AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i246_regulatory_cassete1_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	araC	300	transcriptional regulator for ara operon

Motif number 1

GAGTTGCGATAAAAAGCGTCAGGTAGGATCCGCTAAT	1	16	1	AAAAGCGATG	     0.99252	-285
CTTATGGATAAAAATGCTATGGCATAGCAAAGTGTGA	1	53	1	AAAAGCTGAG	    0.992446	-248
AGCCATGACAAAAACGCGTAACAAAAGTGTCTATAAT	1	127	0	AAAAGCGAAG	    0.998151	-174
GCATTCTGTAACAAAGCGGGACCAAAGCCATGACAAA	1	152	0	ACAAGCGAAG	    0.994962	-149
GAATGCTTTTAATAAGCGGGGTTACCGGTTGGGTTAG	1	183	1	AATAGCGGAG	     0.99525	-118
AAGAGCCAGTAAAAGACGCAGTGACGGCAATGTCTGA	1	224	1	AAAAACGGAG	    0.992439	-77
          **** ***  *  *  *

Masking position 4
Map Score:   7.61527

Number of sites scoring better than the average of aligned sites = 303
Number in coding regions = 270
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

AAAATGCTATGGCATAGCAAAGTGTGACGCCGT	1	63	1	GCAGCAAAGT	    0.990039	-238
GTCTATAATCACGGCAGAAAAGTCCACATTGAT	1	103	0	AGAGAAAAGT	    0.977088	-198
TGACAAAAACGCGTAACAAAAGTGTCTATAATC	1	126	0	GGACAAAAGT	    0.993062	-175
CTGTAACAAAGCGGGACCAAAGCCATGACAAAA	1	151	0	GGACCAAAGC	    0.988053	-150
AAAAGACGCAGTGACGGCAATGTCTGATGCAAT	1	234	1	GGGGCAATGT	    0.979666	-67
TGAATGGTGGGAGTATGAAAAGT          	1	288	1	GGTGAAAAGT	      0.9882	-13
          * *  ********

Masking position 9
Map Score:   3.99395

Number of sites scoring better than the average of aligned sites = 298
Number in coding regions = 273
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 3

      GTAGAGAGTTGCGATAAAAAGCGT	1	5	1	AGAGTTGCGA	    0.953438	-296
TTTATCCATAAGATTAGCGGATCCTACCTG	1	35	0	AGATTAGCGG	    0.992723	-266
TTAATAAGCGGGGTTACCGGTTGGGTTAGC	1	191	1	GGGTTACCGG	     0.99168	-110
GTTACCGGTTGGGTTAGCGAGAAGAGCCAG	1	203	1	GGGTTAGCGA	    0.995256	-98
          **********

Masking position 5
Map Score:   2.23258

Number of sites scoring better than the average of aligned sites = 240
Number in coding regions = 224
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 4

AAAGTGTGACGCCGTGCAAATAATCAATGT	1	81	1	GCCGTGCAAA	    0.985048	-220
GGACTTTTCTGCCGTGATTATAGACACTTT	1	111	1	GCCGTGATTA	    0.991175	-190
CGGGACCAAAGCCATGACAAAAACGCGTAA	1	143	0	GCCATGACAA	    0.987197	-158
ATCAGACATTGCCGTCACTGCGTCTTTTAC	1	232	0	GCCGTCACTG	    0.985302	-69
          **********

Masking position 5
Map Score:   1.40132

Number of sites scoring better than the average of aligned sites = 321
Number in coding regions = 302
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 5

TGCAAATAATCAATGTGGACTTTTCTGCCG	1	95	1	CAATGTGGAC	    0.996957	-206
ATGTCTGATGCAATATGGACAATTGGTTTC	1	253	1	CAATATGGAC	    0.995493	-48
          **********

Masking position 6
Map Score:   0.50812

Number of sites scoring better than the average of aligned sites = 4
Number in coding regions = 3
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 6

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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 8

          **********

No masking
Map Score:   7.91135e-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