AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i338_weak1_ecoli_reg_300.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

AATCTTTTCAATTTGGTTTACAAGTCGATT	1	11	0	ATTTGGTTTA	    0.993368	-76
ATTGAAAAGATTTAGGTTTACAAGTCTACA	1	29	1	TTTAGGTTTA	    0.988349	-58
TTTGTTGTTAATTCGGTGTAGACTTGTAAA	1	45	0	ATTCGGTGTA	    0.994975	-42
AAAACGTGTTTTTTGTTGTTAATTCGGTGT	1	56	0	TTTTGTTGTT	     0.96572	-31
AAAAAACACGTTTTGGAGAAGCCCC     	1	72	1	TTTTGGAGAA	    0.977861	-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

     AATCGACTTGTAAACCAAATTGAAA	1	6	1	ACTTGTAAAC	    0.996063	-81
TAAACCTAAATCTTTTCAATTTGGTTTACA	1	19	0	TCTTTTCAAT	    0.975048	-68
TTCGGTGTAGACTTGTAAACCTAAATCTTT	1	34	0	ACTTGTAAAC	    0.996063	-53
ACGTGTTTTTTGTTGTTAATTCGGTGTAGA	1	53	0	TGTTGTTAAT	    0.975048	-34
          **********

Masking position 6
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	    0.993453	-86
ACTTGTAAACCAAATTGAAAAGATTTAGGT	1	16	1	CAAATTGAAA	    0.972951	-71
TTTAGGTTTACAAGTCTACACCGAATTAAC	1	39	1	CAAGTCTACA	     0.99317	-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