AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i290_oxidoreductase_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	b1970	84	orf, hypothetical protein
#2	b1971	108	putative reductase

Motif number 1

ATCCTTGTCATGTGAATGAGTTTTGAGGAT	1	59	0	TGTGAATGAG	    0.982019	-26
CTCATTCACATGACAAGGATATAAAC    	1	69	1	TGACAAGGAT	    0.974648	-16
TCTCTGCTACTGTTAGGGAGGACACTCCCT	2	33	1	TGTTAGGGAG	    0.993851	-76
ACTGTTAATCTGTCAGGGAGTGTCCTCCCT	2	47	0	TGTCAGGGAG	    0.997735	-62
GACAAAAAAGTGTGATGGCTT         	2	98	1	TGTGATGGCT	    0.969954	-11
          **********

Masking position 5
Map Score:   5.90977

Number of sites scoring better than the average of aligned sites = 158
Number in coding regions = 125
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

GTAATGCTGCTGTAAGGTTACCCTGGACGCTTTT	1	20	1	TGTGTTACCT	    0.996507	-65
CCCTGGACGCTTTTTCGCTATCCTCAAAACTCAT	1	40	1	TTTGCTACCT	    0.996445	-45
GCAAGAGCCGTTTACTGTTAATCTGTCAGGGAGT	2	56	0	TTTGTTATCT	    0.991907	-53
ATCACACTTTTTTGTCGTTAGCCAGCAAGAGCCG	2	80	0	TTTGTTACCA	    0.994797	-29
          ***   **** ***

Masking position 9
Map Score:   2.34024

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 44
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

CAAAATTGTAATGCTGCTGTAAGGTTACCC	1	13	1	ATGCTGCTGT	    0.988172	-72
AAGCAGATCTCTGCTACTGTTAGGGAGGAC	2	26	1	CTGCTACTGT	    0.995359	-83
CAGCAAGAGCCGTTTACTGTTAATCTGTCA	2	62	0	CGTTTACTGT	    0.967567	-47
CAGTAAACGGCTCTTGCTGGCTAACGACAA	2	73	1	CTCTTGCTGG	     0.98559	-36
          **********

Masking position 5
Map Score:   1.6479

Number of sites scoring better than the average of aligned sites = 820
Number in coding regions = 790
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

          TACAAAATTGTAATGCTGCTG	1	1	1	TAAAAATTGT	    0.956208	-84
TTGAGGATAGCGAAAAAGCGTCCAGGGTAAC	1	36	0	CGAAAAGCGT	    0.987867	-49
        TGCATAAATATGTAAAAGCAGAT	2	3	1	CAAAATATGT	    0.971699	-106
TGGCTAACGACAAAAAAGTGTGATGGCTT  	2	90	1	CAAAAAGTGT	    0.995792	-19
          ** ********

Masking position 6
Map Score:   0.932639

Number of sites scoring better than the average of aligned sites = 174
Number in coding regions = 135
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 5

          **********

No masking
Map Score:   4.00336e-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:   4.00336e-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:   4.00336e-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