AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_Mannose_Metabolism_aquae_reg_100.orf -o039_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	RAA01343	83	Aquifex_aeolicus
#2	RAA01344	45	Aquifex_aeolicus
#3	RAA01346	58	Aquifex_aeolicus
#4	RAA01406	33	Aquifex_aeolicus

Motif number 1

ATGCATTAAAAATAGGAAAAAAGCAA    	1	7	0	AATAGGAAAA	    0.889586	-77
TATTATTTAAAGTAGGGAGATGTATTACAC	1	40	1	AGTAGGGAGA	    0.994695	-44
GTATTACACCTTTTCGGAGACAGCAGGTTT	1	61	1	TTTTCGGAGA	    0.737895	-23
AAGATTATGTTGTAGGGAGAATTCTTAAGA	2	13	0	TGTAGGGAGA	    0.994348	-33
TACAACATAATCTTGGAAGATGGAGAT   	2	29	1	TCTTGGAAGA	    0.715927	-17
GTTTAAAATTTATACGGACACTCAATTTAG	3	16	1	TATACGGACA	    0.946265	-43
          **********

Masking position 3
Map Score:   5.82131

Number of sites scoring better than the average of aligned sites = 323
Number in coding regions = 312
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

CTCCCTACTTTAAATAATACACATGCATTAAA	1	27	0	TAAATATAAC	    0.972959	-57
CGAAAAGGTGTAATACATCTCCCTACTTTAAA	1	45	0	TAATAATCCC	    0.964626	-39
     GCTCTTAAGAATTCTCCCTACAACATA	2	6	1	TAAGATTCCC	    0.955782	-40
AGTGTCCGTATAAATTTTAAACTTACA     	3	6	0	TAAATTTAAC	    0.950702	-53
AGCATCATATAAAATGATATCCAGT       	3	44	1	AAAATATACC	     0.98278	-15
TTAGCAGTTTAAAATTATCCCCT         	4	2	0	AAAATATCCC	     0.98898	-32
          ***** *** **

Masking position 8
Map Score:   3.79155

Number of sites scoring better than the average of aligned sites = 154
Number in coding regions = 132
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

CCGTATAAATTTTAAACTTACA        	3	3	0	TTTAAACTTA	    0.953237	-56
TTTATATGATGCTAAATTGAGTGTCCGTAT	3	27	0	GCTAAATTGA	    0.961112	-32
TTTAGCATCATATAAAATGATATCCAGT  	3	41	1	TATAAAATGA	    0.955092	-18
ATTTTAGCAGTTTAAAATTATCCCCT    	4	7	0	TTTAAAATTA	    0.972029	-27
ATTTTAAACTGCTAAAATTCTAAGT     	4	19	1	GCTAAAATTC	    0.963152	-15
          **********

Masking position 5
Map Score:   2.31807

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 56
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

          **********

No masking
Map Score:   -7.57276e-14

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:   -7.57276e-14

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:   -7.57276e-14

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