT	1	56	1	CAGAGGTAGA	    0.977183	-84
CGACCTCCTGCTTGGGAAGCAGGTGCTCTA	1	72	0	CTTGGGAAGC	    0.926462	-68
CTTCCCAAGCAGGAGGTCGCCGGTTCGAGT	1	83	1	AGGAGGTCGC	     0.99456	-57
AAATTTGGAGCGGGCGACGGGACTCGAACC	1	104	0	CGGGCGACGG	    0.987962	-36
          **********

Masking position 6
Map Score:   6.01779

Number of sites scoring better than the average of aligned sites = 412
Number in coding regions = 347
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 3

CTTAAAACACCATTATAAAATTTAATAATA	1	20	1	CATTATAAAA	    0.975558	-120
TATAAAATTTAATAATAAAAAGCGGGCGTA	1	33	1	AATAATAAAA	    0.974068	-107
    AAGCAAAATTGTACAAAAATTTGGAG	1	124	0	AATTGTACAA	    0.979567	-16
          **********

Masking position 7
Map Score:   0.454689

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 16
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

          **********

No masking
Map Score:   -1.82309e-13

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:   -1.82309e-13

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 6

          **********

No masking
Map Score:   -1.82309e-13

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