AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00600_tpal_reg_100.orf -o00600_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	TP0524	135	ATP-dependent protease LA (lon-2)
#2	TP0852	150	prolipoprotein diacylglyceryl transferase (lgt)

Motif number 1

CTGCGCCCCCGCAGGTCGTGCAAGACGTTTAC	1	33	0	GAGGTCGTGA	    0.980325	-103
CACGACCTGCGGGGGCGCAGTATACCGCGCAG	1	45	1	GGGGCGCAGA	    0.992702	-91
         AGGGCGCCTAGTATCCAGGCAAG	1	123	0	GGCGCCTAGA	    0.970135	-13
   ACTTCATGAGGGTGGGGTATAACCCCTAT	2	8	1	GGGGTGGGGA	    0.997669	-143
AGTTTACGCGGAGCGTGGTGAATGGTGACAGG	2	66	1	GGCGTGGTGA	    0.998067	-85
AACGGAAAACGGTGGCGGGGTAGTGCGCGGTG	2	101	1	GTGGCGGGGA	     0.99413	-50
TGGCGGGGTAGTGCGCGGTGCATTTCCTTACG	2	113	1	GGCGCGGTGA	    0.999243	-38
GTGCATTTCCTTACGCGGTGGAGGTTGTGTG 	2	130	1	TACGCGGTGA	    0.975727	-21
          * ******** *

Masking position 12
Map Score:   16.2344

Number of sites scoring better than the average of aligned sites = 634
Number in coding regions = 564
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 62
Fraction of orfs with sites within 600 bp upstream = 0.00995824


Motif number 2

CTGCGCCCCCGCAGGTCGTGCAAGACGTTT	1	35	0	GCAGGTCGTG	    0.910382	-101
CACGACCTGCGGGGGCGCAGTATACCGCGC	1	45	1	GGGGGCGCAG	    0.986289	-91
GGCCTCGAATGGAGGCATTGACTTTTCGTC	1	92	1	GGAGGCATTG	    0.925782	-44
         AGGGCGCCTAGTATCCAGGCA	1	125	0	GGGCGCCTAG	    0.962224	-11
   ACTTCATGAGGGTGGGGTATAACCCCT	2	8	1	GAGGGTGGGG	    0.985622	-143
CCCTATTTGTGGGGGTGTTTTTGGGAGAAT	2	34	1	GGGGGTGTTT	    0.927052	-117
AGTTTACGCGGAGCGTGGTGAATGGTGACA	2	66	1	GAGCGTGGTG	    0.987937	-85
AACGGAAAACGGTGGCGGGGTAGTGCGCGG	2	101	1	GGTGGCGGGG	    0.987078	-50
TGGCGGGGTAGTGCGCGGTGCATTTCCTTA	2	113	1	GTGCGCGGTG	    0.994644	-38
GTGCATTTCCTTACGCGGTGGAGGTTGTGT	2	130	1	TTACGCGGTG	    0.845874	-21
          **********

Masking position 5
Map Score:   12.5765

Number of sites scoring better than the average of aligned sites = 2263
Number in coding regions = 1994
Number in noncoding regions = 269
Number of orfs with sites within 600 bp upstream = 172
Fraction of orfs with sites within 600 bp upstream = 0.0276261


Motif number 3

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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