AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i007_bsub_mtub_100.orf -o007_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	nadB	102	L-aspartate oxidase
#2	nadA	48	nadA

Motif number 1

      CCGGTCTTCCTCCATCCGTTCTCC	1	5	1	TCTTCCTCCA	    0.993206	-98
CTTCCTCCATCCGTTCTCCATAAAAAACTC	1	16	1	CCGTTCTCCA	     0.99827	-87
       ATGCCATCCTCCTGTTGTTTACA	1	90	0	CCATCCTCCT	    0.995672	-13
GCCGCCCCTTCCGCGCTCCAACAGGTTTTC	2	28	0	CCGCGCTCCA	    0.997745	-21
          **********

Masking position 7
Map Score:   6.48409

Number of sites scoring better than the average of aligned sites = 137
Number in coding regions = 125
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

TTACACCTGTCTTGACACCTATATTTACAC	1	65	0	CTTGACACCT	    0.978136	-38
TCCTCCTGTTGTTTACACCTGTCTTGACAC	1	77	0	GTTTACACCT	    0.995132	-26
          GTTTTCGATTATAAGTCGAA	2	1	1	GTTTTCGATT	    0.980936	-48
GCTCCAACAGGTTTTCGACTTATAATCGAA	2	14	0	GTTTTCGACT	    0.995131	-35
          **********

Masking position 3
Map Score:   3.41394

Number of sites scoring better than the average of aligned sites = 403
Number in coding regions = 359
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 3

AGTTTATTTTATCCTTGTGTAAATATAGGT	1	49	1	ATCCTTGTGT	    0.969831	-54
CCTTGTGTAAATATAGGTGTCAAGACAGGT	1	61	1	ATATAGGTGT	    0.978309	-42
ATAGGTGTCAAGACAGGTGTAAACAACAGG	1	73	1	AGACAGGTGT	    0.975219	-30
  ATGCCATCCTCCTGTTGTTTACACCTGT	1	85	0	CTCCTGTTGT	    0.974468	-18
TTCCGCGCTCCAACAGGTTTTCGACTTATA	2	20	0	CAACAGGTTT	     0.93467	-29
          **********

Masking position 8
Map Score:   2.89547

Number of sites scoring better than the average of aligned sites = 723
Number in coding regions = 628
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 4

CGGTCTTCCTCCATCCGTTCTCCATAAAAA	1	12	1	CCATCCGTTC	    0.995889	-91
       ATGCCATCCTCCTGTTGTTTACA	1	90	0	CCATCCTCCT	    0.992466	-13
   TGCCGCCCCTTCCGCGCTCCAACAGGT	2	32	0	CCTTCCGCGC	    0.998202	-17
          **********

Masking position 4
Map Score:   1.45524

Number of sites scoring better than the average of aligned sites = 114
Number in coding regions = 101
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

          **********

No masking
Map Score:   1.51646e-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 6

          **********

No masking
Map Score:   1.51646e-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 7

          **********

No masking
Map Score:   1.51646e-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