AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -iaraC_mpneu_opreg_100.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

GCCAAAGAGCACCCTGATTTTGTGATGTTATCG	1	64	0	ACCCTGATGT	    0.995486	-237
TGGCTTCCGGACCCCAATTCTTAATTAAATGAT	1	93	1	ACCCCAATTA	    0.968645	-208
GGGGACATTGACCCTAAGGATTTAGGTATTTGT	1	136	0	ACCCTAATTT	    0.995585	-165
GGGTCAATGTCCCCTAAAACTGTTCTTACAAAT	1	155	1	CCCCTAATGT	     0.99564	-146
TATTGAAATAACCCTAATAATGTGTAAGCTACT	1	225	1	ACCCTAATGT	     0.99573	-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

GCTATTAAAGAGTGTTTGTAATTTGTCCACC	1	24	0	AGGTTTGTAA	    0.930458	-277
TAGAAATGAAAAGATTTGTAAGAACAGTTTT	1	170	0	AAATTTGTAA	    0.984223	-131
AATAACCCTAATAATGTGTAAGCTACTGGAT	1	231	1	ATATGTGTAA	    0.940894	-70
AAGCTACTGGATAATTTGCCATTAACAGTTG	1	250	1	ATATTTGCCA	    0.967661	-51
ATTTGCCATTAACAGTTGTAAAGCTGGCAAC	1	263	1	AAAGTTGTAA	    0.981031	-38
TGATTCTAAAAATAGTTGCCAGCTTTACAAC	1	277	0	AAAGTTGCCA	    0.972637	-24
          ** ********

Masking position 7
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

         CTCCGACCACCATGGTGGACAA	1	2	1	TCCGCCACCA	    0.998611	-299
GTGTTTGTAATTTGTCCACCATGGTGGTCGG	1	13	0	TTTGCCACCA	     0.98979	-288
CTCTTTGGCTTCCGGACCCCAATTCTTAATT	1	88	1	TCCGACCCCA	    0.994128	-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