AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i008_Uracil_Utilization_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI1227	104	uracil permease (uraA)
#2	HI1228	123	uracil phosphoribosyltransferase (upp)

Motif number 1

     TCCCCAAAACAAGACGGCATTTAAGCC	1	6	1	AAACAAGAGG	    0.981643	-99
TCAACGCACGGAAAAAAGACGGCTTAAATGCC	1	26	0	GAAAAAGAGG	    0.919606	-79
GTTGAAACACAAGAAAAACTGACCGCACTTTT	1	53	1	AAAAAAACGA	    0.865427	-52
TGTTTGAATTAACTTAAAAGTGCGGTCAGTTT	1	68	0	AATTAAAATG	    0.894689	-37
CTTTTAAGTTAATTCAAACAGAGAGTTGAAAC	1	80	1	AATCAAACGA	    0.959449	-25
TTCAAACAGAGAGTTGAAACTAA         	1	92	1	GATTGAAATA	    0.615882	-13
GGGAGTTTTCAATACAATATTGTCT       	2	4	0	AAACAATATG	    0.829247	-120
AAAATATTCTGACTTGAAACGGGAGTTTTCAA	2	24	0	GATTGAAAGG	    0.924877	-100
AGATTAAAAAAATACAAAATGGTAGAGGTTTA	2	58	0	AAACAAAAGG	    0.992024	-66
TGACTCTTAAAAAACAAATTGACAAATTCTAG	2	88	0	AAACAAATGA	    0.911568	-36
TGTTTTTTAAGAGTCAAAAGGAGAGTAAAA  	2	104	1	GATCAAAAGA	    0.980938	-20
          ** ****** **

Masking position 7
Map Score:   9.32464

Number of sites scoring better than the average of aligned sites = 1520
Number in coding regions = 1246
Number in noncoding regions = 274
Number of orfs with sites within 600 bp upstream = 211
Fraction of orfs with sites within 600 bp upstream = 0.0338901


Motif number 2

CAGTTTTTCTTGTGTTTCAACGCACGGAAA	1	44	0	TGTGTTTCAA	    0.975297	-61
GTTTCAACTCTCTGTTTGAATTAACTTAAA	1	82	0	TCTGTTTGAA	    0.955463	-23
CAAGTCAGAATATTTTTATAAACCTCTACC	2	40	1	TATTTTTATA	    0.917393	-84
TACCATTTTGTATTTTTTTAATCTAGAATT	2	66	1	TATTTTTTTA	    0.951521	-58
TTTGTCAATTTGTTTTTTAAGAGTCAAAAG	2	94	1	TGTTTTTTAA	    0.977535	-30
          **********

Masking position 5
Map Score:   1.85347

Number of sites scoring better than the average of aligned sites = 415
Number in coding regions = 300
Number in noncoding regions = 115
Number of orfs with sites within 600 bp upstream = 103
Fraction of orfs with sites within 600 bp upstream = 0.0165435


Motif number 3

CCCAAAACAAGACGGCATTTAAGCCGTCTT	1	13	1	GACGGCATTT	    0.990145	-92
AAGAAAAACTGACCGCACTTTTAAGTTAAT	1	63	1	GACCGCACTT	    0.989055	-42
TCTGACTTGAAACGGGAGTTTTCAATACAA	2	19	0	AACGGGAGTT	    0.934032	-105
          **********

Masking position 7
Map Score:   0.351526

Number of sites scoring better than the average of aligned sites = 454
Number in coding regions = 327
Number in noncoding regions = 127
Number of orfs with sites within 600 bp upstream = 113
Fraction of orfs with sites within 600 bp upstream = 0.0181497


Motif number 4

          **********

No masking
Map Score:   1.87173e-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 5

          **********

No masking
Map Score:   1.87173e-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:   1.87173e-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