AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i343_weak4_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yiaY	189	putative oxidoreductase

Motif number 1

    GGAAATGATTAATTAAGTTTTAAAAT	1	7	1	GATTAATTAA	    0.987355	-183
AAGAATTTTGTATTAATTTATTTTAAAACT	1	26	0	TATTAATTTA	    0.989492	-164
ACAAAATTCTTATGAATTTAAAAAAAGCAC	1	45	1	TATGAATTTA	    0.971779	-145
AAGCACATTGTATTCATTAAACAATGTGCT	1	70	0	TATTCATTAA	    0.976973	-120
CTTTTTATTAGATTAATTTTGATAATCAAT	1	97	1	GATTAATTTT	    0.976662	-93
TGATCAGTATTATTGATTATCAAAATTAAT	1	108	0	TATTGATTAT	    0.957876	-82
          **********

Masking position 6
Map Score:   8.71427

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 56
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 2

TAATTAAGTTTTAAAATAAATTAATACAAA	1	20	1	TTAAAATAAA	     0.76106	-170
TAAAATAAATTAATACAAAATTCTTATGAA	1	31	1	TAATACAAAA	    0.916132	-159
TCTTATGAATTTAAAAAAAGCACATTGTTT	1	52	1	TTAAAAAAAG	     0.98253	-138
ATTGTATTCATTAAACAATGTGCTTTTTTT	1	64	0	TTAAACAATG	    0.973264	-126
ATTGTTTAATGAATACAATGTGCTTTTTAT	1	75	1	GAATACAATG	    0.935265	-115
AAAATTAATCTAATAAAAAGCACATTGTAT	1	87	0	TAATAAAAAG	    0.970735	-103
TCCTGAAAGTGTAAAAAAGGGCGGGCAGCT	1	163	0	GTAAAAAAGG	    0.944598	-27
          **********

Masking position 5
Map Score:   5.81614

Number of sites scoring better than the average of aligned sites = 771
Number in coding regions = 497
Number in noncoding regions = 274
Number of orfs with sites within 600 bp upstream = 287
Fraction of orfs with sites within 600 bp upstream = 0.046097


Motif number 3

TTAAATTCATAAGAATTTTGTATTAATTTA	1	36	0	AAGAATTTTG	    0.960525	-154
AATTTAAAAAAAGCACATTGTTTAATGAAT	1	59	1	AAGCACATTG	    0.992108	-131
ATCTAATAAAAAGCACATTGTATTCATTAA	1	80	0	AAGCACATTG	    0.992108	-110
TTTTTATTAGATTAATTTTGATAATCAATA	1	98	1	ATTAATTTTG	    0.811868	-92
TTTGATAATCAATAATACTGATCATATTTT	1	114	1	AATAATACTG	    0.960629	-76
AAAGGGCGGGCAGCTTACTGAGGATTTTCA	1	148	0	CAGCTTACTG	    0.906448	-42
          **********

Masking position 9
Map Score:   5.15799

Number of sites scoring better than the average of aligned sites = 619
Number in coding regions = 543
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 88
Fraction of orfs with sites within 600 bp upstream = 0.0141343


Motif number 4

TCATTAAACAATGTGCTTTTTTTAAATTCA	1	57	0	ATGTGCTTTT	    0.995921	-133
AATGAATACAATGTGCTTTTTATTAGATTA	1	82	1	ATGTGCTTTT	    0.995921	-108
          **********

Masking position 4
Map Score:   2.55313

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:   -3.24418e-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 6

          **********

No masking
Map Score:   -3.24418e-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 7

          **********

No masking
Map Score:   -3.24418e-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