AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i034_bsub_mtub_100.orf -o034_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	yvgQ	25	similar to sulfite reductase
#2	yvgR	170	similar to sulfite reductase

Motif number 1

AAAAACTCCTTTCAAGTCAAA         	1	2	0	TTCAAGTCAA	    0.981462	-24
ACGGCTATGCTTCATGTAAATAGAAAAAAG	2	29	0	TTCATGTAAA	    0.986796	-142
AATAGTTATCATCATGTAAATATATTTTAC	2	77	1	ATCATGTAAA	     0.98023	-94
GAATACTAGGCTTAAGTAAAATATATTTAC	2	92	0	CTTAAGTAAA	      0.9197	-79
AAGCCTAGTATTCCGGTAAAGTTCAATTAG	2	109	1	TTCCGGTAAA	     0.98044	-62
TCCGGTAAAGTTCAATTAGATGCAATTTTC	2	120	1	TTCAATTAGA	     0.91617	-51
          **********

Masking position 7
Map Score:   6.60586

Number of sites scoring better than the average of aligned sites = 386
Number in coding regions = 327
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 2

TGACTTGAAAGGAGTTTTTCAAC       	1	13	1	GGAGTTTTTC	    0.990893	-13
   AGAGAAGGGAGTCCTTCTCTTTTTTCT	2	8	1	GGAGTCCTTC	    0.977598	-163
TTTATCATTAGGATTCTTAATAGTTATCAT	2	59	1	GGATTCTTAA	    0.965411	-112
          **********

Masking position 3
Map Score:   0.305657

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 91
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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