AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00460_tpal_reg_100.orf -o00460_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	TP0329	117	serine hydroxymethyltransferase (glyA)
#2	TP0556	104	asparagine synthetase (asnA)

Motif number 1

TTACGCACGACGGGTATCGGGCATGCGGCG	1	26	1	CGGGTATCGG	    0.968067	-92
GGGCATGCGGCGCGCGGCGTTTTGTCCATT	1	44	1	CGCGCGGCGT	    0.983059	-74
TTCTCTCCTCAGGTAGGCAGAATATTGTTC	1	94	0	AGGTAGGCAG	    0.982559	-24
ATCTGACAGCAGGGAGGTGGT         	2	2	0	AGGGAGGTGG	    0.994043	-103
ATTATTTAATAGGGTGGCGGTGTAGTGCAA	2	42	0	AGGGTGGCGG	     0.99928	-63
ACAAGGTAAAAGGTTGGCGTTAACT     	2	90	1	AGGTTGGCGT	    0.994278	-15
          **********

Masking position 2
Map Score:   9.52096

Number of sites scoring better than the average of aligned sites = 345
Number in coding regions = 286
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 2

CGTCGTGCGTAACAGGGGAACATACCA     	1	6	0	AACAGGAACA	    0.986076	-112
TTCTAGCGCAAAGAATGGACAAAACGCCGCGC	1	55	0	AAGAAGACAA	    0.990967	-63
GCGCTAGAAACAGAGCGAACAATATTCTGCCT	1	78	1	CAGAGGACAA	    0.991099	-40
TGCCTACCTGAGGAGAGAAAAAC         	1	105	1	AGGAGGAAAA	    0.990399	-13
CAGTTTACTCAACAAGGTAAAAGGTTGGCGTT	2	79	1	AACAAGAAAA	     0.98587	-26
          ***** * ****

Masking position 4
Map Score:   2.82646

Number of sites scoring better than the average of aligned sites = 66
Number in coding regions = 51
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

AAAGAATGGACAAAACGCCGCGCGCCGCATG	1	47	0	CAAAACCCGC	    0.995739	-71
ACAGAGCGAACAATATTCTGCCTACCTGAGG	1	87	1	CAATATCTGC	    0.985303	-31
        ACCACCTCCCTGCTGTCAGATTA	2	3	1	CACCTCCTGC	    0.992757	-102
TTGAGTATTGCACTACACCGCCACCCTATTA	2	35	1	CACTACCCGC	    0.998433	-70
          ****** ****

Masking position 2
Map Score:   3.38543

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 80
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

GCATGCGGCGCGCGGCGTTTTGTCCATTCT	1	46	1	CGCGGCGTTT	    0.958547	-72
TTTGTCCATTCTTTGCGCTAGAAACAGAGC	1	64	1	CTTTGCGCTA	    0.970311	-54
GCAGAATATTGTTCGCTCTGTTTCTAGCGC	1	78	0	GTTCGCTCTG	    0.954348	-40
TATTTAATAGGGTGGCGGTGTAGTGCAATA	2	40	0	GGTGGCGGTG	    0.994146	-65
AAGGTAAAAGGTTGGCGTTAACT       	2	92	1	GTTGGCGTTA	     0.99189	-13
          **********

Masking position 9
Map Score:   0.39799

Number of sites scoring better than the average of aligned sites = 433
Number in coding regions = 404
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 5

          **********

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 6

          **********

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 7

          **********

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