AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00380_tpal_reg_100.orf -o00380_tpal_100.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	TP0632	104	tryptophanyl-tRNA synthetase (trsA)

Motif number 1

TCTATATCACGGGTGCGTGTCCGTC     	1	6	0	GGGTGCGTGT	    0.961141	-99
TATAGAGGAGGGCTGCGCGGTCGGCGCACG	1	30	1	GGCTGCGCGG	    0.993294	-75
GCGCAGGAACACGTGCGCCGACCGCGCAGC	1	41	0	ACGTGCGCCG	    0.914661	-64
GCGCACGTGTTCCTGCGCCTGCACTCTTGA	1	53	1	TCCTGCGCCT	    0.986851	-52
CTGTAAATCAAGGTCCGTCCAGTATTCAAG	1	78	0	AGGTCCGTCC	    0.978254	-27
          **********

Masking position 4
Map Score:   7.01978

Number of sites scoring better than the average of aligned sites = 818
Number in coding regions = 755
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 2

ACCGCGCAGCCCTCCTCTATATCACGGGTG	1	21	0	CCTCCTCTAT	    0.997061	-84
TGTTCCTGCGCCTGCACTCTTGAATACTGG	1	60	1	CCTGCACTCT	    0.996345	-45
AATCAAGGTCCGTCCAGTATTCAAGAGTGC	1	73	0	CGTCCAGTAT	    0.994363	-32
          **********

Masking position 3
Map Score:   2.30435

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 25
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

AGCCCTCCTCTATATCACGGGTGCGTGTCC	1	14	0	TATATCACGG	    0.997201	-91
GGGGAGACTGTAAATCAAGGTCCGTCCAGT	1	85	0	TAAATCAAGG	    0.995858	-20
          **********

Masking position 5
Map Score:   1.0373

Number of sites scoring better than the average of aligned sites = 1
Number in coding regions = 0
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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 6

          **********

No masking
Map Score:   -1.17788e-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