AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -irhaS_bbur_opreg_300.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	BB0665	42	B. burgdorferi predicted coding region BB0665
#2	BB0668	70	flagellar filament outer layer protein (flaA)

Motif number 1

TATAATTAAATTATAATAATCAT       	1	4	0	TTATAATAAT	    0.984864	-39
TTTAAAATCCTTATAATTAAATTATAATAA	1	15	0	TTATAATTAA	    0.936739	-28
ATTATAAGGATTTTAAAAGTAATTT     	1	28	1	TTTTAAAAGT	     0.97791	-15
TTTTAATTATTTTTATTAGTAAAATTTAAT	2	14	0	TTTTATTAGT	     0.97791	-57
AATTTTCGTTTTTTAATTATTTTTATTAGT	2	24	0	TTTTAATTAT	    0.984864	-47
AAAACGAAAATTTTATAAAAGATTTATATA	2	42	1	TTTTATAAAA	    0.499197	-29
TATAAAAGATTTATATATATAAGGAG    	2	55	1	TTATATATAT	    0.707925	-16
          **********

Masking position 5
Map Score:   13.1495

Number of sites scoring better than the average of aligned sites = 2022
Number in coding regions = 1226
Number in noncoding regions = 796
Number of orfs with sites within 600 bp upstream = 158
Fraction of orfs with sites within 600 bp upstream = 0.0253774


Motif number 2

AATCCTTATAATTAAATTATAATAATCAT 	1	10	0	ATTAAATTAT	    0.925512	-33
        AAATTACTTTTAAAATCCTTAT	1	31	0	ATTACTTTTA	    0.924673	-12
       TAAATTAAATTTTACTAATAAAA	2	4	1	ATTAAATTTT	    0.980313	-67
TTCGTTTTTTAATTATTTTTATTAGTAAAA	2	20	0	AATTATTTTT	    0.851486	-51
TAAATCTTTTATAAAATTTTCGTTTTTTAA	2	38	0	ATAAAATTTT	    0.817134	-33
CCTTATATATATAAATCTTTTATAAAATTT	2	49	0	ATAAATCTTT	    0.799308	-22
          **********

Masking position 8
Map Score:   7.80499

Number of sites scoring better than the average of aligned sites = 2203
Number in coding regions = 1435
Number in noncoding regions = 768
Number of orfs with sites within 600 bp upstream = 163
Fraction of orfs with sites within 600 bp upstream = 0.0261805


Motif number 3

          **********

No masking
Map Score:   -5.44113e-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:   -5.44113e-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 5

          **********

No masking
Map Score:   -5.44113e-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