AlignACE version 2.2  July 7, 1998
alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jlacI.reg -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 = 	182

Input sequences:
#1	lacZ 122 bp lacZ 1024 1-3075 CDS

Motif number 1

   GCGCAACGCAATTAATGTGAGTTAGCTCA	1	8	1	GCAAAATGTG	    0.940383	-115
AGCCTGGGGTGCCTAATGAGTGAGCTAACTCA	1	28	0	GCCTTGAGTG	    0.994546	-95
CGAGCCGGAAGCATAAAGTGTAAAGCCTGGGG	1	51	0	GCATAGTGTA	    0.984601	-72
CTTCCGGCTCGTATGTTGTGTGGAATTGTGAG	1	72	1	GTATTGTGTG	    0.997086	-51
ATGTTGTGTGGAATTGTGAGCGGATAACAATT	1	84	1	GAATTGAGCG	     0.97438	-39
      AGCTGTTTCCTGTGTGAAATTGTTAT	1	107	0	GTTTTGTGTG	    0.990477	-16
          ****  ******

Masking position 10
Map Score:   5.81393

Number of sites scoring better than the average of aligned sites = 681
Number in coding regions = 613
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 2

ACCCCAGGCTTTACACTTTATGCTTCCGGC	1	50	1	TTACACTTTA	    0.973125	-73
TGTTATCCGCTCACAATTCCACACAACATA	1	83	0	TCACAATTCC	    0.993309	-40
TGTGAGCGGATAACAATTTCACACAGGAAA	1	98	1	TAACAATTTC	    0.991405	-25
          **********

Masking position 5
Map Score:   0.688411

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 69
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 3

          **********

No masking
Map Score:   1.23224e-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:   1.23224e-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:   1.23224e-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