AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i176_cobalamin_biosynthesis_1_aful_reg_300.orf -o176_aful_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	RAG13740	100	Archaeoglobus_fulgidus

Motif number 1

GCTCAAGAAATCTGGAGGTGTTGTG        	1	3	0	TCTGAGTGTG	    0.998875	-98
CCTCCAGATTTCTTGAGCTTGTGTCAGATTGAC	1	18	1	TCTGAGTTTG	    0.998261	-83
ATTTAAATTTTTTGGATTTTCAGTAAGATTTAT	1	54	1	TTTGATTTAG	    0.989405	-47
TTTAACTGAGTTTAGAGTTGCAGCA        	1	86	1	TTTGAGTGAG	    0.998244	-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

CAACACCTCCAGATTTCTTGAGCTTGTGTC	1	13	1	AGATTTCTTG	    0.994689	-88
AGCTTGTGTCAGATTGACTTTATTTAAATT	1	33	1	AGATTGACTT	    0.979304	-68
GACTTTATTTAAATTTTTTGGATTTTCAGT	1	48	1	AAATTTTTTG	    0.968788	-53
ATTTTCAGTAAGATTTATTTAACTGAGTTT	1	69	1	AGATTTATTT	    0.976083	-32
          **********

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

CAGATTGACTTTATTTAAATTTTTTGGATT	1	42	1	TTATTTAAAT	    0.970805	-59
TTTTGGATTTTCAGTAAGATTTATTTAACT	1	63	1	TCAGTAAGAT	    0.991629	-38
AACTCTAAACTCAGTTAAATAAATCTTACT	1	75	0	TCAGTTAAAT	    0.995999	-26
          **********

Masking position 7
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