AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i100_Ion_Transporter_bbur_reg_100.orf -o100_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	RBB00043	87	3615

Motif number 1

  ATATTAAAAATAATGTAATTATGATAAT	1	9	1	AATAATGTAA	    0.993222	-79
TAATTATGATAATATTTCAATGTTAAAATA	1	26	1	AATATTTCAA	    0.990346	-62
TATATAGCATAATATTTTAACATTGAAATA	1	38	0	AATATTTTAA	    0.995605	-50
TTAAATTATTAAAAATTTATCTTATATAGC	1	60	0	AAAAATTTAT	     0.88561	-28
ATAAATTTTTAATAATTTAAACAACTTT  	1	70	1	AATAATTTAA	    0.996516	-18
          **********

Masking position 6
Map Score:   11.9754

Number of sites scoring better than the average of aligned sites = 264
Number in coding regions = 162
Number in noncoding regions = 102
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

          ATATTAAAAATAATGTAATT	1	1	1	ATATTAAAAA	    0.897804	-87
CATTGAAATATTATCATAATTACATTATTT	1	18	0	TTATCATAAT	     0.97331	-70
TAATATTTCAATGTTAAAATATTATGCTAT	1	35	1	ATGTTAAAAT	    0.824259	-53
TTTATCTTATATAGCATAATATTTTAACAT	1	45	0	ATAGCATAAT	     0.97161	-43
ATTATGCTATATAAGATAAATTTTTAATAA	1	55	1	ATAAGATAAA	    0.925363	-33
GTTGTTTAAATTATTAAAAATTTATCTTAT	1	65	0	TTATTAAAAA	    0.887245	-23
          **********

Masking position 6
Map Score:   7.38464

Number of sites scoring better than the average of aligned sites = 1413
Number in coding regions = 893
Number in noncoding regions = 520
Number of orfs with sites within 600 bp upstream = 112
Fraction of orfs with sites within 600 bp upstream = 0.0179891


Motif number 3

          **********

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 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