AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_Mannose_Metabolism_aquae_reg_300.orf -o039_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	RAA01343	83	Aquifex_aeolicus
#2	RAA01344	45	Aquifex_aeolicus
#3	RAA01346	58	Aquifex_aeolicus
#4	RAA01406	33	Aquifex_aeolicus

Motif number 1

    TTGCTTTTTTCCTATTTTTAATGCAT	1	7	1	TTTTCCTATT	    0.876592	-77
GTGTAATACATCTCCCTACTTTAAATAATA	1	40	0	TCTCCCTACT	    0.994021	-44
AAACCTGCTGTCTCCGAAAAGGTGTAATAC	1	61	0	TCTCCGAAAA	    0.750525	-23
TCTTAAGAATTCTCCCTACAACATAATCTT	2	13	1	TCTCCCTACA	    0.994316	-33
   ATCTCCATCTTCCAAGATTATGTTGTA	2	29	0	TCTTCCAAGA	     0.72856	-17
CTAAATTGAGTGTCCGTATAAATTTTAAAC	3	16	0	TGTCCGTATA	    0.945572	-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

GCTTTTTTCCTATTTTTAATGCATGTGTAT	1	13	1	TATTTTTAAT	    0.953348	-71
TACATCTCCCTACTTTAAATAATACACATG	1	34	0	TACTTTAAAT	    0.933073	-50
TTGTAGGGAGAATTCTTAAGAGC       	2	4	0	AATTCTTAAG	    0.948828	-42
TGTCCGTATAAATTTTAAACTTACA     	3	6	0	AATTTTAAAC	    0.987095	-53
   AGGGGATAATTTTAAACTGCTAAAATT	4	8	1	AATTTTAAAC	    0.987095	-26
AAACTGCTAAAATTCTAAGT          	4	24	1	AATTCTAAGT	    0.954998	-10
          **********

Masking position 6
Map Score:   5.59558

Number of sites scoring better than the average of aligned sites = 153
Number in coding regions = 113
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 3

TTTAATGCATGTGTATTATTTAAAGTAGGGA	1	27	1	GTGTATATTT	    0.984824	-57
TTTAAAGTAGGGAGATGTATTACACCTTTTC	1	45	1	GGAGATTATT	    0.904179	-39
     TGTAAGTTTAAAATTTATACGGACAC	3	6	1	GTTTAAATTT	    0.878607	-53
       ACTGGATATCATTTTATATGATGC	3	45	0	GGATATATTT	     0.98953	-14
         AGGGGATAATTTTAAACTGCTA	4	2	1	GGGGATATTT	     0.99371	-32
          ****** ****

Masking position 5
Map Score:   2.15269

Number of sites scoring better than the average of aligned sites = 111
Number in coding regions = 99
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

  ATCTCCATCTTCCAAGATTATGTTGTAG	2	28	0	CTTCCAAGAT	    0.949231	-18
ATTGAGTGTCCGTATAAATTTTAAACTTAC	3	12	0	CGTATAAATT	    0.943523	-47
ATTTTATATGATGCTAAATTGAGTGTCCGT	3	29	0	ATGCTAAATT	    0.928478	-30
AATTTAGCATCATATAAAATGATATCCAGT	3	39	1	CATATAAAAT	    0.939481	-20
TAATTTTAAACTGCTAAAATTCTAAGT   	4	17	1	CTGCTAAAAT	    0.989794	-17
          **********

Masking position 6
Map Score:   0.387288

Number of sites scoring better than the average of aligned sites = 191
Number in coding regions = 166
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


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


Motif number 7

          **********

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