AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00440_bbur_reg_300.orf -o00440_bbur_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e 
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 =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	BB0590	36	dimethyladenosine transferase (ksgA)
#2	BB0591	115	competence locus E, putative

Motif number 1

          AATAATTTTAAAATATCTGT	1	1	1	AATAATTTTA	    0.707546	-36
          ATTATTCTTAATAATGACAG	1	27	0	ATTATTCTTA	    0.971841	-10
ATTGTAATTAAATAATTATTAATTGTCAAC	2	16	1	AATAATTATT	    0.499263	-100
TTAATCAATCAATAATCATTCGTTGACAAT	2	37	0	AATAATCATT	    0.675647	-79
TTATTGATTGATTAATCAAAACAAATTAAA	2	52	1	ATTAATCAAA	    0.942618	-64
AAAACAAATTAAAATTCAAAATATAATTAT	2	69	1	AAAATTCAAA	    0.861916	-47
TTTATTTATAAATAATTATATTTTGAATTT	2	80	0	AATAATTATA	    0.551709	-36
TATTCTTATTTTTATTTATAAATAATTATA	2	90	0	TTTATTTATA	    0.755826	-26
      TTATAATATTCTTATTTTTATTTA	2	102	0	AATATTCTTA	    0.984463	-14
          **********

Masking position 6
Map Score:   15.8414

Number of sites scoring better than the average of aligned sites = 1131
Number in coding regions = 745
Number in noncoding regions = 386
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 2

          **********

No masking
Map Score:   7.34864e-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 3

          **********

No masking
Map Score:   7.34864e-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 4

          **********

No masking
Map Score:   7.34864e-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