AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00471_tpal_reg_300.orf -o00471_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	TP0406	190	glutamate racemase (murI)

Motif number 1

GTATGTGTGTTGACGTATGCATGAGCTTAGC	1	16	1	TGACGTTGCA	    0.986443	-175
GACGTATGCATGAGCTTAGCAAAGTCCGACG	1	27	1	TGAGCTAGCA	     0.97621	-164
CGTAGAGCAATACGGTGTGGGTTCGAACATG	1	56	1	TACGGTTGGG	    0.992822	-135
CCAGCCCGTATAAGCTTTGCGCGCATGTTCG	1	79	0	TAAGCTTGCG	    0.988766	-112
GCAAAGCTTATACGGGCTGGACGGGTGTGGT	1	90	1	TACGGGTGGA	    0.983716	-101
TGTCAATGTATGCGGTGTGCAGGACCTGGGG	1	120	1	TGCGGTTGCA	    0.967335	-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	     0.93225	-149
GTAGAGCAATACGGTGTGGGTTCGAACATG	1	57	1	ACGGTGTGGG	    0.996328	-134
CAAAGCTTATACGGGCTGGACGGGTGTGGT	1	91	1	ACGGGCTGGA	     0.99466	-100
ACGGGCTGGACGGGTGTGGTGTCAATGTAT	1	101	1	CGGGTGTGGT	    0.968583	-90
TGCGGTGTGCAGGACCTGGGGATAACACGG	1	130	1	AGGACCTGGG	    0.985678	-61
TTTTCAAAGAACAGGCTAGGATGATGTCT 	1	172	1	ACAGGCTAGG	    0.955714	-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

CGTCAACACACATACACGGC          	1	1	0	CATACACGGC	    0.976508	-190
TTGCTAAGCTCATGCATACGTCAACACACA	1	19	0	CATGCATACG	    0.971457	-172
TGGGTTCGAACATGCGCGCAAAGCTTATAC	1	73	1	CATGCGCGCA	    0.984459	-118
ACACCGCATACATTGACACCACACCCGTCC	1	108	0	CATTGACACC	     0.97472	-83
ATCCCCAGGTCCTGCACACCGCATACATTG	1	123	0	CCTGCACACC	    0.992859	-68
          **********

Masking position 3
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