AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i002_Purine_Nucleotides_Metabolism_bbur_reg_300.orf -o002_borburg_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	RBB00142	87	3615

Motif number 1

     GTTTTTAGCTTATTTTACATTGACTAT	1	6	1	TATTATTTTA	    0.942897	-82
TTTATTTTATTGAAATATTGTAATATAGTCAA	1	30	0	TGATATTGTA	    0.528227	-58
TTAGCCATTGTGGTTTATTTTATTGAAATATT	1	43	0	TGTTATTTTA	    0.993905	-45
ATTTCCCACCTGTTATATTTTATTAGCCATTG	1	65	0	TGATATTTTA	     0.94921	-23
          **  ********

Masking position 6
Map Score:   7.36366

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 36
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

AGTCAATGTAAAATAAGCTAAAAAC     	1	6	0	AAATAAGCTA	    0.975055	-82
AGCTTATTTTACATTGACTATATTACAATA	1	17	1	ACATTGACTA	    0.994702	-71
AAAATAAACCACAATGGCTAATAAAATATA	1	54	1	ACAATGGCTA	    0.996578	-34
          **********

Masking position 3
Map Score:   2.13028

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 12
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

  GTTTTTAGCTTATTTTACATTGACTATA	1	9	1	CTTATTTTAC	    0.961931	-79
TTTTACATTGACTATATTACAATATTTCAA	1	23	1	ACTATATTAC	    0.982658	-65
ATTGTGGTTTATTTTATTGAAATATTGTAA	1	39	0	ATTTTATTGA	    0.961083	-49
CACCTGTTATATTTTATTAGCCATTGTGGT	1	61	0	ATTTTATTAG	    0.982166	-27
          **********

Masking position 5
Map Score:   1.5045

Number of sites scoring better than the average of aligned sites = 474
Number in coding regions = 312
Number in noncoding regions = 162
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 4

          **********

No masking
Map Score:   5.21701e-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:   5.21701e-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 6

          **********

No masking
Map Score:   5.21701e-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