AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00471_tpal_reg_100.orf -o00471_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	TP0406	190	glutamate racemase (murI)

Motif number 1

GTATGTGTGTTGACGTATGCATGAGCTTAGC	1	16	1	TGACGTTGCA	     0.98604	-175
GACGTATGCATGAGCTTAGCAAAGTCCGACG	1	27	1	TGAGCTAGCA	    0.975506	-164
CGTAGAGCAATACGGTGTGGGTTCGAACATG	1	56	1	TACGGTTGGG	    0.992605	-135
CCAGCCCGTATAAGCTTTGCGCGCATGTTCG	1	79	0	TAAGCTTGCG	    0.988427	-112
GCAAAGCTTATACGGGCTGGACGGGTGTGGT	1	90	1	TACGGGTGGA	    0.983236	-101
TGTCAATGTATGCGGTGTGCAGGACCTGGGG	1	120	1	TGCGGTTGCA	    0.968132	-71
          ****** ****

Masking position 1
Map Score:   6.85012

Number of sites scoring better than the average of aligned sites = 313
Number in coding regions = 280
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 2

TTAGCAAAGTCCGACGTAGAGCAATACGGT	1	42	1	CCGACGTAGA	     0.92731	-149
GTAGAGCAATACGGTGTGGGTTCGAACATG	1	57	1	ACGGTGTGGG	    0.995839	-134
CAAAGCTTATACGGGCTGGACGGGTGTGGT	1	91	1	ACGGGCTGGA	    0.993951	-100
ACGGGCTGGACGGGTGTGGTGTCAATGTAT	1	101	1	CGGGTGTGGT	    0.964206	-90
TGCGGTGTGCAGGACCTGGGGATAACACGG	1	130	1	AGGACCTGGG	    0.984054	-61
TTTTCAAAGAACAGGCTAGGATGATGTCT 	1	172	1	ACAGGCTAGG	    0.950256	-19
          **********

Masking position 7
Map Score:   4.19227

Number of sites scoring better than the average of aligned sites = 526
Number in coding regions = 459
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

          GCCGTGTATGTGTGTTGACG	1	1	1	GCCGTGTATG	    0.979534	-190
TGTGTGTTGACGTATGCATGAGCTTAGCAA	1	19	1	CGTATGCATG	    0.974212	-172
GTATAAGCTTTGCGCGCATGTTCGAACCCA	1	73	0	TGCGCGCATG	    0.986306	-118
GGACGGGTGTGGTGTCAATGTATGCGGTGT	1	108	1	GGTGTCAATG	     0.97798	-83
CAATGTATGCGGTGTGCAGGACCTGGGGAT	1	123	1	GGTGTGCAGG	    0.992937	-68
          **********

Masking position 8
Map Score:   2.43643

Number of sites scoring better than the average of aligned sites = 610
Number in coding regions = 562
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 4

          **********

No masking
Map Score:   -2.32047e-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:   -2.32047e-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:   -2.32047e-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