AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i206_nucleases_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	addB	183	ATP-dependent deoxyribonuclease (subunit B)
#2	yrrC	24	similar to conjugation transfer protein
#3	yrrB	85	similar to hypothetical proteins
#4	yrrA	116	similar to hypothetical proteins

Motif number 1

CATATACTTTTACAGAAGCCCAATTCCTAAGAATGG	1	23	0	TCAACCCATC	    0.994991	-161
GATCTATTGGTAAAAACGGCCTTTTCACATATAAAA	1	93	0	TAAAGCCTTC	    0.981739	-91
         ATTAGAAGACCCCTCTCTTTTTATCTC	1	167	0	TAGACCCTTC	    0.988568	-17
      AAGATGAAAAACCTCAACACTGAGTTGGGG	3	5	1	TAAACTCAAC	    0.892437	-81
TTCCTTTCATTAAAAAACCCCAACTCAGTGTTGAGG	3	22	0	TAAACCCATC	    0.995097	-64
CAGTTTTTCATAAAGATTCCGATTACATCATAGCCC	4	39	0	TAAACCGTAC	    0.980504	-78
TCTGTCGCCGTGCAAAAACCGTTTTCGTCCGTATCA	4	78	0	TCAACCGTTC	    0.992629	-39
       ATCTTCATAATCCTCTGTCGCCGTGCAAA	4	98	0	TCAACCTTTC	    0.980102	-19
          * ** *  *** * **

Masking position 6
Map Score:   9.84065

Number of sites scoring better than the average of aligned sites = 271
Number in coding regions = 220
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 2

CCCAATTCCTAAGAATGGAGTTGAATCCCC  	1	9	0	AAGAAGAGTT	    0.934595	-175
CTCCATTCTTAGGAATTGGGCTTCTGTAAAAG	1	21	1	AGGAAGGGCT	    0.994046	-163
GAGAGATAAAAAGAGAGGGGTCTTCTAAT   	1	165	1	AAGAGGGGTC	    0.993814	-19
   CAGGCACAGGAGGAGGGACAGCTC     	2	8	1	AGGAGGGGAC	    0.990835	-17
CTGTTCTTTTAACAGCAGGGCCGCCACAG   	4	8	0	AACAGGGGCC	    0.988093	-109
CTGCTGTTAAAAGAACAGGGCTATGATGTAAT	4	22	1	AAGAAGGGCT	    0.995986	-95
AATCTTTATGAAAAACTGGGATGATACGGACG	4	57	1	AAAAAGGGAT	    0.944577	-60
          *****  *****

Masking position 4
Map Score:   8.79991

Number of sites scoring better than the average of aligned sites = 346
Number in coding regions = 297
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

    GGGGATTCAACTCCATTCTTAGGAAT	1	7	1	TCAACTCCAT	    0.947505	-177
TTATCTCCGCACATCTCTCCCTGCCCAACA	1	57	0	ACATCTCTCC	    0.801839	-127
AAAAAGCTGATTATCTCCGCACATCTCTCC	1	67	0	TTATCTCCGC	    0.955373	-117
ATCAGATTGGTCATTTTCGTCAACATTCGA	1	126	1	TCATTTTCGT	    0.811092	-58
CCCTCTCTTTTTATCTCTCTATATTTTATC	1	154	0	TTATCTCTCT	    0.900952	-30
TTAAAAAACCCCAACTCAGTGTTGAGGTTT	3	19	0	CCAACTCAGT	    0.912824	-67
AATCCACCGATCATCTTCCTTTCATTAAAA	3	43	0	TCATCTTCCT	    0.964183	-43
TGGATTATAATCAACTCGGTATAGAGGCG 	3	67	1	TCAACTCGGT	    0.970705	-19
TTCGTCCGTATCATCCCAGTTTTTCATAAA	4	61	0	TCATCCCAGT	    0.946119	-56
          **********

Masking position 3
Map Score:   3.81481

Number of sites scoring better than the average of aligned sites = 1731
Number in coding regions = 1492
Number in noncoding regions = 239
Number of orfs with sites within 600 bp upstream = 243
Fraction of orfs with sites within 600 bp upstream = 0.0390299


Motif number 4

TATATGTTGGGCAGGGAGAGATGTGCGGAG	1	53	1	GCAGGGAGAG	    0.996037	-131
AGGCACAGGAGGAGGGACAGCTC       	2	12	1	GGAGGGACAG	    0.989448	-13
TCTTTTAACAGCAGGGCCGCCACAG     	4	6	0	GCAGGGCCGC	    0.992738	-111
AACGGTTTTTGCACGGCGACAGAGGATTAT	4	91	1	GCACGGCGAC	    0.993138	-26
          **********

Masking position 3
Map Score:   2.8408

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 58
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

          **********

No masking
Map Score:   -6.86222e-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:   -6.86222e-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:   -6.86222e-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