AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i228_6_1_1_17_aful_reg_100.orf -o228_aful_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAG50068	112	Archaeoglobus_fulgidus

Motif number 1

      TGGATTTTGCTTGAAGTTGAGGTT	1	5	1	TTTTGCTTGA	    0.986791	-108
TTGCTTGAAGTTGAGGTTAAAATTTTTTAG	1	17	1	TTGAGGTTAA	    0.970104	-96
GTTAAAATTTTTTAGGTTGGGTGATGCGCT	1	32	1	TTTAGGTTGG	    0.996983	-81
  TGATGTTGTTCTGGTTGGGCCGATAAAA	1	95	0	TTCTGGTTGG	    0.996464	-18
          **********

Masking position 7
Map Score:   5.01796

Number of sites scoring better than the average of aligned sites = 243
Number in coding regions = 213
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

GTTGGGTGATGCGCTAAATACTTCAAGACA	1	47	1	GCGCTAAATA	     0.99434	-66
TAAAAATTTACCGCTAAAAGGCCTGTCTTG	1	70	0	CCGCTAAAAG	    0.997745	-43
TCTGGTTGGGCCGATAAAAATTTACCGCTA	1	84	0	CCGATAAAAA	    0.995226	-29
          **********

Masking position 6
Map Score:   3.65423

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 7
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

          **********

No masking
Map Score:   1.3033e-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 4

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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