AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -idnaA_aful_opreg_300.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	    0.989827	-109
GAGATGCTGTAAGAAAAATTTTTCTATTCA	1	59	1	AAGAAAAATT	    0.996292	-89
CATCTATTGAAGGAAAAATTGAATAGAAAA	1	78	0	AGGAAAAATT	    0.996633	-70
CTCGAAGGGCAGGCAAAATTGTTTTATCTT	1	110	1	AGGCAAAATT	    0.992538	-38
TATGGTAGATAAGAAAGATAAAACAATTTT	1	124	0	AAGAAAGATA	    0.974065	-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

TAACTTTAATACTTTTCAAGAAGACAGGAC	1	14	0	ACTTTTCAAG	    0.985461	-134
TTTTCTTACAGCATCTCAAGAAAACTTGAC	1	46	0	GCATCTCAAG	    0.961997	-102
GAAAAATTTTTCTATTCAATTTTTCCTTCA	1	71	1	TCTATTCAAT	    0.958164	-77
TTCGAGAGCATCTATTGAAGGAAAAATTGA	1	86	0	TCTATTGAAG	    0.987959	-62
TTCAATAGATGCTCTCGAAGGGCAGGCAAA	1	97	1	GCTCTCGAAG	    0.979611	-51
          **********

Masking position 8
Map Score:   2.36786

Number of sites scoring better than the average of aligned sites = 758
Number in coding regions = 716
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 3

TTTTCAAGAAGACAGGACATC         	1	2	0	GACAGGACAT	     0.97985	-146
AAGAAAACTTGACATTAACTTTAATACTTT	1	29	0	GACATTAACT	     0.95678	-119
AAATTTTTCTTACAGCATCTCAAGAAAACT	1	50	0	TACAGCATCT	    0.990695	-98
CCTGCCCTTCGAGAGCATCTATTGAAGGAA	1	93	0	GAGAGCATCT	    0.993701	-55
          **********

Masking position 4
Map Score:   0.892565

Number of sites scoring better than the average of aligned sites = 394
Number in coding regions = 362
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


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


Motif number 6

          **********

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