AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i008_Uracil_Utilization_ecoli_reg_100.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	    0.996509	-70
CGACTTTAAGAGTCGGCTTTTTTTTGAGTA	1	31	1	AGTCGGCTTT	    0.996509	-55
GTCTCGCAAACGTTTGCTTTCCCTGTTAGA	2	63	0	CGTTTGCTTT	    0.976652	-235
AACGTTTGCGAGACTGCTTTACACAACCTT	2	79	1	AGACTGCTTT	    0.972182	-219
CCCTGGCACAAGTCTTCTTTCGCCGCGCGC	2	129	0	AGTCTTCTTT	    0.990771	-169
CGGATGGAATAATCTTCTTTCATAACCATC	2	173	1	AATCTTCTTT	    0.954828	-125
ATATTCTTTTCGTTGACTTTAGTCAAAATG	2	236	0	CGTTGACTTT	    0.947909	-62
TCAAGGCGGCAATATTCTTTTCGTTGACTT	2	247	0	AATATTCTTT	    0.732748	-51
AGGTATAATCCGTCGATTTTTTTT      	2	284	1	CGTCGATTTT	    0.886358	-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

   TGCTTGGGTCCCCACGCGTTACTTGCG	2	8	1	GTCCCCACGC	    0.997051	-290
TGCACGTCTTTTCCCCAGGCGCGCGGCGAA	2	111	1	TTCCCCAGGC	    0.998267	-187
CAAGTCTTCTTTCGCCGCGCGCCTGGGGAA	2	121	0	TTCGCCGCGC	    0.994509	-177
AAACTAACCTTTACCCTGGCACAAGTCTTC	2	142	0	TTACCCTGGC	    0.988018	-156
          **********

Masking position 2
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

ATAATTAAAGCCGACTTTAAGAGTCGGCTT	1	20	1	CCGACTTTAA	    0.989876	-66
TTTGAGTAAAGCGCCTATAACACATAATAC	1	53	1	GCGCCTATAA	    0.960942	-33
TATTTTTCTACCGCAAGTAACGCGTGGGGA	2	19	0	CCGCAAGTAA	    0.933993	-279
TAGAATTGCGCCGAATTTTATTTTTCTACC	2	37	0	CCGAATTTTA	    0.938804	-261
TCATAACCATCTGAATATAAAATAACTTTA	2	192	1	CTGAATATAA	    0.870357	-106
AAGAATATTGCCGCCTTGAAGAAAGGAGGT	2	258	1	CCGCCTTGAA	    0.982523	-40
          **********

Masking position 10
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	    0.879162	-38
TTCCCTGTTAGAATTGCGCCGAATTTTATT	2	45	0	GAATTGCGCC	    0.990556	-253
CTTTTTGCACGTCTTTTCCCCAGGCGCGCG	2	106	1	GTCTTTTCCC	    0.943943	-192
GGCACAAGTCTTCTTTCGCCGCGCGCCTGG	2	125	0	TTCTTTCGCC	    0.947014	-173
GGCGAAAGAAGACTTGTGCCAGGGTAAAGG	2	135	1	GACTTGTGCC	    0.992431	-163
TCTTTTCGTTGACTTTAGTCAAAATGATAA	2	232	0	GACTTTAGTC	    0.742181	-66
TCAACGAAAAGAATATTGCCGCCTTGAAGA	2	250	1	GAATATTGCC	    0.958939	-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

GCGCCTATAACACATAATACAGAGGATAAT	1	63	1	CACATAATAC	    0.954694	-23
CATAATACAGAGGATAATACT         	1	75	1	AGGATAATAC	    0.982605	-11
GTTATGAAAGAAGATTATTCCATCCGAAAA	2	169	0	AAGATTATTC	    0.935287	-129
AAAAAATCGACGGATTATACCTCCTTTCTT	2	276	0	CGGATTATAC	    0.988685	-22
          **********

Masking position 5
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