AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -iglpR_aquae_opreg_100.orf -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	ribD2	139	riboflavin specific deaminase
#2	aq_1327	29	hypothetical protein

Motif number 1

TTAATAATAAAAAGCGGGCGTAGCTCAGAG	1	41	1	AAAGCGGGCG	    0.997958	-99
TCCTGCTTGGGAAGCAGGTGCTCTACCTCT	1	67	0	GAAGCAGGTG	    0.995518	-73
ACCTGCTTCCCAAGCAGGAGGTCGCCGGTT	1	78	1	CAAGCAGGAG	    0.995515	-62
CGACGGGACTCGAACCGGCGACCTCCTGCT	1	90	0	CGAACCGGCG	    0.993336	-50
ACAAAAATTTGGAGCGGGCGACGGGACTCG	1	108	0	GGAGCGGGCG	    0.999131	-32
          **********

Masking position 3
Map Score:   10.8383

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	     0.98469	-138
TAATAAAAAGCGGGCGTAGCTCAGAGGTAG	1	45	1	CGGGCGTAGC	     0.99654	-95
GGGCGTAGCTCAGAGGTAGAGCACCTGCTT	1	56	1	CAGAGGTAGA	    0.979963	-84
CTTCCCAAGCAGGAGGTCGCCGGTTCGAGT	1	83	1	AGGAGGTCGC	    0.996198	-57
AAATTTGGAGCGGGCGACGGGACTCGAACC	1	104	0	CGGGCGACGG	    0.984313	-36
          **********

Masking position 6
Map Score:   5.17444

Number of sites scoring better than the average of aligned sites = 152
Number in coding regions = 119
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

AAACACCATTATAAAATTTAATAATAAAAA	1	24	1	ATAAAATTTA	    0.975055	-116
CAAAATTGTACAAAAATTTGGAGCGGGCGA	1	117	0	CAAAAATTTG	    0.646505	-23
       AAGCAAAATTGTACAAAAATTTG	1	127	0	CAAAATTGTA	    0.899576	-13
TTTTTCTCCTATAAAATGTATTTTTACT  	2	12	1	ATAAAATGTA	    0.984328	-18
          **********

Masking position 5
Map Score:   2.29619

Number of sites scoring better than the average of aligned sites = 40
Number in coding regions = 31
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

          **********

No masking
Map Score:   -1.68098e-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:   -1.68098e-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:   -1.68098e-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