AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00650_tpal_reg_100.orf -o00650_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	TP0251	153	DNA-binding protein II
#2	TP0417	26	apolipoprotein N-acyltransferase (cutE)

Motif number 1

AGCGAAAACACCTTTCCGGGCAGCGGTGTCAA	1	17	0	CCTTCCGGCA	    0.992909	-137
GCGAGCCACAGCCTTTCTAGCGAAAACACCTT	1	35	0	GCTTTCAGCG	    0.997026	-119
TACACATTCGGGACTTCTGGCGAGCCACAGCC	1	54	0	GGCTTCGGCG	    0.997548	-100
CAAACGCGCACCACCTCGGGTGAAGAGAACAC	1	100	0	CCCCTCGGTG	    0.981543	-54
GAGGTGGTGCGCGTTTGAGGCGGCTGTTTGCC	1	115	1	GCTTTGGGCG	    0.997974	-39
      AAATGCTTTTCTGGCAGGGGAAAGTT	2	5	1	GCTTTCGGCA	     0.99864	-22
          ** **** ****

Masking position 10
Map Score:   9.54421

Number of sites scoring better than the average of aligned sites = 237
Number in coding regions = 211
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

CCTTTCCGGGCAGCGGTGTCAAGTCGCT  	1	9	0	CAGCGGTGTC	     0.98554	-145
GCTGCCCGGAAAGGTGTTTTCGCTAGAAAG	1	25	1	AAGGTGTTTT	    0.941644	-129
TTCGCTAGAAAGGCTGTGGCTCGCCAGAAG	1	43	1	AGGCTGTGGC	    0.986729	-111
AGACTGTACAACGGTGTGTTCTCTTCACCC	1	85	1	ACGGTGTGTT	    0.989184	-69
TTCTCTTCACCCGAGGTGGTGCGCGTTTGA	1	103	1	CCGAGGTGGT	    0.955557	-51
GCGTTTGAGGCGGCTGTTTGCCCGCGTGTG	1	125	1	CGGCTGTTTG	    0.971287	-29
GCTGTTTGCCCGCGTGTGTTTCTTGTC   	1	137	1	CGCGTGTGTT	    0.981449	-17
          **********

Masking position 7
Map Score:   5.93626

Number of sites scoring better than the average of aligned sites = 956
Number in coding regions = 879
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 3

CTAGCGAAAACACCTTTCCGGGCAGCGGTG	1	21	0	CACCTTTCCG	    0.977857	-133
GGCGAGCCACAGCCTTTCTAGCGAAAACAC	1	38	0	AGCCTTTCTA	    0.961201	-116
GAAGAGAACACACCGTTGTACAGTCTACAC	1	81	0	CACCGTTGTA	    0.940907	-73
CGAGGTGGTGCGCGTTTGAGGCGGCTGTTT	1	114	1	CGCGTTTGAG	    0.983756	-40
GCTGTTTGCCCGCGTGTGTTTCTTGTC   	1	137	1	CGCGTGTGTT	    0.948385	-17
       AAATGCTTTTCTGGCAGGGGAAA	2	4	1	TGCTTTTCTG	    0.933546	-23
          **********

Masking position 7
Map Score:   0.431639

Number of sites scoring better than the average of aligned sites = 942
Number in coding regions = 874
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 4

          **********

No masking
Map Score:   -4.02577e-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:   -4.02577e-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:   -4.02577e-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