AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i290_ecoli_bsub_300.orf -o290_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 
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 =  	0.47
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	b1970	84	orf, hypothetical protein
#2	b1971	108	putative reductase

Motif number 1

ATCCTTGTCATGTGAATGAGTTTTGAGGAT	1	59	0	TGTGAATGAG	    0.981813	-26
CTCATTCACATGACAAGGATATAAAC    	1	69	1	TGACAAGGAT	     0.97436	-16
TCTCTGCTACTGTTAGGGAGGACACTCCCT	2	33	1	TGTTAGGGAG	     0.99378	-76
ACTGTTAATCTGTCAGGGAGTGTCCTCCCT	2	47	0	TGTCAGGGAG	    0.997709	-62
GACAAAAAAGTGTGATGGCTT         	2	98	1	TGTGATGGCT	    0.969615	-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

AAAAGCGTCCAGGGTAACCTTACAGCAGCATTAC	1	20	0	AGGTAACACA	     0.99679	-65
ATGAGTTTTGAGGATAGCGAAAAAGCGTCCAGGG	1	40	0	AGGTAGCAAA	    0.996723	-45
ACTCCCTGACAGATTAACAGTAAACGGCTCTTGC	2	56	1	AGATAACAAA	    0.992562	-53
CGGCTCTTGCTGGCTAACGACAAAAAAGTGTGAT	2	80	1	TGGTAACAAA	    0.995211	-29
          *** ****   ***

Masking position 6
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	    0.989597	-72
AAGCAGATCTCTGCTACTGTTAGGGAGGAC	2	26	1	CTGCTACTGT	     0.99592	-83
CAGCAAGAGCCGTTTACTGTTAATCTGTCA	2	62	0	CGTTTACTGT	    0.971402	-47
CAGTAAACGGCTCTTGCTGGCTAACGACAA	2	73	1	CTCTTGCTGG	    0.987322	-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	    0.957754	-84
TTGAGGATAGCGAAAAAGCGTCCAGGGTAAC	1	36	0	CGAAAAGCGT	    0.988308	-49
        TGCATAAATATGTAAAAGCAGAT	2	3	1	CAAAATATGT	    0.972713	-106
TGGCTAACGACAAAAAAGTGTGATGGCTT  	2	90	1	CAAAAAGTGT	    0.995946	-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