AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00900_ecoli_reg_100.orf -o00900_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 =  	0.51
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	caiA	30	probable carnitine operon oxidoreductase
#2	caiT	300	probable carnitine transporter
#3	xseB	205	exonuclease VII, small subunit

Motif number 1

         TTAACCCCCAAAATATCAAGAGGT	1	2	1	TACCCAAAAT	    0.976164	-29
AAATAACATCTGACTTTCAATATTGGTGATCCA	2	43	0	TACTCAATAT	    0.978394	-258
ATGTTATTTTTTACTCACAACAGAGCATAACAA	2	67	1	TACCCAACAG	    0.986541	-234
CGTTAATGGCTAACTCATAATGGGTATTCAATA	2	182	0	TACCTAATGG	    0.973544	-119
TTATTTTTGTTAACATTTAATATAATTATTATT	2	228	0	TACTTAATAT	    0.925112	-73
AAATAGCAAATAACGCGCAATGGTAAGGTGATG	3	128	0	TACCCAATGG	    0.992641	-78
AATGAATGTCTGACTCTCAATATTTTTCGCCCC	3	183	0	TACCCAATAT	    0.994012	-23
          * ** * ******

Masking position 9
Map Score:   7.63506

Number of sites scoring better than the average of aligned sites = 161
Number in coding regions = 140
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

       CGTAGCAAAAAGAAATTTTCAATAT	2	4	1	ACAAAAAAAA	    0.950833	-297
AATATTGGTGATCCATAAAACAATATTGAAAA	2	26	0	ACCATAAACA	    0.918609	-275
ATGCTCTGTTGTGAGTAAAAAATAACATCTGA	2	63	0	GGAGTAAAAA	    0.930284	-238
ACTCACAACAGAGCATAACAAACTGATTATTA	2	79	1	GGCATAAAAA	    0.969497	-222
CCCTCTATTCACCCGAAACAAAAATGTGATAC	2	132	1	ACCGAAAAAA	    0.969079	-169
ATTAAATGTTAACAAAAATAAAACAAACGGGA	2	240	1	ACAAAAAAAA	    0.950833	-61
ACAAACGGGAACGCAAAATAAATATTCGTTTT	2	262	1	AGCAAAAAAA	    0.979194	-39
GACTTGTATAGGGAAAAATACAGCAGCCCACA	3	42	1	GGAAAAAACA	     0.94584	-164
TACCATGACGGGGCGAAAAATATTGAGAGTCA	3	174	1	GGCGAAAATA	    0.912094	-32
          * ****** ***

Masking position 7
Map Score:   7.23038

Number of sites scoring better than the average of aligned sites = 490
Number in coding regions = 356
Number in noncoding regions = 134
Number of orfs with sites within 600 bp upstream = 151
Fraction of orfs with sites within 600 bp upstream = 0.0242531


Motif number 3

GAAAGTCAGATGTTATTTTTTACTCACAAC	2	58	1	TGTTATTTTT	    0.907155	-243
GGCGTTTTTTCGTTAATTTTGATTAATAAT	2	104	0	CGTTAATTTT	    0.933701	-197
AGCTGTATTCTGTGATTGGTATCACATTTT	2	152	0	TGTGATTGGT	     0.88233	-149
CTCGTGGACGCGTTAATGGCTAACTCATAA	2	195	0	CGTTAATGGC	    0.959409	-106
TTTGCGTTCCCGTTTGTTTTATTTTTGTTA	2	249	0	CGTTTGTTTT	    0.818925	-52
AGCAAAGCGATGTTAGTGGTATACTTCCGC	3	93	0	TGTTAGTGGT	    0.963379	-113
TACCATTGCGCGTTATTTGCTATTTGCCCT	3	136	1	CGTTATTTGC	    0.965572	-70
          **********

Masking position 7
Map Score:   2.69265

Number of sites scoring better than the average of aligned sites = 713
Number in coding regions = 645
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 79
Fraction of orfs with sites within 600 bp upstream = 0.0126887


Motif number 4

GCAGGTGTGGGCTGCTGTATTTTTCCCTAT	3	49	0	GCTGCTGTAT	    0.989855	-157
GCCCACACCTGCGGCTGCATCCAGGCGCGG	3	67	1	GCGGCTGCAT	    0.995548	-139
GCATCCAGGCGCGGAAGTATACCACTAACA	3	83	1	GCGGAAGTAT	    0.982248	-123
          **********

Masking position 9
Map Score:   0.321129

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 88
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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:   -1.75204e-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