AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -iaraC_mpneu_opreg_300.orf -g0.400 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	araD	300	L-ribulose-5-phosphate 4-epimerase; similar to Swiss-Prot Accession Number P08203, from E. coli

Motif number 1

CGATAACATCACAAAATCAGGGTGCTCTTTGGC	1	64	1	ACATCAGGGT	    0.995942	-237
ATCATTTAATTAAGAATTGGGGTCCGGAAGCCA	1	93	0	TAATTGGGGT	    0.971998	-208
ACAAATACCTAAATCCTTAGGGTCAATGTCCCC	1	136	1	AAATTAGGGT	    0.996068	-165
ATTTGTAAGAACAGTTTTAGGGGACATTGACCC	1	155	0	ACATTAGGGG	    0.996115	-146
AGTAGCTTACACATTATTAGGGTTATTTCAATA	1	225	0	ACATTAGGGT	    0.995661	-76
          ***   *******

Masking position 7
Map Score:   5.96614

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 18
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

GGTGGACAAATTACAAACACTCTTTAATAGC	1	24	1	TTACAAACCT	    0.935923	-277
AAAACTGTTCTTACAAATCTTTTCATTTCTA	1	170	1	TTACAAATTT	    0.985528	-131
ATCCAGTAGCTTACACATTATTAGGGTTATT	1	231	0	TTACACATAT	    0.945587	-70
CAACTGTTAATGGCAAATTATCCAGTAGCTT	1	250	0	TGGCAAATAT	    0.970296	-51
GTTGCCAGCTTTACAACTGTTAATGGCAAAT	1	263	0	TTACAACTTT	    0.982596	-38
GTTGTAAAGCTGGCAACTATTTTTAGAATCA	1	277	1	TGGCAACTTT	    0.974877	-24
          ******** **

Masking position 5
Map Score:   3.13026

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 73
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

TTGTCCACCATGGTGGTCGGAG         	1	2	0	TGGTGGCGGA	    0.998665	-299
CCGACCACCATGGTGGACAAATTACAAACAC	1	13	1	TGGTGGCAAA	    0.990185	-288
AATTAAGAATTGGGGTCCGGAAGCCAAAGAG	1	88	0	TGGGGTCGGA	    0.994246	-213
          ****** ****

Masking position 11
Map Score:   0.23734

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 4
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 4

          **********

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 5

          **********

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 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