AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00480_tpal_reg_100.orf -o00480_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	TP0477	60	glucose-6-phosphate 1-dehydrogenase, putative
#2	TP0478	72	glucose-6-phosphate 1-dehydrogenase (zwf)
#3	TP0479	111	T. pallidum predicted coding region TP0479

Motif number 1

      CGGTAATGCCGAGCCTTGAACGAC	1	5	1	AATGCCGAGC	    0.891616	-56
ACGTAGCGGGAGAGAGGAGGATGTTCGCCC	1	41	1	AGAGAGGAGG	    0.968226	-20
  TGCCTTAGGGAGCGGAGAGTCTGCCTGC	2	9	1	GGAGCGGAGA	    0.973758	-64
CCCTTCTTTCAACGGTGCGACCTACACCGG	2	46	0	AACGGTGCGA	    0.974457	-27
ACCGTTGAAAGAAGGGGCGGTTT       	2	60	1	GAAGGGGCGG	    0.990897	-13
CCTTTAGAAAAAGGAGGAGCTC        	3	3	0	AAGGAGGAGC	    0.983264	-109
CCTTTTTCTAAAGGCTGCGAGGCAATTATT	3	19	1	AAGGCTGCGA	    0.959097	-93
AGAAAAACTTGACGGCGCGCGCTAAACGCC	3	50	0	GACGGCGCGC	    0.978951	-62
GAGTATGCCAAACGGTGAGAAAAACTTGAC	3	67	0	AACGGTGAGA	    0.976072	-45
CCTTCCTTGCGAAGAGGAGTATGCCAAACG	3	83	0	GAAGAGGAGT	    0.919691	-29
TTCGCAAGGAAGGGGGGAGGGC        	3	100	1	AGGGGGGAGG	    0.989489	-12
          **********

Masking position 4
Map Score:   17.2103

Number of sites scoring better than the average of aligned sites = 1266
Number in coding regions = 1116
Number in noncoding regions = 150
Number of orfs with sites within 600 bp upstream = 119
Fraction of orfs with sites within 600 bp upstream = 0.0191134


Motif number 2

GCCGAGCCTTGAACGACACTAGAACGTAGC	1	18	1	GAACGACACT	    0.869309	-43
     GGGCGAACATCCTCCTCTCTCCCGC	1	46	0	AACATCCTCC	    0.972534	-15
ATGTGCCGCAGGCAGACTCTCCGCTCCCTA	2	16	0	GGCAGACTCT	     0.96133	-57
TCAACGGTGCGACCTACACCGGATGTGCCG	2	38	0	GACCTACACC	    0.992579	-35
         AAACCGCCCCTTCTTTCAACG	2	62	0	AACCGCCCCT	    0.966421	-11
          GAGCTCCTCCTTTTTCTAAA	3	1	1	GAGCTCCTCC	    0.986697	-111
CTCACCGTTTGGCATACTCCTCTTCGCAAG	3	78	1	GGCATACTCC	      0.9837	-34
          GCCCTCCCCCCTTCCTTGCG	3	102	0	GCCCTCCCCC	    0.991698	-10
          **********

Masking position 7
Map Score:   10.5747

Number of sites scoring better than the average of aligned sites = 631
Number in coding regions = 555
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 3

          **********

No masking
Map Score:   1.16119e-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 4

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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