AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i288_moxr_hypothetical_bbur_reg_100.orf -o288_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	RBB00563	35	3615
#2	RBB00560	83	3615

Motif number 1

          TATTATTATCGTTTAAGTTC	1	1	1	TATTATTATC	    0.870722	-35
      TCTAAAATATAAACTGAACTTAAA	1	22	0	AAATATAAAC	    0.978151	-14
TTATGAAATTAATTATAAGCTATTATAAAC	2	13	1	AATTATAAGC	    0.962403	-71
AATTATAAGCTATTATAAACATATTTACAA	2	23	1	TATTATAAAC	    0.888501	-61
 ACTTTAATGTATTATAACACAATAAAAAA	2	65	0	TATTATAACA	    0.614367	-19
          **********

Masking position 5
Map Score:   7.50434

Number of sites scoring better than the average of aligned sites = 168
Number in coding regions = 96
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

CTGAACTTAAACGATAATAATA        	1	3	0	ACGATAATAA	    0.941008	-33
       TCTAAAATATAAACTGAACTTAA	1	23	0	AAAATATAAA	    0.925517	-13
   TTTTATGAAATTAATTATAAGCTATTA	2	8	1	AAATTAATTA	    0.858871	-76
AGCTATTATAAACATATTTACAAATCAATT	2	30	1	AACATATTTA	     0.97349	-54
AATGTATTATAACACAATAAAAAAGACAAA	2	59	0	AACACAATAA	    0.985197	-25
ATTGTGTTATAATACATTAAAGT       	2	71	1	AATACATTAA	    0.960593	-13
          **********

Masking position 6
Map Score:   4.26647

Number of sites scoring better than the average of aligned sites = 1431
Number in coding regions = 926
Number in noncoding regions = 505
Number of orfs with sites within 600 bp upstream = 109
Fraction of orfs with sites within 600 bp upstream = 0.0175072


Motif number 3

          **********

No masking
Map Score:   1.16119e-13

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:   1.16119e-13

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:   1.16119e-13

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