AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i228_6_1_1_17_bbur_reg_100.orf -o228_borburg_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	RBB00375	124	3615

Motif number 1

CATGGTTAATAGAGCTTAATTTCAAGGGAAT	1	13	0	AGGCTTAATT	    0.980974	-112
ATATCATATTATTTATTAATTGTCTATCTAT	1	45	1	ATTATTAATT	    0.932326	-80
TTTATTAATTGTCTATCTATTAGTATAATGT	1	56	1	GTTATCTATT	    0.934539	-69
TATTAGTATAATGTATTTATTATATCTCAAT	1	73	1	ATTATTTATT	    0.978985	-52
TGTATTTATTATATCTCAATTTTTGAATTAA	1	84	1	ATTCTCAATT	    0.991325	-41
TCTCTTCAAAAAAGCTTAATTCAAAAATTGA	1	99	0	AAGCTTAATT	    0.971756	-26
          ** ********

Masking position 6
Map Score:   6.62815

Number of sites scoring better than the average of aligned sites = 328
Number in coding regions = 211
Number in noncoding regions = 117
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

TAGAGCTTAATTTCAAGGGAATAA      	1	5	0	TTTCAAGGGA	    0.990531	-120
TATCTCAATTTTTGAATTAAGCTTTTTTGA	1	95	1	TTTGAATTAA	     0.96092	-30
ATTAAGCTTTTTTGAAGAGATTTTT     	1	110	1	TTTGAAGAGA	    0.992024	-15
          **********

Masking position 5
Map Score:   0.588863

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 80
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

          **********

No masking
Map Score:   -6.15168e-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:   -6.15168e-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:   -6.15168e-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