AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i282_hypothetical7_aquae_reg_300.orf -o282_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	RAA00475	120	Aquifex_aeolicus

Motif number 1

       GGTTTCCACCTCCTTTTACTTTA	1	4	1	TTCCACCTCC	    0.996898	-117
TTCCACCTCCTTTTACTTTAAGTATTTTGG	1	14	1	TTTTACTTTA	    0.891259	-107
GAGTTAGAATTTTTAATACCAAAATACTTA	1	32	0	TTTTAATACC	    0.928929	-89
GTATTAAAAATTCTAACTCAAGTTATTTAA	1	43	1	TTCTAACTCA	    0.993663	-78
CTATACTTAATTTTAACTCAGAATATGACT	1	89	0	TTTTAACTCA	    0.990071	-32
       TTTGTCCACCTCCTATACTTAAT	1	108	0	GTCCACCTCC	    0.991562	-13
          **********

Masking position 5
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

TAATACCAAAATACTTAAAGTAAAAGGAGG	1	19	0	ATACTTAAAG	    0.942094	-102
AATTCTAACTCAAGTTATTTAAAAACTCAT	1	51	1	CAAGTTATTT	    0.940799	-70
AGTTATTTAAAAACTCATATGTCAAAAGTC	1	63	1	AAACTCATAT	    0.986989	-58
TCATATGTCAAAAGTCATATTCTGAGTTAA	1	77	1	AAAGTCATAT	    0.981462	-44
TCCACCTCCTATACTTAATTTTAACTCAGA	1	97	0	ATACTTAATT	    0.961776	-24
          **********

Masking position 5
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