AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i194_aful_mthe_300.orf -o194_aful_mthe_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

CCCCACCAAAAGGAAATGGTAGGGCAGGCA	1	27	1	AGGAAATGGT	    0.998085	-34
ATGGTAGGGCAGGCATCGGTGAGAGGAGC 	1	42	1	AGGCATCGGT	    0.997782	-19
         GAGGAAAAGGTTAAGAGGCAA	2	29	0	AGGAAAAGGT	     0.99848	-11
          **********

Masking position 5
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

ATTTTTTACACAGCCCCACCAAAAGGAAAT	1	14	1	CAGCCCCACC	    0.999605	-47
TCACCGATGCCTGCCCTACCATTTCCTTTT	1	34	0	CTGCCCTACC	    0.999414	-27
          **********

Masking position 8
Map Score:   2.96342

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 28
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

GGCAGGCATCGGTGAGAGGAGC        	1	49	1	GGTGAGAGGA	    0.998074	-12
 GAGGAAAAGGTTAAGAGGCAAAATAAAGA	2	21	0	GTTAAGAGGC	    0.997122	-19
          **********

Masking position 5
Map Score:   0.341791

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 36
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          AAAATTTTTTACACAGCCCC	1	1	1	AAAATTTTTT	    0.613066	-60
     CTCAGAAAACTCTTTATTTTGCCTC	2	6	1	AAAACTCTTT	    0.880489	-34
ATTTTGCCTCTTAACCTTTTCCTC      	2	26	1	TTAACCTTTT	    0.959961	-14
          **********

Masking position 4
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 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


Motif number 7

          **********

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