AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i194_dna_replication_aful_reg_300.orf -o194_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	RAG17482	60	Archaeoglobus_fulgidus
#2	RAG17481	39	Archaeoglobus_fulgidus

Motif number 1

TGCCTGCCCTACCATTTCCTTTTGGTGGGG	1	27	0	ACCATTTCCT	       0.998	-34
 GCTCCTCTCACCGATGCCTGCCCTACCAT	1	42	0	ACCGATGCCT	    0.997624	-19
TTGCCTCTTAACCTTTTCCTC         	2	29	1	ACCTTTTCCT	    0.998365	-11
          **********

Masking position 1
Map Score:   5.88794

Number of sites scoring better than the average of aligned sites = 31
Number in coding regions = 26
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

GCCCCACCAAAAGGAAATGGTAGGGCAGGC	1	26	1	AAGGAAATGG	    0.991026	-35
AATGGTAGGGCAGGCATCGGTGAGAGGAGC	1	41	1	CAGGCATCGG	    0.993269	-20
AAAAGGTTAAGAGGCAAAATAAAGAGTTTT	2	16	0	GAGGCAAAAT	     0.98115	-24
          GAGGAAAAGGTTAAGAGGCA	2	30	0	GAGGAAAAGG	    0.998121	-10
          **********

Masking position 6
Map Score:   3.94445

Number of sites scoring better than the average of aligned sites = 758
Number in coding regions = 718
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 3

GGGGCTGTGTAAAAAATTTT          	1	1	0	AAAAAATTTT	    0.613404	-60
GAGGCAAAATAAAGAGTTTTCTGAG     	2	6	0	AAAGAGTTTT	    0.880819	-34
      GAGGAAAAGGTTAAGAGGCAAAAT	2	26	0	AAAAGGTTAA	    0.959902	-14
          **********

Masking position 3
Map Score:   0.387054

Number of sites scoring better than the average of aligned sites = 153
Number in coding regions = 93
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 4

          **********

No masking
Map Score:   -1.88842e-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:   -1.88842e-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 6

          **********

No masking
Map Score:   -1.88842e-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