AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i206_nucleases_bsub_reg_300.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	    0.995126	-161
GATCTATTGGTAAAAACGGCCTTTTCACATATAAAA	1	93	0	TAAAGCCTTC	    0.982226	-91
         ATTAGAAGACCCCTCTCTTTTTATCTC	1	167	0	TAGACCCTTC	    0.988877	-17
      AAGATGAAAAACCTCAACACTGAGTTGGGG	3	5	1	TAAACTCAAC	    0.895066	-81
TTCCTTTCATTAAAAAACCCCAACTCAGTGTTGAGG	3	22	0	TAAACCCATC	     0.99523	-64
CAGTTTTTCATAAAGATTCCGATTACATCATAGCCC	4	39	0	TAAACCGTAC	    0.981026	-78
TCTGTCGCCGTGCAAAAACCGTTTTCGTCCGTATCA	4	78	0	TCAACCGTTC	    0.992828	-39
       ATCTTCATAATCCTCTGTCGCCGTGCAAA	4	98	0	TCAACCTTTC	    0.980632	-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

GGGGATTCAACTCCATTCTTAGGAATTGGG	1	11	1	CTCCATTCTT	    0.939836	-173
TTTACAGAAGCCCAATTCCTAAGAATGGAG	1	21	0	CCCAATTCCT	    0.970658	-163
TCTCTCCCTGCCCAACATATACTTTTACAG	1	44	0	CCCAACATAT	    0.812236	-140
AGCTGATTATCTCCGCACATCTCTCCCTGC	1	63	0	CTCCGCACAT	    0.880517	-121
CTTTTTATCTCTCTATATTTTATCGAATGT	1	148	0	CTCTATATTT	    0.671862	-36
 ATTAGAAGACCCCTCTCTTTTTATCTCTC	1	165	0	CCCCTCTCTT	    0.941498	-19
   GAGCTGTCCCTCCTCCTGTGCCTG   	2	8	0	CCCTCCTCCT	    0.952544	-17
ATTAAAAAACCCCAACTCAGTGTTGAGGTT	3	20	0	CCCAACTCAG	    0.920577	-66
       CGCCTCTATACCGAGTTGATTAT	3	73	0	CTCTATACCG	    0.702471	-13
 CTGTGGCGGCCCTGCTGTTAAAAGAACAG	4	10	1	CCCTGCTGTT	    0.925619	-107
TACATCATAGCCCTGTTCTTTTAACAGCAG	4	22	0	CCCTGTTCTT	    0.981662	-95
TCCGTATCATCCCAGTTTTTCATAAAGATT	4	57	0	CCCAGTTTTT	    0.914989	-60
          **********

Masking position 3
Map Score:   9.03111

Number of sites scoring better than the average of aligned sites = 2488
Number in coding regions = 2065
Number in noncoding regions = 423
Number of orfs with sites within 600 bp upstream = 381
Fraction of orfs with sites within 600 bp upstream = 0.061195


Motif number 3

ATATAAAAAGCTGATTATCTCCGCACATCT	1	71	0	CTGATTATCT	    0.984498	-113
AGATAATCAGCTTTTTATATGTGAAAAGGC	1	81	1	CTTTTTATAT	    0.931726	-103
AGACCCCTCTCTTTTTATCTCTCTATATTT	1	158	0	CTTTTTATCT	    0.975838	-26
AGTGTTGAGGTTTTTCATCTT         	3	2	0	TTTTTCATCT	    0.838185	-84
TTATAATCCACCGATCATCTTCCTTTCATT	3	47	0	CCGATCATCT	    0.977603	-39
CATAAAGATTCCGATTACATCATAGCCCTG	4	37	0	CCGATTACAT	    0.866755	-80
          **********

Masking position 5
Map Score:   2.66149

Number of sites scoring better than the average of aligned sites = 500
Number in coding regions = 435
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 4

CAGCTTTTTATATGTGAAAAGGCCGTTTTT	1	88	1	TATGTGAAAA	     0.88055	-96
ATCTGATCTATTGGTAAAAACGGCCTTTTC	1	103	0	TTGGTAAAAA	    0.919208	-81
TTATCGAATGTTGACGAAAATGACCAATCT	1	129	0	TTGACGAAAA	    0.948744	-55
TTCGTCAACATTCGATAAAATATAGAGAGA	1	141	1	TTCGATAAAA	    0.757931	-43
          AAGATGAAAAACCTCAACAC	3	1	1	AAGATGAAAA	    0.799678	-85
TCATCTTCCTTTCATTAAAAAACCCCAACT	3	33	0	TTCATTAAAA	    0.938949	-53
CTATACCGAGTTGATTATAATCCACCGATC	3	61	0	TTGATTATAA	    0.840748	-25
AATCGGAATCTTTATGAAAAACTGGGATGA	4	51	1	TTTATGAAAA	    0.951115	-66
          **********

Masking position 7
Map Score:   2.77065

Number of sites scoring better than the average of aligned sites = 2002
Number in coding regions = 1717
Number in noncoding regions = 285
Number of orfs with sites within 600 bp upstream = 318
Fraction of orfs with sites within 600 bp upstream = 0.0510761


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