AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i097_aful_mthe_300.orf -o097_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	RAG29809	87	Archaeoglobus_fulgidus

Motif number 1

          GATATATAGCCATTTATTGGATATA	1	1	1	GATATACCTT	    0.999513	-87
CCATTTATTGGATATATATCCCTATCGATATTCTA	1	20	1	GATATACCTT	    0.999513	-68
TATCCCTATCGATATTCTACCGTTTAAGGAAAAGG	1	36	1	GATATTCCTT	      0.9984	-52
TTCGAACTCTGATATATATCCTTTTCCTTAAACGG	1	55	0	GATATACCTT	    0.999513	-33
ATATATATCAGAGTTCGAACGCTCTGC        	1	71	1	GAGTTACGTT	    0.987629	-17
          *****  * ** * *

Masking position 5
Map Score:   13.5178

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 4
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

     GATATATAGCCATTTATTGGATATA	1	6	1	ATAGCCATTT	    0.935841	-82
TATTGGATATATATCCCTATCGATATTCTA	1	25	1	ATATCCCTAT	    0.771317	-63
ACTCTGATATATATCCTTTTCCTTAAACGG	1	55	0	ATATCCTTTT	    0.989863	-33
          **********

Masking position 3
Map Score:   4.35519

Number of sites scoring better than the average of aligned sites = 28
Number in coding regions = 24
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

 GATATATAGCCATTTATTGGATATATATC	1	10	1	CCATTTATTG	    0.783465	-78
CGATATTCTACCGTTTAAGGAAAAGGATAT	1	45	1	CCGTTTAAGG	    0.836732	-43
          **********

Masking position 5
Map Score:   0.0325993

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 9
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

No masking
Map Score:   5.21701e-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:   5.21701e-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:   5.21701e-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