AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_folate_biosynthesis_aful_reg_100.orf -o179_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	RAG46815	38	Archaeoglobus_fulgidus
#2	RAG26652	64	Archaeoglobus_fulgidus

Motif number 1

AAACTTGAAATATAACTTTTTGC        	1	3	0	TAAACTTTTT	    0.977686	-36
AGATAACTCTTAAAACCTTTGCCTTCTTACG	2	17	0	TAAACCTTTG	    0.993988	-48
ACCTCAGGCGTAGAACTTCTGAGATAACTCT	2	38	0	TAAACTTCTG	    0.934207	-27
        GATATCACCTCAGGCGTAGAACT	2	52	0	TACACCTCAG	    0.992589	-13
          ** ********

Masking position 5
Map Score:   5.39823

Number of sites scoring better than the average of aligned sites = 60
Number in coding regions = 51
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

TCAAGTTTCTGTGAGGTGGACAC       	1	26	1	GTGAGGTGGA	    0.997431	-13
          GTGTGGCGTAAGAAGGCAAA	2	1	1	GTGTGGCGTA	    0.998605	-64
  GATATCACCTCAGGCGTAGAACTTCTGA	2	47	0	CTCAGGCGTA	    0.997313	-18
          **********

Masking position 10
Map Score:   3.54156

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 34
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

          **********

No masking
Map Score:   -6.15168e-14

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:   -6.15168e-14

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:   -6.15168e-14

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