AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -ihipB_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	BB0434	118	stage 0 sporulation protein J (spo0J)

Motif number 1

      AGAATTGGTTTTTCTTGTTTAAGAAT	1	5	1	TTGTTTTCTT	    0.978858	-114
ATGTTCCACGTGGAACATTCTTAAACAAGAAA	1	21	0	TGGAATTCTT	    0.997561	-98
ATGTTCCACGTGGAACATTCTTTTTTTTTATT	1	35	1	TGGAATTCTT	    0.997561	-84
AACATTCTTTTTTTTTATTCTTAAATTGTAAT	1	48	1	TTTTATTCTT	    0.967029	-71
TATTATAACCTGGTAAAATTTTGTGTTGTAGG	1	84	1	TGGAAATTTT	    0.966423	-35
          *** * ******

Masking position 9
Map Score:   6.25819

Number of sites scoring better than the average of aligned sites = 178
Number in coding regions = 126
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

AAAAAAAGAATGTTCCACGTGGAACATTCT	1	32	0	TGTTCCACGT	    0.993666	-87
AACACAAAATTTTACCAGGTTATAATATTG	1	81	0	TTTACCAGGT	    0.994694	-38
AATTTTGTGTTGTAGGAGGTTTTGACAAT 	1	100	1	TGTAGGAGGT	    0.993414	-19
          **********

Masking position 7
Map Score:   1.41859

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 5
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

          **********

No masking
Map Score:   1.16119e-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 4

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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