AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i282_hypothetical7_aquae_reg_100.orf -o282_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	RAA00475	120	Aquifex_aeolicus

Motif number 1

TAAAGTAAAAGGAGGTGGAAACC       	1	4	0	GGAGGTGGAA	    0.996579	-117
CCAAAATACTTAAAGTAAAAGGAGGTGGAA	1	14	0	TAAAGTAAAA	    0.881359	-107
TAAGTATTTTGGTATTAAAAATTCTAACTC	1	32	1	GGTATTAAAA	    0.922159	-89
TTAAATAACTTGAGTTAGAATTTTTAATAC	1	43	0	TGAGTTAGAA	    0.993012	-78
AGTCATATTCTGAGTTAAAATTAAGTATAG	1	89	1	TGAGTTAAAA	    0.989056	-32
ATTAAGTATAGGAGGTGGACAAA       	1	108	1	GGAGGTGGAC	    0.990699	-13
          **********

Masking position 6
Map Score:   8.33084

Number of sites scoring better than the average of aligned sites = 964
Number in coding regions = 791
Number in noncoding regions = 173
Number of orfs with sites within 600 bp upstream = 163
Fraction of orfs with sites within 600 bp upstream = 0.0261805


Motif number 2

CCTCCTTTTACTTTAAGTATTTTGGTATTA	1	19	1	CTTTAAGTAT	    0.939571	-102
ATGAGTTTTTAAATAACTTGAGTTAGAATT	1	51	0	AAATAACTTG	    0.938258	-70
GACTTTTGACATATGAGTTTTTAAATAACT	1	63	0	ATATGAGTTT	    0.986455	-58
TTAACTCAGAATATGACTTTTGACATATGA	1	77	0	ATATGACTTT	    0.980679	-44
TCTGAGTTAAAATTAAGTATAGGAGGTGGA	1	97	1	AATTAAGTAT	    0.960079	-24
          **********

Masking position 6
Map Score:   2.67509

Number of sites scoring better than the average of aligned sites = 180
Number in coding regions = 153
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

          **********

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 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