AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i319_aful_mthe_300.orf -o319_aful_mthe_300.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	RAG50028	105	Archaeoglobus_fulgidus

Motif number 1

         GATGAGAGGATGATTGAACAAT	1	2	1	ATGAAGGATG	    0.992415	-104
ATGATTGAACAATATAAAATGTTTTTCAATG	1	20	1	AATAAAAATG	    0.989674	-86
AAGTGAAAGAATGACAAAATGAACATTGAAA	1	43	0	ATGAAAAATG	    0.997377	-63
GGTATTTAAAATTAAAAAATGTTTCGTGTAA	1	74	0	ATTAAAAATG	    0.995948	-32
          **** ******

Masking position 6
Map Score:   6.45899

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 17
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

GAGAGGATGATTGAACAATATAAAATGTTT	1	14	1	TTGAACAATA	    0.903163	-92
ATGAACATTGAAAAACATTTTATATTGTTC	1	26	0	AAAAACATTT	    0.965327	-80
GAATGACAAAATGAACATTGAAAAACATTT	1	36	0	ATGAACATTG	    0.979366	-70
CGTGTAAAAGTGAAAGAATGACAAAATGAA	1	51	0	TGAAAGAATG	    0.928976	-55
CACTTTTACACGAAACATTTTTTAATTTTA	1	69	1	CGAAACATTT	    0.985266	-37
          CAGAAGATTTCGGTATTTAA	1	96	0	CAGAAGATTT	    0.972627	-10
          **********

Masking position 5
Map Score:   4.03088

Number of sites scoring better than the average of aligned sites = 460
Number in coding regions = 397
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 3

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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:   -1.9652e-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