AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i132_tpal_bbur_300.orf -o132_tpal_bbur_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -x5 -e 
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 = 	1

Input sequences:
#1	RTP00337	109	AE000520

Motif number 1

ACTCGGCAACGCACTCCCTACGAAACTTTG	1	16	0	GCACTCCCTA	    0.994331	-94
CGCGCAGGCCACACCACCCTCCTGAACTCG	1	41	0	ACACCACCCT	    0.980744	-69
TGGCCTGCGCGCACTCAGGTACATACCGCG	1	60	1	GCACTCAGGT	    0.979824	-50
GTAGAGACGAGCACTACCTTAACCGCGGTA	1	83	0	GCACTACCTT	     0.99813	-27
GTAGTGCTCGTCTCTACCGTTGTC      	1	96	1	TCTCTACCGT	      0.9841	-14
          **********

Masking position 4
Map Score:   5.06719

Number of sites scoring better than the average of aligned sites = 686
Number in coding regions = 207
Number in noncoding regions = 479
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 2

CCACCCTCCTGAACTCGGCAACGCACTCCC	1	28	0	GAACTCGGCA	    0.991627	-82
GCACTACCTTAACCGCGGTATGTACCTGAG	1	73	0	AACCGCGGTA	    0.536713	-37
          GACAACGGTAGAGACGAGCA	1	100	0	GACAACGGTA	    0.974019	-10
          **********

Masking position 2
Map Score:   1.52442

Number of sites scoring better than the average of aligned sites = 90
Number in coding regions = 33
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

          **********

No masking
Map Score:   1.16119e-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 4

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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