AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i274_hypothetical19_aful_reg_100.orf -o274_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	RAG45764	139	Archaeoglobus_fulgidus

Motif number 1

TCTGAAGCTCATTCTGACAGAAAAATGAAA	1	11	0	ATTCTGACAG	     0.94259	-129
GAGCTTCAGAATTCCACCTGAAATTGCGTC	1	31	1	ATTCCACCTG	    0.983509	-109
TCCACCTGAAATTGCGTCTGATTTCCTTTG	1	43	1	ATTGCGTCTG	    0.997237	-97
ATTGCGTCTGATTTCCTTTGAAATTCTATC	1	53	1	ATTTCCTTTG	    0.968466	-87
ATAAAGCCTTATTGAGTTTGAGAGGTAAAC	1	98	0	ATTGAGTTTG	    0.958986	-42
GGCTTTATGCATTCCCTCAGCAAATCTGCT	1	120	1	ATTCCCTCAG	     0.99486	-20
          **********

Masking position 3
Map Score:   6.57253

Number of sites scoring better than the average of aligned sites = 384
Number in coding regions = 356
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

CAGGTGGAATTCTGAAGCTCATTCTGACAG	1	21	0	TCTGAAGCTC	    0.996698	-119
TCTGATTTCCTTTGAAATTCTATCCAGCTC	1	59	1	TTTGAAATTC	    0.946568	-81
TTTGAAATTCTATCCAGCTCATCTTCGGTG	1	69	1	TATCCAGCTC	     0.98254	-71
GGTGTTTACCTCTCAAACTCAATAAGGCTT	1	95	1	TCTCAAACTC	    0.994818	-45
ATGCATTCCCTCAGCAAATCTGCT      	1	126	1	TCAGCAAATC	    0.958496	-14
          **********

Masking position 6
Map Score:   5.3702

Number of sites scoring better than the average of aligned sites = 661
Number in coding regions = 613
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

          **********

No masking
Map Score:   -1.82309e-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 4

          **********

No masking
Map Score:   -1.82309e-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:   -1.82309e-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