AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00052_aquae_reg_300.orf -o00052_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	aq_503	83	hypothetical protein
#2	otnA'	30	polysaccharide biosynthesis protein (fragment)
#3	metE	44	tetrahydropteroyltriglutamate methyltransferase

Motif number 1

TTGCTTTTTTCCTATTTTTAATGCATGTGT	1	11	1	CCTATTTTTA	     0.99505	-73
AATACATCTCCCTACTTTAAATAATACACA	1	36	0	CCTACTTTAA	    0.996793	-48
TTTAGAACTTCTTATTTTAAAATATCTTTT	3	11	0	CTTATTTTAA	     0.98061	-34
  GGATTTCTCCTCCTTTTAGAACTTCTTA	3	27	0	CCTCCTTTTA	    0.994547	-18
          **********

Masking position 6
Map Score:   7.55958

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 54
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

TGCATTAAAAATAGGAAAAAAGCAA     	1	6	0	ATAGGAAAAA	    0.983052	-78
ATTATTTAAAGTAGGGAGATGTATTACACC	1	41	1	GTAGGGAGAT	    0.995437	-43
 GATTATGTTGTAGGGAGAATTCTTAAGAG	2	12	0	GTAGGGAGAA	    0.998189	-19
AGTTCTAAAAGGAGGAGAAATCC       	3	32	1	GGAGGAGAAA	    0.987546	-13
          **********

Masking position 3
Map Score:   4.49909

Number of sites scoring better than the average of aligned sites = 198
Number in coding regions = 180
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

TAAATAATACACATGCATTAAAAATAGGAAA	1	18	0	ACATGCTTAA	    0.970899	-66
TAAAGTAGGGAGATGTATTACACCTTTTCGG	1	47	1	AGATGTTTAC	    0.991557	-37
TGTTGTAGGGAGAATTCTTAAGAGC      	2	5	0	AGAATTTTAA	    0.978495	-26
       AAAAGATATTTTAAAATAAGAAGT	3	4	1	AGATATTTAA	    0.984992	-41
TTTTAAAATAAGAAGTTCTAAAAGGAGGAGA	3	19	1	AGAAGTCTAA	    0.987946	-26
          ****** ****

Masking position 3
Map Score:   4.21897

Number of sites scoring better than the average of aligned sites = 168
Number in coding regions = 145
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

TTAAAAATAGGAAAAAAGCAA         	1	2	0	GAAAAAAGCA	    0.965075	-82
ACACCTTTTCGGAGACAGCAGGTTTGCT  	1	66	1	GGAGACAGCA	    0.996079	-18
TATGTTGTAGGGAGAATTCTTAAGAGC   	2	8	0	GGAGAATTCT	    0.982774	-23
TCTAAAAGGAGGAGAAATCC          	3	35	1	GGAGAAATCC	    0.987085	-10
          **********

Masking position 5
Map Score:   3.49408

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 154
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


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


Motif number 7

          **********

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