AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ideoR_ecoli_hinf_300.orf -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	deoC	257	2-deoxyribose-5-phosphate aldolase
#2	HI1116	110	deoxyribose-phosphate aldolase (deoC)

Motif number 1

CTTACAATGGCGCATCACCTTCGGCATAAAA	1	21	0	CGCATCACCT	    0.997316	-237
TGGTGGCAAACGCATCAGGATCAAAGTGAAC	1	64	0	CGCATCAGGT	    0.990612	-194
TGAACCAGATCGCATTACAGTGATGCAAACT	1	124	1	CGCATTACAT	    0.991832	-134
CACTTCGATACACATCACAATTAAGGAAATC	1	163	0	CACATCACAT	    0.991832	-95
ACATCTACTCCGCAACACACTTCGATACACA	1	180	0	CGCAACACAT	    0.994834	-78
          ********* *

Masking position 7
Map Score:   7.74934

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 88
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

ATCACGAAACTTCTTACAATGGCGCATCACCTTCGGC	1	27	0	TCTCACGCAT	    0.996263	-231
CTGATGCGTTTGCCACCACTGACGCATTCATTTGAAA	1	77	1	TCACCCGCAT	    0.994725	-181
AAGTGAATTATTTGAACCAGATCGCATTACAGTGATG	1	112	1	TTACACGCAT	    0.989564	-146
TAAGGAAATCTACTTACAAGTTTGCATCACTGTAATG	1	136	0	TCTCATGCAT	    0.971899	-122
CGCAACACACTTCGATACACATCACAATTAAGGAAAT	1	164	0	TCAAACACAA	    0.887888	-94
GTTAGTATTCTAACATCTACTCCGCAACACACTTCGA	1	186	0	TAACACGCAA	    0.986453	-72
GATGTTAGAATACTAACAAACTCGCAAGGTGAATTTT	1	206	1	TCACACGCAA	     0.99788	-52
          * * * * *   *****

Masking position 16
Map Score:   7.25925

Number of sites scoring better than the average of aligned sites = 275
Number in coding regions = 250
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

CGAAGGTGATGCGCCATTGTAAGAAGTTTCGTGAT	1	29	1	GCGTGTAAGA	    0.997944	-229
TCAAATGAATGCGTCAGTGGTGGCAAACGCATCAG	1	77	0	GCGTGGTGGA	    0.992964	-181
TTACAGTGATGCAAACTTGTAAGTAGATTTCCTTA	1	138	1	GCATGTAAGA	    0.989361	-120
GTGTGTTGCGGAGTAGATGTTAGAATACTAACAAA	1	191	1	GAGTGTTAGA	    0.992552	-67
AATTCACCTTGCGAGTTTGTTAGTATTCTAACATC	1	206	0	GCGTGTTAGA	    0.998564	-52
          ***    ****** *

Masking position 8
Map Score:   4.80864

Number of sites scoring better than the average of aligned sites = 79
Number in coding regions = 72
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

CCTTCGGCATAAAAGGAAAAGAAG      	1	5	0	AAAAGGAAAA	     0.95848	-253
CACATCACAATTAAGGAAATCTACTTACAA	1	154	0	TTAAGGAAAT	    0.925219	-104
TCTCAACAAGATAAGGAATAAATAAA    	2	7	0	ATAAGGAATA	     0.98045	-104
ATAGTCAAAAATAAAGAATTTTTGCTACAA	2	60	1	ATAAAGAATT	    0.900817	-51
TTTTGCTACAATAGGTAAAACATAAATAAA	2	79	1	ATAGGTAAAA	    0.920388	-32
TAGGTAAAACATAAATAAAAGGAGGAAAAT	2	90	1	ATAAATAAAA	    0.914403	-21
          **********

Masking position 7
Map Score:   2.88627

Number of sites scoring better than the average of aligned sites = 441
Number in coding regions = 277
Number in noncoding regions = 164
Number of orfs with sites within 600 bp upstream = 196
Fraction of orfs with sites within 600 bp upstream = 0.0314809


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


Motif number 6

          **********

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 7

          **********

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