AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i104_Cobalt_Transport_aful_reg_100.orf -o104_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	RAG13761	100	Archaeoglobus_fulgidus

Motif number 1

TTTAACTGAGTTTAGAGTTGCAGCA        	1	3	0	TTTGAGTGAG	    0.998146	-98
ATTTAAATTTTTTGGATTTTCAGTAAGATTTAT	1	35	0	TTTGATTTAG	    0.988805	-66
CCTCCAGATTTCTTGAGCTTGTGTCAGATTGAC	1	71	0	TCTGAGTTTG	    0.998162	-30
GCTCAAGAAATCTGGAGGTGTTGTG        	1	86	1	TCTGAGTGTG	    0.998811	-15
          *** *** ** **

Masking position 6
Map Score:   5.25883

Number of sites scoring better than the average of aligned sites = 96
Number in coding regions = 85
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

ATTTTCAGTAAGATTTATTTAACTGAGTTT	1	23	0	AGATTTATTT	    0.977282	-78
GACTTTATTTAAATTTTTTGGATTTTCAGT	1	44	0	AAATTTTTTG	    0.964505	-57
AGCTTGTGTCAGATTGACTTTATTTAAATT	1	59	0	AGATTGACTT	     0.97655	-42
CAACACCTCCAGATTTCTTGAGCTTGTGTC	1	79	0	AGATTTCTTG	    0.993903	-22
          **********

Masking position 5
Map Score:   4.01642

Number of sites scoring better than the average of aligned sites = 76
Number in coding regions = 65
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

AGTAAGATTTATTTAACTGAGTTTAGAGTT	1	17	0	ATTTAACTGA	    0.996141	-84
AGTTAAATAAATCTTACTGAAAATCCAAAA	1	29	1	ATCTTACTGA	    0.991924	-72
AATCCAAAAAATTTAAATAAAGTCAATCTG	1	50	1	ATTTAAATAA	    0.971804	-51
          **********

Masking position 6
Map Score:   2.40182

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 2
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

          **********

No masking
Map Score:   -1.04149e-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:   -1.04149e-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:   -1.04149e-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