AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i343_weak4_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	yiaY	189	putative oxidoreductase

Motif number 1

ATTTTAAAACTTAATTAATCATTTCC    	1	7	0	TTAATTAATC	     0.98611	-183
AGTTTTAAAATAAATTAATACAAAATTCTT	1	26	1	TAAATTAATA	    0.988455	-164
GTGCTTTTTTTAAATTCATAAGAATTTTGT	1	45	0	TAAATTCATA	    0.969049	-145
AGCACATTGTTTAATGAATACAATGTGCTT	1	70	1	TTAATGAATA	    0.974732	-120
ATTGATTATCAAAATTAATCTAATAAAAAG	1	97	0	AAAATTAATC	    0.974392	-93
ATTAATTTTGATAATCAATAATACTGATCA	1	108	1	ATAATCAATA	    0.953865	-82
          **********

Masking position 5
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

TTTGTATTAATTTATTTTAAAACTTAATTA	1	20	0	TTTATTTTAA	     0.76106	-170
TTCATAAGAATTTTGTATTAATTTATTTTA	1	31	0	TTTTGTATTA	    0.916132	-159
AAACAATGTGCTTTTTTTAAATTCATAAGA	1	52	0	CTTTTTTTAA	     0.98253	-138
AAAAAAAGCACATTGTTTAATGAATACAAT	1	64	1	CATTGTTTAA	    0.973264	-126
ATAAAAAGCACATTGTATTCATTAAACAAT	1	75	0	CATTGTATTC	    0.935265	-115
ATACAATGTGCTTTTTATTAGATTAATTTT	1	87	1	CTTTTTATTA	    0.970735	-103
AGCTGCCCGCCCTTTTTTACACTTTCAGGA	1	163	1	CCTTTTTTAC	    0.944598	-27
          **********

Masking position 6
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

TAAATTAATACAAAATTCTTATGAATTTAA	1	36	1	CAAAATTCTT	    0.960555	-154
ATTCATTAAACAATGTGCTTTTTTTAAATT	1	59	0	CAATGTGCTT	     0.99175	-131
TTAATGAATACAATGTGCTTTTTATTAGAT	1	80	1	CAATGTGCTT	     0.99175	-110
TATTGATTATCAAAATTAATCTAATAAAAA	1	98	0	CAAAATTAAT	    0.804902	-92
AAAATATGATCAGTATTATTGATTATCAAA	1	114	0	CAGTATTATT	     0.95922	-76
TGAAAATCCTCAGTAAGCTGCCCGCCCTTT	1	148	1	CAGTAAGCTG	    0.903626	-42
          **********

Masking position 2
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

TGAATTTAAAAAAAGCACATTGTTTAATGA	1	57	1	AAAAGCACAT	    0.995979	-133
TAATCTAATAAAAAGCACATTGTATTCATT	1	82	0	AAAAGCACAT	    0.995979	-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