AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i028_tpal_bbur_100.orf -o028_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTP00065	121	AE000520

Motif number 1

CTATCTTGCTTTGCCGATCCG         	1	2	0	TTGCCGATCC	    0.989667	-120
CTGCTGCTGTTTGCCTCTCACGGTTCTGAG	1	42	0	TTGCCTCTCA	    0.994312	-80
TTCAGATGACTCGCTGCTGCTGTTTGCCTC	1	55	0	TCGCTGCTGC	    0.994162	-67
TATGTGAGTGTTGCTTCAGATGACTCGCTG	1	69	0	TTGCTTCAGA	    0.958345	-53
GGAAGCGATATTGTCGCCCCCTATGTGAGT	1	90	0	TTGTCGCCCC	    0.990162	-32
GGCGACAATATCGCTTCCCTGAGAACGCAA	1	102	1	TCGCTTCCCT	    0.982591	-20
          **********

Masking position 1
Map Score:   7.44586

Number of sites scoring better than the average of aligned sites = 1999
Number in coding regions = 576
Number in noncoding regions = 1423
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 2

TGCCTCTCACGGTTCTGAGGATCACTTTTC	1	31	0	GGTTCTGAGG	    0.998399	-91
CAGATGACTCGCTGCTGCTGTTTGCCTCTC	1	53	0	GCTGCTGCTG	    0.992932	-69
TGTGAGTGTTGCTTCAGATGACTCGCTGCT	1	67	0	GCTTCAGATG	    0.993836	-55
       TTGCGTTCTCAGGGAAGCGATAT	1	109	0	CGTTCTCAGG	     0.98578	-13
          **********

Masking position 3
Map Score:   3.99548

Number of sites scoring better than the average of aligned sites = 218
Number in coding regions = 54
Number in noncoding regions = 164
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

          CGGATCGGCAAAGCAAGATA	1	1	1	CGGATCGGCA	     0.99381	-121
AGATAGAAAAGTGATCCTCAGAACCGTGAG	1	26	1	GTGATCCTCA	    0.963169	-96
CCTCAGAACCGTGAGAGGCAAACAGCAGCA	1	41	1	GTGAGAGGCA	    0.990864	-81
CACTCACATAGGGGGCGACAATATCGCTTC	1	89	1	GGGGGCGACA	    0.997044	-33
GCGTTCTCAGGGAAGCGATATTGTCGCCCC	1	100	0	GGAAGCGATA	    0.968015	-22
          **********

Masking position 10
Map Score:   4.05536

Number of sites scoring better than the average of aligned sites = 1364
Number in coding regions = 442
Number in noncoding regions = 922
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 4

          **********

No masking
Map Score:   -1.46782e-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:   -1.46782e-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:   -1.46782e-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