AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -idnaA_aful_opreg_100.orf -g0.49 -x5 
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 = 	0

Input sequences:
#1	AF1664	147	ribonucleotide reductase (nrd)

Motif number 1

ACAGCATCTCAAGAAAACTTGACATTAACT	1	39	0	AAGAAAACTT	    0.989567	-109
GAGATGCTGTAAGAAAAATTTTTCTATTCA	1	59	1	AAGAAAAATT	    0.996136	-89
CATCTATTGAAGGAAAAATTGAATAGAAAA	1	78	0	AGGAAAAATT	    0.996485	-70
CTCGAAGGGCAGGCAAAATTGTTTTATCTT	1	110	1	AGGCAAAATT	    0.992213	-38
TATGGTAGATAAGAAAGATAAAACAATTTT	1	124	0	AAGAAAGATA	    0.972951	-24
          **********

Masking position 5
Map Score:   10.9974

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 29
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

TGTCCTGTCTTCTTGAAAAGTATTAAAGTT	1	13	1	TCTTGAAAAG	    0.991674	-135
TGTCAAGTTTTCTTGAGATGCTGTAAGAAA	1	45	1	TCTTGAGATG	    0.968335	-103
TTGAAGGAAAAATTGAATAGAAAAATTTTT	1	72	0	AATTGAATAG	    0.904721	-76
CGAGAGCATCTATTGAAGGAAAAATTGAAT	1	84	0	TATTGAAGGA	    0.960303	-64
CAATAGATGCTCTCGAAGGGCAGGCAAAAT	1	99	1	TCTCGAAGGG	    0.992433	-49
          **********

Masking position 6
Map Score:   2.36786

Number of sites scoring better than the average of aligned sites = 784
Number in coding regions = 747
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

          **********

No masking
Map Score:   5.92755e-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:   5.92755e-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:   5.92755e-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