AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i253_chemotaxis2_ecoli_reg_300.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	motA	126	proton conductor component of motor; no effect on switching
#2	flhD	300	regulator of flagellar biosynthesis, acting on class 2 operons; transcriptional initiation factor

Motif number 1

GCAACATTCCAGCAGCGGTAACGACGTACC	1	26	1	AGCAGCGGTA	    0.996483	-101
GGCAAAAAAAAGCAGCGGTACGTCGTTACC	1	42	0	AGCAGCGGTA	    0.996483	-85
AACGGAGGGGGGCTGCGATTTTCAATAATG	2	59	0	GGCTGCGATT	    0.977471	-242
AGTTGCGATAAGCTGCAATAAGCAGAACCA	2	192	0	AGCTGCAATA	    0.971575	-109
GCATTAGAATAGTTGCGATAAGCTGCAATA	2	202	0	AGTTGCGATA	    0.976165	-99
GTCGCCGGGAAGCCCCGGTAAAAAATAATT	2	233	0	AGCCCCGGTA	    0.979248	-68
CGACATCACGGGGTGCGGTGAAACCGCATA	2	259	1	GGGTGCGGTG	    0.968643	-42
          **********

Masking position 9
Map Score:   9.88875

Number of sites scoring better than the average of aligned sites = 937
Number in coding regions = 898
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

TAACGACGTACCGCTGCTTTTTTTTGCCCCAAT	1	44	1	CCGCTCTTTT	    0.921745	-83
         TACCCATTTATGTTAAGTAATTGA	2	2	1	ACCCATTTTT	     0.98233	-299
TCCTAAATCGACGCAACTGTACTCGTCACTACA	2	98	0	ACGCACTTCT	    0.990513	-203
AAGTGTAAAGACCCATTTCTATTTGTAAGGACA	2	143	1	ACCCATTTTT	    0.982331	-158
CAATAAGCAGAACCACCTTTTTGGTTTAATATG	2	174	0	AACCACTTTG	    0.944772	-127
TTGCAGCTTATCGCAACTATTCTAATGCTAATT	2	204	1	TCGCACTTCT	     0.96263	-97
   CCAGAATAACCAACTTTATTTTTATGCGGT	2	281	0	AACCACTTTT	     0.98223	-20
          ***** ** * **

Masking position 8
Map Score:   4.43418

Number of sites scoring better than the average of aligned sites = 322
Number in coding regions = 268
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

    CTGATACGGTGAGGCGCAACATTCCA	1	7	1	CGGTGAGGCG	    0.983298	-120
AACAGTGGAAGGATGATGTC          	1	117	1	GGATGATGTC	    0.882404	-10
TTTCAATAATGCGTGATGCAGATCACACAA	2	40	0	GCGTGATGCA	    0.970538	-261
TACAACGGAGGGGGGCTGCGATTTTCAATA	2	62	0	GGGGGCTGCG	    0.957866	-239
CGTTGTATGTGCGTGTAGTGACGAGTACAG	2	85	1	GCGTGTAGTG	     0.89079	-216
CGTGATGTCGCCGGGAAGCCCCGGTAAAAA	2	239	0	CCGGGAAGCC	    0.986799	-62
TCACCGCACCCCGTGATGTCGCCGGGAAGC	2	250	0	CCGTGATGTC	    0.985336	-51
TCACGGGGTGCGGTGAAACCGCATAAAAAT	2	264	1	CGGTGAAACC	     0.93601	-37
          **********

Masking position 5
Map Score:   5.0293

Number of sites scoring better than the average of aligned sites = 3679
Number in coding regions = 3499
Number in noncoding regions = 180
Number of orfs with sites within 600 bp upstream = 169
Fraction of orfs with sites within 600 bp upstream = 0.0271442


Motif number 4

GACCATGACAGGATGTTCAGTCGTCAGGCG	1	87	0	GGATGTTCAG	    0.986271	-40
AAACCAAAAAGGTGGTTCTGCTTATTGCAG	2	180	1	GGTGGTTCTG	    0.994702	-121
AAATAAAGTTGGTTATTCTGG         	2	290	1	GGTTATTCTG	    0.987936	-11
          **********

Masking position 6
Map Score:   0.597686

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 96
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   6.34815e-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:   6.34815e-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:   6.34815e-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