AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ifnr_tpal_opreg_300.orf -g0.528 -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 =  	0.528
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	TP0382	83	T. pallidum predicted coding region TP0382
#2	TP0383	27	conserved hypothetical protein
#3	TP0390	45	cell division protein (ftsZ)

Motif number 1

          ACGTCCACCCCCCCCCCCCCG	1	1	1	ACGTCACCCC	    0.978458	-83
CGTCCACCCCCCCCCCCCCGACGAGAAAAAG	1	12	1	CCCCCCCCGA	    0.998847	-72
GAACATTGTCACCCATACCGTTGCCGGTTGT	1	42	1	ACCCTACCGT	    0.978278	-42
  GATTTCCTACCTTCCCCTATATTTTTC  	2	9	0	ACCTCCCCTA	     0.98564	-19
         ACCGCGCACAGCATGCGGCACG	3	2	1	CCGCCACAGC	    0.994648	-44
CCTCCCATTCCCCTACACCGCGTGCCGCATG	3	22	0	CCCTCACCGC	    0.998724	-24
         TCCCCTCCCATTCCCCTACACC	3	34	0	CCCCCCCATT	    0.987635	-12
          **** ******

Masking position 8
Map Score:   12.3514

Number of sites scoring better than the average of aligned sites = 1027
Number in coding regions = 861
Number in noncoding regions = 166
Number of orfs with sites within 600 bp upstream = 100
Fraction of orfs with sites within 600 bp upstream = 0.0160617


Motif number 2

          **********

No masking
Map Score:   2.15595e-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 3

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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