AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -ilacI_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	BB0351	106	B. burgdorferi predicted coding region BB0351

Motif number 1

ACATAATTTATTGTAAAATAAAAGAAAAAA	1	12	0	TTGTAAAATA	    0.974831	-95
TAATATAACTATAAAAATTATACATAATTT	1	33	0	ATAAAAATTA	    0.961005	-74
CCAATTAAGCATGGAAATTAATATAACTAT	1	51	0	ATGGAAATTA	     0.99627	-56
CCATGCTTAATTGGAAATTAGAGTAAGGTG	1	67	1	TTGGAAATTA	    0.996265	-40
          **********

Masking position 5
Map Score:   6.10373

Number of sites scoring better than the average of aligned sites = 202
Number in coding regions = 128
Number in noncoding regions = 74
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

TTTATTGTAAAATAAAAGAAAAAAC     	1	6	0	AATAAAAGAA	    0.972497	-101
TAACTATAAAAATTATACATAATTTATTGT	1	28	0	AATTATACAT	    0.950506	-79
CATGGAAATTAATATAACTATAAAAATTAT	1	42	0	AATATAACTA	    0.916008	-65
TCTAATTTCCAATTAAGCATGGAAATTAAT	1	59	0	AATTAAGCAT	    0.958608	-48
CTTAATTGGAAATTAGAGTAAGGTGGCTTA	1	72	1	AATTAGAGTA	    0.953812	-35
          **********

Masking position 3
Map Score:   1.57549

Number of sites scoring better than the average of aligned sites = 912
Number in coding regions = 556
Number in noncoding regions = 356
Number of orfs with sites within 600 bp upstream = 89
Fraction of orfs with sites within 600 bp upstream = 0.0142949


Motif number 3

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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