AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i346_weak7_aquae_reg_300.orf -o346_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	RAA01468	39	Aquifex_aeolicus
#2	RAA01493	138	Aquifex_aeolicus

Motif number 1

TCGACTCCGCCCTGGGCCACCA        	2	3	0	CCTGGGCCAC	    0.992027	-136
CGGGGTGTCGGCGGTTCGACTCCGCCCTGG	2	18	0	GCGGTTCGAC	    0.972369	-121
CGGCTGAAAACCGGGGTGTCGGCGGTTCGA	2	29	0	CCGGGGTGTC	    0.995753	-110
CGGTTTTCAGCCGGGTGCTCTACCACCTGA	2	46	1	CCGGGTGCTC	    0.998336	-93
GTCGTAAGGCCCGGTAGCTCAGGTGGTAGA	2	64	0	CCGGTAGCTC	     0.99325	-75
          **********

Masking position 4
Map Score:   6.14821

Number of sites scoring better than the average of aligned sites = 99
Number in coding regions = 82
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

TTCTAAAGCTATAAAATTTTGAGT      	1	5	0	ATAAAATTTT	    0.713591	-35
   AATCTGGATAATAAATTCTAAAGCTAT	1	23	0	ATAATAAATT	    0.971527	-17
AATGGAATATATAATATATTTTTGTCGTAA	2	87	0	ATAATATATT	    0.915472	-52
TTCAAGTGTCATAATTTAATTGT       	2	126	1	ATAATTTAAT	    0.713591	-13
          **********

Masking position 4
Map Score:   2.96425

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 21
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 3

GGTGCTCTACCACCTGAGCTACCGGGCCTT	2	59	1	CACCTGAGCT	    0.998032	-80
TAAATTATGACACTTGAACTCAAAGGGAAT	2	114	0	CACTTGAACT	    0.995804	-25
          **********

Masking position 5
Map Score:   0.325101

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 6
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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:   -1.75204e-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