AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i030_Glycerol_Uptake_aquae_reg_100.orf -o030_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	RAA01298	139	Aquifex_aeolicus

Motif number 1

CTCTGAGCTACGCCCGCTTTTTATTATTAA	1	41	0	CGCCCGCTTT	    0.998178	-99
AGAGGTAGAGCACCTGCTTCCCAAGCAGGA	1	67	1	CACCTGCTTC	    0.996024	-73
AACCGGCGACCTCCTGCTTGGGAAGCAGGT	1	78	0	CTCCTGCTTG	    0.996021	-62
AGCAGGAGGTCGCCGGTTCGAGTCCCGTCG	1	90	1	CGCCGGTTCG	    0.994042	-50
CGAGTCCCGTCGCCCGCTCCAAATTTTTGT	1	108	1	CGCCCGCTCC	    0.999183	-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

         ATCAACCTCCTTAAAACACCA	1	2	1	TCAACCTCCT	    0.967913	-138
CTACCTCTGAGCTACGCCCGCTTTTTATTA	1	45	0	GCTACGCCCG	    0.997537	-95
AAGCAGGTGCTCTACCTCTGAGCTACGCCC	1	56	0	TCTACCTCTG	    0.977357	-84
TAGAGCACCTGCTTCCCAAGCAGGAGGTCG	1	72	1	GCTTCCCAAG	    0.926995	-68
ACTCGAACCGGCGACCTCCTGCTTGGGAAG	1	83	0	GCGACCTCCT	    0.994602	-57
GGTTCGAGTCCCGTCGCCCGCTCCAAATTT	1	104	1	CCGTCGCCCG	     0.98804	-36
          **********

Masking position 5
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

TATTATTAAATTTTATAATGGTGTTTTAAG	1	20	0	TTTTATAATG	    0.976689	-120
TACGCCCGCTTTTTATTATTAAATTTTATA	1	33	0	TTTTATTATT	    0.977233	-107
CTCCAAATTTTTGTACAATTTTGCTT    	1	124	1	TTGTACAATT	    0.982207	-16
          **********

Masking position 5
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