AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i008_Uracil_Utilization_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	uraA	85	uracil transport
#2	upp	297	uracil phosphoribosyltransferase

Motif number 1

CGACTCTTAAAGTCGGCTTTAATTATTTTT	1	16	0	AGTCGGCTTT	    0.996751	-70
CGACTTTAAGAGTCGGCTTTTTTTTGAGTA	1	31	1	AGTCGGCTTT	    0.996751	-55
GTCTCGCAAACGTTTGCTTTCCCTGTTAGA	2	63	0	CGTTTGCTTT	    0.978239	-235
AACGTTTGCGAGACTGCTTTACACAACCTT	2	79	1	AGACTGCTTT	    0.974064	-219
CCCTGGCACAAGTCTTCTTTCGCCGCGCGC	2	129	0	AGTCTTCTTT	    0.991406	-169
CGGATGGAATAATCTTCTTTCATAACCATC	2	173	1	AATCTTCTTT	    0.957834	-125
ATATTCTTTTCGTTGACTTTAGTCAAAATG	2	236	0	CGTTGACTTT	    0.951352	-62
TCAAGGCGGCAATATTCTTTTCGTTGACTT	2	247	0	AATATTCTTT	    0.746611	-51
AGGTATAATCCGTCGATTTTTTTT      	2	284	1	CGTCGATTTT	    0.893412	-14
          **********

Masking position 8
Map Score:   15.5104

Number of sites scoring better than the average of aligned sites = 775
Number in coding regions = 700
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


Motif number 2

CGCAAGTAACGCGTGGGGACCCAAGCA   	2	8	0	GCGTGGGGAC	     0.99663	-290
TTCGCCGCGCGCCTGGGGAAAAGACGTGCA	2	111	0	GCCTGGGGAA	     0.99802	-187
TTCCCCAGGCGCGCGGCGAAAGAAGACTTG	2	121	1	GCGCGGCGAA	    0.993725	-177
GAAGACTTGTGCCAGGGTAAAGGTTAGTTT	2	142	1	GCCAGGGTAA	    0.986319	-156
          **********

Masking position 9
Map Score:   4.52583

Number of sites scoring better than the average of aligned sites = 139
Number in coding regions = 90
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

AAGCCGACTCTTAAAGTCGGCTTTAATTAT	1	20	0	TTAAAGTCGG	    0.990264	-66
GTATTATGTGTTATAGGCGCTTTACTCAAA	1	53	0	TTATAGGCGC	    0.962396	-33
TCCCCACGCGTTACTTGCGGTAGAAAAATA	2	19	1	TTACTTGCGG	    0.936384	-279
GGTAGAAAAATAAAATTCGGCGCAATTCTA	2	37	1	TAAAATTCGG	    0.941032	-261
TAAAGTTATTTTATATTCAGATGGTTATGA	2	192	0	TTATATTCAG	    0.874744	-106
ACCTCCTTTCTTCAAGGCGGCAATATTCTT	2	258	0	TTCAAGGCGG	    0.983188	-40
          **********

Masking position 1
Map Score:   2.68234

Number of sites scoring better than the average of aligned sites = 833
Number in coding regions = 763
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 81
Fraction of orfs with sites within 600 bp upstream = 0.01301


Motif number 4

TTTTTTTTGAGTAAAGCGCCTATAACACAT	1	48	1	GTAAAGCGCC	    0.886884	-38
TTCCCTGTTAGAATTGCGCCGAATTTTATT	2	45	0	GAATTGCGCC	     0.99123	-253
CTTTTTGCACGTCTTTTCCCCAGGCGCGCG	2	106	1	GTCTTTTCCC	    0.947768	-192
GGCACAAGTCTTCTTTCGCCGCGCGCCTGG	2	125	0	TTCTTTCGCC	    0.950644	-173
GGCGAAAGAAGACTTGTGCCAGGGTAAAGG	2	135	1	GACTTGTGCC	    0.992918	-163
TCTTTTCGTTGACTTTAGTCAAAATGATAA	2	232	0	GACTTTAGTC	    0.743707	-66
TCAACGAAAAGAATATTGCCGCCTTGAAGA	2	250	1	GAATATTGCC	     0.96162	-48
          **********

Masking position 10
Map Score:   5.00684

Number of sites scoring better than the average of aligned sites = 1942
Number in coding regions = 1835
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 5

ATTATCCTCTGTATTATGTGTTATAGGCGC	1	63	0	GTATTATGTG	    0.955416	-23
         AGTATTATCCTCTGTATTATG	1	75	0	GTATTATCCT	     0.98289	-11
TTTTCGGATGGAATAATCTTCTTTCATAAC	2	169	1	GAATAATCTT	    0.936298	-129
AAGAAAGGAGGTATAATCCGTCGATTTTTT	2	276	1	GTATAATCCG	    0.988871	-22
          **********

Masking position 6
Map Score:   0.723255

Number of sites scoring better than the average of aligned sites = 81
Number in coding regions = 59
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 6

          **********

No masking
Map Score:   -4.09683e-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:   -4.09683e-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:   -4.09683e-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