AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i031_2_7_1_29_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	b1200	188	putative dihydroxyacetone kinase (EC 2.7.1.2)

Motif number 1

AATACACGTAAAAGTTTCAATATGGAACAT	1	53	1	AAAGTTTCAA	    0.945233	-136
TGCTTTAATGAATGTTCCATATTGAAACTT	1	64	0	AATGTTCCAT	    0.990816	-125
CATTAAAGCATATGTTTCACTATGAAACAT	1	84	1	TATGTTTCAC	    0.993585	-105
TAGCCCAAATTATGTTTCATAGTGAAACAT	1	95	0	TATGTTTCAT	    0.990112	-94
      GGATGATGTTCAACGACACGGCGA	1	175	0	GATGTTCAAC	    0.963894	-14
          **********

Masking position 5
Map Score:   5.42622

Number of sites scoring better than the average of aligned sites = 155
Number in coding regions = 125
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

ACGTAAAAGTTTCAATATGGAACATTCATT	1	58	1	TTCAATATGG	    0.990721	-131
AAGCATATGTTTCACTATGAAACATAATTT	1	89	1	TTCACTATGA	     0.99072	-100
CCTTGCCTGATGCACAATGGATTCATCGGC	1	136	1	TGCACAATGG	    0.992848	-53
          **********

Masking position 4
Map Score:   1.88524

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 40
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

          **********

No masking
Map Score:   6.63809e-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 4

          **********

No masking
Map Score:   6.63809e-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:   6.63809e-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