AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00072_ecoli_reg_100.orf -o00072_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	atoD	195	acetyl-CoA:acetoacetyl-CoA transferase alpha subunit
#2	atoB	30	acetyl-CoA acetyltransferase
#3	yqeF	251	putative acyltransferase

Motif number 1

AATTGCGCACTGTGCAAATTTCTGCATAGCAAGTTTTGGT	1	12	0	TGGATGCAAC	    0.998587	-184
ATTTGCACAGTGCGCAATTTTCTGCATAGCCGCTCATTCT	1	33	1	TGGATGCAAC	    0.998587	-163
CCCTTGCTATTGCCTGACTGTACCCACAACGGTGTATGCA	1	153	1	TGCATCCAAC	    0.992783	-43
AGGTTAAGTATGGGAGATTAACGCCCTATCTACCCCTCTA	3	67	1	TGGATCCCAC	    0.995445	-185
CCTCTATTGGTGGGTTAGTGGTTGCAAACCTTACGTGCCA	3	101	1	TGGATGCAAC	    0.998587	-151
          ** *  * *    *** * *

Masking position 9
Map Score:   5.40323

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 26
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

AGGGATAAATTGGATGGGGATTTATAAGGA	1	72	0	TGGATGGGGA	    0.952473	-124
TAATTGAATATGAAGGGATAAATTGGATGG	1	85	0	TGAAGGGATA	    0.966681	-111
CGGTGTATGCAAGAGGGATAAAAA      	1	182	1	AAGAGGGATA	     0.91395	-14
TCCTTCTGTTTGTAGGGGTGCCG       	2	4	0	TGTAGGGGTG	    0.952638	-27
TTAAACAAAATGGAGGGCAATTTACCATAA	3	34	1	TGGAGGGCAA	    0.974929	-218
AACCCACCAATAGAGGGGTAGATAGGGCGT	3	87	0	TAGAGGGGTA	    0.991398	-165
ACCCCTCTATTGGTGGGTTAGTGGTTGCAA	3	98	1	TGGTGGGTTA	    0.956672	-154
          **********

Masking position 6
Map Score:   4.5334

Number of sites scoring better than the average of aligned sites = 401
Number in coding regions = 342
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 3

CCAAAACTTGCTATGCAGAAATTTGCACAG	1	13	1	CTATGCAGAA	    0.990996	-183
AAATTGCGCACTGTGCAAATTTCTGCATAG	1	23	0	CTGTGCAAAT	    0.890847	-173
GAATGAGCGGCTATGCAGAAAATTGCGCAC	1	42	0	CTATGCAGAA	    0.990996	-154
ATGGGGATTTATAAGGAGAATGAGCGGCTA	1	59	0	ATAAGGAGAA	    0.841846	-137
GGAAATATGCCTGAGCAGCAGTCAGAGACA	3	145	0	CTGAGCAGCA	    0.979404	-107
          **********

Masking position 7
Map Score:   2.5292

Number of sites scoring better than the average of aligned sites = 219
Number in coding regions = 203
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 4

TAGTTATTTAACTAATTGAATATGAAGGGA	1	97	0	ACTAATTGAA	    0.950458	-99
CAATTAGTTAAATAACTAAATCCAATAATC	1	109	1	AATAACTAAA	    0.745306	-87
CGGCACCCCTACAAACAGAAGGAATATAAA	2	11	1	ACAAACAGAA	    0.849293	-20
CGTATCATCTACAAATTAAACAAAATGGAG	3	19	1	ACAAATTAAA	    0.940968	-233
CCACTAACCCACCAATAGAGGGGTAGATAG	3	92	0	ACCAATAGAG	    0.939908	-160
ACTTTTTTTAAACAATTAAGATAACTGTAA	3	190	1	AACAATTAAG	    0.890308	-62
  AACCTCGCACCAATTAACAGTGCAATAG	3	234	0	ACCAATTAAC	    0.941709	-18
          **********

Masking position 5
Map Score:   1.13015

Number of sites scoring better than the average of aligned sites = 406
Number in coding regions = 338
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 5

          **********

No masking
Map Score:   5.06917e-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:   5.06917e-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:   5.06917e-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