AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00650_bbur_reg_300.orf -o00650_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	BB0109	136	acetyl-CoA C-acetyltransferase (fadA)

Motif number 1

CATTTTAGCTTGTTTATTAAATAATTCAGG	1	24	1	TGTTTATTAA	    0.985074	-113
CAGGTTAAATAGTTTATTTTTATTAAATAA	1	50	1	AGTTTATTTT	    0.989531	-87
ATAAAAACTAAGTTTATTTAATAAAAATAA	1	63	0	AGTTTATTTA	    0.996795	-74
AAATAAACTTAGTTTTTATATGATCTATTG	1	74	1	AGTTTTTATA	    0.966417	-63
TAATTCAATAAGTTTATTAAGACTTTAGGA	1	111	1	AGTTTATTAA	    0.995416	-26
          **********

Masking position 5
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

     TTTAAAATTATAACATTTTAGCTTGT	1	6	1	AATTATACAT	    0.932929	-131
ATTTAACCTGAATTATTTAATAAACAAGCTA	1	29	0	AATTATTAAT	    0.981983	-108
AATAAAAATAAACTATTTAACCTGAATTATT	1	43	0	AACTATTAAC	    0.974557	-94
AATAGTTTATTTTTATTAAATAAACTTAGTT	1	57	1	TTTTATTAAT	    0.796581	-80
TTTTTATATGATCTATTGTATTGTATAATTC	1	86	1	ATCTATTTAT	    0.955953	-51
GTCTTAATAAACTTATTGAATTATACAATAC	1	103	0	ACTTATTAAT	    0.976589	-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