AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i303_mixed18_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	msrA	205	peptide methionine sulfoxide reductase

Motif number 1

TGGATTTTTGTTAAGCCGTTTAACGGCGTTCCAGGG	1	40	0	TTAACCTACG	    0.999464	-166
AGTCTGCTTTTTAATCCATATTACTGGATTTTTGTT	1	64	0	TTAACCTACG	    0.999464	-142
ATGTTTTACTTTAGACCTATTCACGGTGGTTATTGT	1	118	1	TTAGCCTACG	    0.999086	-88
TGTTACAACCTTAACCCCAATGACCGATTTTCGGGA	1	170	1	TTAACCTACG	    0.999464	-36
          **** **   * ** *

Masking position 11
Map Score:   8.80942

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 11
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

TATTACTGGATTTTTGTTAAGCCGTTTAACG	1	51	0	TTTTGTTAAG	    0.989229	-155
TAAGAAATATTTGGGGTTTAGTCTGCTTTTT	1	88	0	TTGGGTTTAG	    0.995501	-118
ATTTCTTATGTTTTACTTTAGACCTATTCAC	1	111	1	TTTTCTTTAG	     0.97146	-95
AAATCGGTCATTGGGGTTAAGGTTGTAACAA	1	169	0	TTGGGTTAAG	    0.995492	-37
          **** ******

Masking position 7
Map Score:   3.47454

Number of sites scoring better than the average of aligned sites = 57
Number in coding regions = 45
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

GGCAGGAAAAAAGGATATTCAGGAGAAAAT     	1	6	0	AAGGTTCGGG	    0.997864	-200
AAGCCGTTTAACGGCGTTCCAGGGGCAGGAAAAAA	1	29	0	ACGGTCCGGG	    0.999081	-177
AGACCTATTCACGGTGGTTATTGTGTGCAAATACG	1	130	1	ACGGTTATGG	    0.991567	-76
AACCCCAATGACCGATTTTCGGGAGAGCGACACC 	1	182	1	ACCGTTCGGG	    0.998558	-24
          ****   *** ** *

Masking position 8
Map Score:   2.19863

Number of sites scoring better than the average of aligned sites = 219
Number in coding regions = 209
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

AAAGGATATTCAGGAGAAAAT         	1	2	0	CAGGAGAAAA	    0.993771	-204
GTTCCAGGGGCAGGAAAAAAGGATATTCAG	1	19	0	CAGGAAAAAA	    0.983191	-187
CGTTAAACGGCTTAACAAAAATCCAGTAAT	1	51	1	CTTAACAAAA	    0.934803	-155
TAAAGTAAAACATAAGAAATATTTGGGGTT	1	101	0	CATAAGAAAT	    0.963489	-105
          **********

Masking position 5
Map Score:   1.40483

Number of sites scoring better than the average of aligned sites = 337
Number in coding regions = 279
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 5

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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