AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00780_tpal_reg_300.orf -o00780_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	TP0997	33	protease IV (sppA)
#2	TP0998	71	sodium/proton-dependent alanine transporter

Motif number 1

        TGTAACCTCCACCTCATGTGTG	1	22	0	TAACCTCCAC	    0.995329	-12
      GCATTGTCCTGAACAGTTAATCTG	2	5	1	TGTCCTGAAC	    0.988264	-67
GTTAATCTGTTAGCTTGCACGCCCTGCAGG	2	26	1	TAGCTTGCAC	    0.997264	-46
TCGGGGTCGGTAGCCTGCAGGGCGTGCAAG	2	39	0	TAGCCTGCAG	     0.99809	-33
          **********

Masking position 6
Map Score:   6.23692

Number of sites scoring better than the average of aligned sites = 125
Number in coding regions = 114
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

GCATAACACACATGAGGTGGAGGTTACA  	1	16	1	CATGAGGTGG	    0.993693	-18
ATTAACTGTTCAGGACAATGC         	2	2	0	CAGGACAATG	    0.974537	-70
CGGTAGCCTGCAGGGCGTGCAAGCTAACAG	2	32	0	CAGGGCGTGC	    0.997284	-40
CCGACCCCGACAGAAGGAGCCGA       	2	59	1	CAGAAGGAGC	    0.993711	-13
          **********

Masking position 2
Map Score:   2.98785

Number of sites scoring better than the average of aligned sites = 621
Number in coding regions = 569
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

          **********

No masking
Map Score:   8.76972e-14

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:   8.76972e-14

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:   8.76972e-14

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