AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i338_weak1_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -x5 
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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

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

Motif number 1

AATCGACTTGTAAACCAAATTGAAAAGATT	1	11	1	TAAACCAAAT	    0.993165	-76
TGTAGACTTGTAAACCTAAATCTTTTCAAT	1	29	0	TAAACCTAAA	    0.987994	-58
TTTACAAGTCTACACCGAATTAACAACAAA	1	45	1	TACACCGAAT	    0.994821	-42
ACACCGAATTAACAACAAAAAACACGTTTT	1	56	1	AACAACAAAA	    0.964698	-31
     GGGGCTTCTCCAAAACGTGTTTTTT	1	72	0	TTCTCCAAAA	    0.977208	-15
          **********

Masking position 8
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	    0.996394	-81
TGTAAACCAAATTGAAAAGATTTAGGTTTA	1	19	1	ATTGAAAAGA	    0.977764	-68
AAAGATTTAGGTTTACAAGTCTACACCGAA	1	34	1	GTTTACAAGT	    0.996394	-53
TCTACACCGAATTAACAACAAAAAACACGT	1	53	1	ATTAACAACA	    0.977764	-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	    0.993771	-86
ACTTGTAAACCAAATTGAAAAGATTTAGGT	1	16	1	CAAATTGAAA	    0.974239	-71
TTTAGGTTTACAAGTCTACACCGAATTAAC	1	39	1	CAAGTCTACA	    0.993501	-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