AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i104_Cobalt_Transport_aful_reg_300.orf -o104_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	RAG13761	100	Archaeoglobus_fulgidus

Motif number 1

        TGCTGCAACTCTAAACTCAGTTAAA	1	3	1	CTCACTCAAA	    0.998124	-98
ATAAATCTTACTGAAAATCCAAAAAATTTAAAT	1	35	1	CTAAATCAAA	    0.988675	-66
GTCAATCTGACACAAGCTCAAGAAATCTGGAGG	1	71	1	CAAACTCAGA	     0.99814	-30
        CACAACACCTCCAGATTTCTTGAGC	1	86	0	CACACTCAGA	    0.998797	-15
          ** ** *** ***

Masking position 8
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	    0.975099	-78
GACTTTATTTAAATTTTTTGGATTTTCAGT	1	44	0	AAATTTTTTG	    0.971173	-57
AGCTTGTGTCAGATTGACTTTATTTAAATT	1	59	0	AGATTGACTT	    0.980825	-42
CAACACCTCCAGATTTCTTGAGCTTGTGTC	1	79	0	AGATTTCTTG	    0.995127	-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

AACTCTAAACTCAGTTAAATAAATCTTACT	1	17	1	TCAGTTAAAT	    0.996509	-84
TTTTGGATTTTCAGTAAGATTTATTTAACT	1	29	0	TCAGTAAGAT	    0.992687	-72
CAGATTGACTTTATTTAAATTTTTTGGATT	1	50	0	TTATTTAAAT	    0.974394	-51
          **********

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