AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00052_aquae_reg_100.orf -o00052_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	aq_503	83	hypothetical protein
#2	otnA'	30	polysaccharide biosynthesis protein (fragment)
#3	metE	44	tetrahydropteroyltriglutamate methyltransferase

Motif number 1

ACACATGCATTAAAAATAGGAAAAAAGCAA	1	11	0	TAAAAATAGG	    0.995651	-73
TGTGTATTATTTAAAGTAGGGAGATGTATT	1	36	1	TTAAAGTAGG	    0.997183	-48
AAAAGATATTTTAAAATAAGAAGTTCTAAA	3	11	1	TTAAAATAAG	    0.982935	-34
TAAGAAGTTCTAAAAGGAGGAGAAATCC  	3	27	1	TAAAAGGAGG	     0.99521	-18
          **********

Masking position 5
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	    0.981029	-78
ATTATTTAAAGTAGGGAGATGTATTACACC	1	41	1	GTAGGGAGAT	    0.994886	-43
 GATTATGTTGTAGGGAGAATTCTTAAGAG	2	12	0	GTAGGGAGAA	     0.99797	-19
AGTTCTAAAAGGAGGAGAAATCC       	3	32	1	GGAGGAGAAA	    0.986052	-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

TTTCCTATTTTTAATGCATGTGTATTATTTA	1	18	1	TTAAGCATGT	    0.974484	-66
CCGAAAAGGTGTAATACATCTCCCTACTTTA	1	47	0	GTAAACATCT	    0.992616	-37
      GCTCTTAAGAATTCTCCCTACAACA	2	5	1	TTAAAATTCT	    0.981124	-26
ACTTCTTATTTTAAAATATCTTTT       	3	4	0	TTAAATATCT	    0.986864	-41
TCTCCTCCTTTTAGAACTTCTTATTTTAAAA	3	19	0	TTAGACTTCT	    0.989452	-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