AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_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	ycaI	129	orf, hypothetical protein
#2	msbA	36	ATP-binding transport protein; multicopy suppressor of htrB
#3	ycaQ	36	orf, hypothetical protein
#4	ycaR	51	orf, hypothetical protein
#5	b2253	274	putative enzyme

Motif number 1

TTTTACTCAAACTTGAACGAGAGAAAAGCACCT	1	14	1	ACTTAACAAG	    0.929047	-116
ATTCAGAAGAATTTAACGAAAGGGTGAAAACTG	1	107	0	ATTTACGAGG	    0.935133	-23
ATATGCGGCTATTTCAACAAATGCTGGTTTTTT	2	12	1	ATTTAACATG	    0.932472	-25
      GTAAACTCCACCTATAGACAAGCGCAA	5	5	1	ACTCACCAAG	    0.925206	-270
ATGTAGCTCAATTTCACGGTAATTGTCTGGTTG	5	35	0	ATTTACGTAT	    0.809819	-240
GATTTTTAATATTACACCAACTGCGAATTATCG	5	74	0	ATTAACCATG	    0.939474	-201
ATTTTGAGGCATTTTGCCGACATCGTAGGATTT	5	102	0	ATTTGCCAAT	    0.922803	-173
ATGCCTCAAAATTTTGCCAAATGCAAAGCCTAA	5	123	1	ATTTGCCATG	    0.971981	-152
AGAAACTAATATTAGACGTAAATATTGAAATTT	5	172	0	ATTAACGAAT	    0.748211	-103
TAGAATATTAACTTAACCTTAAGAAACTAATAT	5	193	0	ACTTACCTAG	    0.954718	-82
TTGGAGCGAAATTTTAAGGATAGAATATTAACT	5	213	0	ATTTAAGAAG	    0.922974	-62
TGTTGTGTATATTTTGCCATTTGGAGCGAAATT	5	233	0	ATTTGCCTTG	     0.92556	-42
          **** *** * **

Masking position 1
Map Score:   10.4754

Number of sites scoring better than the average of aligned sites = 944
Number in coding regions = 819
Number in noncoding regions = 125
Number of orfs with sites within 600 bp upstream = 154
Fraction of orfs with sites within 600 bp upstream = 0.024735


Motif number 2

TATGCGGCTATTTCAACAAATGCTGGTTTTTT	2	13	1	TTCACAAATG	    0.990847	-24
        AGTTCCTCCAGATGGATCGGGTTA	4	38	0	TTCCCAGATG	    0.991535	-14
CTGCGAATTATCGCCAGAAATGTAGCTCAATT	5	55	0	TCCAGAAATG	    0.953657	-220
ATTTTTAATATTACACCAACTGCGAATTATCG	5	74	0	TTCCCAACTG	    0.991536	-201
TGCCTCAAAATTTTGCCAAATGCAAAGCCTAA	5	124	1	TTTCCAAATG	    0.980223	-151
CCTTAAAATTTCGCTCCAAATGGCAAAATATA	5	227	1	TCCCCAAATG	    0.996249	-48
          ** * *******

Masking position 8
Map Score:   7.27258

Number of sites scoring better than the average of aligned sites = 151
Number in coding regions = 134
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

ATTAGAGAAATGAAAAAAGCACCCGACAGG	1	44	0	TGAAAAAAGC	    0.910935	-86
TGAAAACTGTTCAAAACTCTGCGAGGCAGC	1	86	0	TCAAAACTCT	    0.937099	-44
AACGAAAGGGTGAAAACTGTTCAAAACTCT	1	96	0	TGAAAACTGT	    0.862758	-34
          TCAAAAAACCAGCATTTGTT	2	27	0	TCAAAAAACC	    0.960378	-10
          TCATGACTCCATCAATCGAA	3	27	0	TCATGACTCC	    0.931859	-10
ATGGATCGGGTTATGAATGCATAAATCTTA	4	21	0	TTATGAATGC	    0.845054	-31
TGGTGTAATATTAAAAATCCTACGATGTCG	5	88	1	TTAAAAATCC	    0.961133	-187
TAACTTAACCTTAAGAAACTAATATTAGAC	5	188	0	TTAAGAAACT	    0.855197	-87
          **********

Masking position 6
Map Score:   2.15458

Number of sites scoring better than the average of aligned sites = 831
Number in coding regions = 680
Number in noncoding regions = 151
Number of orfs with sites within 600 bp upstream = 165
Fraction of orfs with sites within 600 bp upstream = 0.0265018


Motif number 4

TTACTCAAACTTGAACGAGAGAAAAGCACCT	1	16	1	TTGAACGAAG	    0.992374	-114
TTCAGAAGAATTTAACGAAAGGGTGAAAACT	1	108	0	TTTAACGAAG	    0.993562	-22
GGAGCGAAATTTTAAGGATAGAATATTAACT	5	213	0	TTTAAGGAAG	    0.988252	-62
          ******** **

Masking position 5
Map Score:   0.286522

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 8
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

          **********

No masking
Map Score:   7.2008e-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:   7.2008e-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:   7.2008e-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