AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00061_bbur_reg_100.orf -o00061_bbur_100.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	BB0109	136	acetyl-CoA C-acetyltransferase (fadA)

Motif number 1

CCTGAATTATTTAATAAACAAGCTAAAATG	1	24	0	TTAATAAACA	    0.987142	-113
TTATTTAATAAAAATAAACTATTTAACCTG	1	50	0	AAAATAAACT	    0.990985	-87
TTATTTTTATTAAATAAACTTAGTTTTTAT	1	63	1	TAAATAAACT	    0.997243	-74
CAATAGATCATATAAAAACTAAGTTTATTT	1	74	0	TATAAAAACT	    0.971003	-63
TCCTAAAGTCTTAATAAACTTATTGAATTA	1	111	0	TTAATAAACT	    0.996057	-26
          **********

Masking position 6
Map Score:   11.0481

Number of sites scoring better than the average of aligned sites = 72
Number in coding regions = 42
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

ACAAGCTAAAATGTTATAATTTTAAA     	1	6	0	ATGTATAATT	    0.930843	-131
TAGCTTGTTTATTAAATAATTCAGGTTAAAT	1	29	1	ATTAATAATT	     0.98205	-108
AATAATTCAGGTTAAATAGTTTATTTTTATT	1	43	1	GTTAATAGTT	    0.973714	-94
AACTAAGTTTATTTAATAAAAATAAACTATT	1	57	0	ATTAATAAAA	    0.798933	-80
GAATTATACAATACAATAGATCATATAAAAA	1	86	0	ATAAATAGAT	    0.954587	-51
GTATTGTATAATTCAATAAGTTTATTAAGAC	1	103	1	ATTAATAAGT	    0.976473	-34
          *** *******

Masking position 6
Map Score:   5.13085

Number of sites scoring better than the average of aligned sites = 359
Number in coding regions = 228
Number in noncoding regions = 131
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

          **********

No masking
Map Score:   -9.70439e-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:   -9.70439e-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:   -9.70439e-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