AlignACE version 2.2  July 7, 1998
alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jiclR.reg -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 = 	137

Input sequences:
#1	aceB 268 bp aceB 533 1-1602 CDS
#2	iclR 160 bp iclR 287 1-864 CDS

Motif number 1

GATAACAATATGAATAAAATTTATTCACCTGC	1	97	0	TATAAAATTT	    0.893471	-172
TGATAACTTGTTGATAACAATATGAATAAAAT	1	109	0	TGTAACAATA	    0.977335	-160
ATTTCCATTTTAATTAAAAATACTTGATAACT	1	133	0	TATAAAAATA	    0.968122	-136
AAATGCAAAATCAAAAACAATTTCCATTTTAA	1	152	0	TAAAACAATT	    0.945424	-117
CAACCCAGATTTAATAAAAATTCAACAAACCA	2	29	1	TATAAAAATT	    0.975845	-132
TCGGATCAGTTCAGTAACTATTGCATTAGCTA	2	130	1	TATAACTATT	    0.945424	-31
ACTATTGCATTAGCTAACAATAAAA       	2	146	1	TGTAACAATA	    0.977335	-15
          * * ********

Masking position 6
Map Score:   5.29504

Number of sites scoring better than the average of aligned sites = 171
Number in coding regions = 91
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 93
Fraction of orfs with sites within 600 bp upstream = 0.0149374


Motif number 2

TCAGCACCTTACCTCAGGCACCTTCGGGTGCC	1	40	1	ACCAGGCACC	    0.966226	-229
TTTCGGAAATAAAAAAGGCACCCGAAGGTGCC	1	56	0	AAAAGGCACC	    0.969559	-213
TTTTTTATTTCCGAAACGTACCTCAGCAGGTG	1	72	1	CCAACGTACC	    0.982866	-197
ATATTGTTATCAACAAGTTATCAAGTATTTTT	1	118	1	CAAAGTTATC	    0.877976	-151
ACCATACTGGCATAAACGCATCTGTGGTAAAA	2	57	1	CAAACGCATC	    0.990966	-104
GTAAAAGCGACCACCACGCAACATGAGATTTG	2	83	1	CCCACGCAAC	    0.967711	-78
ATTTGTTCAACATTAACTCATCGGATCAGTTC	2	110	1	CAAACTCATC	    0.977225	-51
TGCAATAGTTACTGAACTGATCCGATGAGTTA	2	123	0	ACAACTGATC	    0.859159	-38
          **  ********

Masking position 6
Map Score:   4.65024

Number of sites scoring better than the average of aligned sites = 1338
Number in coding regions = 1239
Number in noncoding regions = 99
Number of orfs with sites within 600 bp upstream = 118
Fraction of orfs with sites within 600 bp upstream = 0.0189528


Motif number 3

GATAGTCGATCGTTAAGCGATTCAGCACCTTAC	1	19	1	CGTTAAGCTC	    0.993686	-250
GTGCTCTTTTCGTTCAGCACAACTAAGACTACT	1	190	0	CGTTCAGCAC	    0.990645	-79
AACGAAGGATCGTTGTGCTCTTTTCGTTCAGCA	1	204	0	CGTTGTGCTT	     0.95978	-65
          CGTGCAGCTCCTCGTCATGGATC	1	256	0	CGTGCAGCTC	    0.993669	-13
ATTAAATCTGGGTTGAGCGTGTCGGGAGCAAGT	2	11	0	GGTTGAGCTC	      0.9944	-150
GATGAGTTAATGTTGAACAAATCTCATGTTGCG	2	99	0	TGTTGAACTC	    0.948811	-62
          ********   **

Masking position 3
Map Score:   3.30257

Number of sites scoring better than the average of aligned sites = 558
Number in coding regions = 537
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

         TCTTCTGTGATAGTCGATCGT	1	2	1	CTTCTGTGAT	    0.987878	-267
ATTTATTCACCTGCTGAGGTACGTTTCGGA	1	81	0	CTGCTGAGGT	     0.99065	-188
GGCATAAACGCATCTGTGGTAAAAGCGACC	2	65	1	CATCTGTGGT	    0.992129	-96
          **********

Masking position 5
Map Score:   0.582708

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 39
Number in noncoding regions = 5
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:   -3.88366e-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:   -3.88366e-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:   -3.88366e-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