AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i338_ecoli_mtub_300.orf -o338_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 =  	0.58
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	bioB	86	biotin synthesis, sulfur insertion?

Motif number 1

AATCTTTTCAATTTGGTTTACAAGTCGATT	1	11	0	ATTTGGTTTA	    0.992751	-76
ATTGAAAAGATTTAGGTTTACAAGTCTACA	1	29	1	TTTAGGTTTA	    0.987273	-58
TTTGTTGTTAATTCGGTGTAGACTTGTAAA	1	45	0	ATTCGGTGTA	    0.994506	-42
AAAACGTGTTTTTTGTTGTTAATTCGGTGT	1	56	0	TTTTGTTGTT	    0.962624	-31
AAAAAACACGTTTTGGAGAAGCCCC     	1	72	1	TTTTGGAGAA	    0.975878	-15
          **********

Masking position 3
Map Score:   7.34427

Number of sites scoring better than the average of aligned sites = 457
Number in coding regions = 406
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 2

TTTCAATTTGGTTTACAAGTCGATT     	1	6	0	GTTTACAAGT	    0.996022	-81
TGTAAACCAAATTGAAAAGATTTAGGTTTA	1	19	1	ATTGAAAAGA	    0.974719	-68
AAAGATTTAGGTTTACAAGTCTACACCGAA	1	34	1	GTTTACAAGT	    0.996022	-53
TCTACACCGAATTAACAACAAAAAACACGT	1	53	1	ATTAACAACA	    0.974719	-34
          **********

Masking position 5
Map Score:   5.02274

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 45
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

ATTTGGTTTACAAGTCGATT          	1	1	0	CAAGTCGATT	     0.99406	-86
ACTTGTAAACCAAATTGAAAAGATTTAGGT	1	16	1	CAAATTGAAA	    0.975413	-71
TTTAGGTTTACAAGTCTACACCGAATTAAC	1	39	1	CAAGTCTACA	    0.993803	-48
          **********

Masking position 3
Map Score:   0.732487

Number of sites scoring better than the average of aligned sites = 172
Number in coding regions = 148
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

          **********

No masking
Map Score:   -1.88842e-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:   -1.88842e-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:   -1.88842e-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