AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ideoR_ecoli_hinf_100.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

TTTTATGCCGAAGGTGATGCGCCATTGTAAG	1	21	1	AGGTGATGCG	    0.997804	-237
GTTCACTTTGATCCTGATGCGTTTGCCACCA	1	64	1	ACCTGATGCG	    0.992309	-194
AGTTTGCATCACTGTAATGCGATCTGGTTCA	1	124	0	ATGTAATGCG	    0.993311	-134
GATTTCCTTAATTGTGATGTGTATCGAAGTG	1	163	1	ATGTGATGTG	    0.993311	-95
TGTGTATCGAAGTGTGTTGCGGAGTAGATGT	1	180	1	ATGTGTTGCG	    0.995772	-78
          * *********

Masking position 5
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

GCCGAAGGTGATGCGCCATTGTAAGAAGTTTCGTGAT	1	27	1	ATGCGTGAGA	    0.996482	-231
TTTCAAATGAATGCGTCAGTGGTGGCAAACGCATCAG	1	77	0	ATGCGGGTGA	    0.995033	-181
CATCACTGTAATGCGATCTGGTTCAAATAATTCACTT	1	112	0	ATGCGTGTAA	     0.99017	-146
CATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTA	1	136	1	ATGCATGAGA	    0.973505	-122
ATTTCCTTAATTGTGATGTGTATCGAAGTGTGTTGCG	1	164	1	TTGTGTTTGA	    0.893769	-94
TCGAAGTGTGTTGCGGAGTAGATGTTAGAATACTAAC	1	186	1	TTGCGTGTTA	    0.987238	-72
AAAATTCACCTTGCGAGTTTGTTAGTATTCTAACATC	1	206	0	TTGCGTGTGA	    0.998004	-52
          *****   * * * * *

Masking position 17
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

    CTTCTTTTCCTTTTATGCCGAAGGTGA	1	7	1	TTCCTTTTTG	     0.98398	-251
TGTAAGAAGTTTCGTGATGTTCACTTTGATC	1	46	1	TTCGTGATTT	    0.934876	-212
GTAAGTAGATTTCCTTAATTGTGATGTGTAT	1	156	1	TTCCTTAATG	    0.965839	-102
  TTTATTTATTCCTTATCTTGTTGAGATGA	2	9	1	TTCCTTATTT	    0.992818	-102
GTAGCAAAAATTCTTTATTTTTGACTATGGT	2	57	0	TTCTTTATTT	    0.963622	-54
   TATTTTCCTCCTTTTATTTATGTTTTAC	2	93	0	CTCCTTTTTT	    0.964401	-18
          ******** **

Masking position 5
Map Score:   4.63637

Number of sites scoring better than the average of aligned sites = 158
Number in coding regions = 105
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 4

CGAAACTTCTTACAATGGCGCATCACCTTCGGC	1	27	0	TACAACGCAT	    0.993046	-231
TGCGTTTGCCACCACTGACGCATTCATTTGAAA	1	81	1	ACCACCGCAT	    0.977721	-177
GAATTATTTGAACCAGATCGCATTACAGTGATG	1	116	1	AACCACGCAT	    0.991722	-142
GAAATCTACTTACAAGTTTGCATCACTGTAATG	1	136	0	TACAATGCAT	    0.956689	-122
GTATTCTAACATCTACTCCGCAACACACTTCGA	1	186	0	ATCTACGCAA	    0.929533	-72
TTAGAATACTAACAAACTCGCAAGGTGAATTTT	1	210	1	AACAACGCAA	    0.993046	-48
          *****   *****

Masking position 12
Map Score:   3.65533

Number of sites scoring better than the average of aligned sites = 226
Number in coding regions = 200
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 5

CGAAGGTGATGCGCCATTGTAAGAAGTTTCGTG	1	29	1	GCGCTTGTAG	    0.996169	-229
TCACTGTAATGCGATCTGGTTCAAATAATTCAC	1	114	0	GCGATGGTCA	    0.974623	-144
TTACAGTGATGCAAACTTGTAAGTAGATTTCCT	1	138	1	GCAATTGTAG	    0.991121	-120
AATTCACCTTGCGAGTTTGTTAGTATTCTAACA	1	208	0	GCGATTGTAG	     0.99775	-50
          ****  **** **

Masking position 7
Map Score:   0.169847

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 89
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


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


Motif number 8

          **********

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