AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -icspA_bbur_opreg_100.orf -g0.282 -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 =  	0.282
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	BB0436	172	DNA gyrase, subunit B (gyrB)

Motif number 1

ATGTTAAAAGTATAGTGCTAAAACCAACAAG	1	20	0	TAAGTGCTAA	    0.980955	-153
CATTATACTATATAATGTTAAAAGTATAGTG	1	34	0	TAAATGTTAA	    0.993976	-139
CATTATATAGTATAATGTTAAATTAGGATTC	1	48	1	TAAATGTTAA	    0.993976	-125
ACAATTTAGATAGAATCCTAATTTAACATTA	1	60	0	TAAATCCTAA	    0.986675	-113
TTATTTTTTTTTTAATGTAGAATTTATCTGT	1	135	1	TTAATGTAGA	    0.948692	-38
     TTAATTAAAATCTAGACACAGATAAA	1	157	0	TAAATCTAGA	    0.974867	-16
          ** ********

Masking position 6
Map Score:   8.21255

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 69
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

TTTTAGCACTATACTTTTAACATTATATAG	1	28	1	ATACTTTTAA	    0.935953	-145
ATTTAACATTATACTATATAATGTTAAAAG	1	41	0	ATACTATATA	    0.947543	-132
AAAAATTCACAAACAATTTAGATAGAATCC	1	73	0	AAACAATTTA	    0.935953	-100
GAAATACCAAAAACTTTTAAAAATTCACAA	1	91	0	AAACTTTTAA	    0.863702	-82
TAAAAAAAAAATAATATCTATTACATAGGA	1	119	0	ATAATATCTA	    0.970546	-54
CTAGACACAGATAAATTCTACATTAAAAAA	1	142	0	ATAAATTCTA	    0.952655	-31
      TTAATTAAAATCTAGACACAGATA	1	159	0	TTAAAATCTA	    0.824669	-14
          **********

Masking position 3
Map Score:   5.33373

Number of sites scoring better than the average of aligned sites = 779
Number in coding regions = 488
Number in noncoding regions = 291
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 3

AAAACCAACAAGGACAAAAAA         	1	2	0	AGGACAAAAA	    0.976557	-171
GTATAGTGCTAAAACCAACAAGGACAAAAA	1	12	0	AAAACCAACA	    0.987124	-161
TTACATAGGAAATACCAAAAACTTTTAAAA	1	99	0	AATACCAAAA	    0.986687	-74
ATTCTACATTAAAAAAAAAATAATATCTAT	1	128	0	AAAAAAAAAA	    0.955089	-45
          **********

Masking position 4
Map Score:   1.50682

Number of sites scoring better than the average of aligned sites = 474
Number in coding regions = 327
Number in noncoding regions = 147
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 4

          **********

No masking
Map Score:   1.51646e-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:   1.51646e-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 6

          **********

No masking
Map Score:   1.51646e-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