AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_tpal_bbur_100.orf -o113_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	RTP00139	102	AE000520

Motif number 1

TCTGCCGCTAACAGCAAGTGAGTACGGGCG	1	12	0	ACAGCAAGTG	     0.98967	-91
TATCCCCTCCATCGAAAGCGGCATCTGCCG	1	35	0	ATCGAAAGCG	    0.994451	-68
GATGGAGGGGATAGAGCGCGTGCACGTGCT	1	52	1	ATAGAGCGCG	    0.994083	-51
CGCGTACCAAAAAGCACGTGCACGCGCTCT	1	64	0	AAAGCACGTG	    0.992579	-39
GAAAACGGTCAACGTACGCGTACCAAAAAG	1	80	0	AACGTACGCG	    0.968191	-23
          **********

Masking position 1
Map Score:   8.31746

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 5
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

AACAGCAAGTGAGTACGGGCGT        	1	3	0	GAGTACGGGC	    0.988793	-100
CTCACTTGCTGTTAGCGGCAGATGCCGCTT	1	20	1	GTTAGCGGCA	    0.977749	-83
CCCCTCCATCGAAAGCGGCATCTGCCGCTA	1	32	0	GAAAGCGGCA	    0.994692	-71
GGAGGGGATAGAGCGCGTGCACGTGCTTTT	1	55	1	GAGCGCGTGC	    0.690754	-48
GTGCTTTTTGGTACGCGTACGTTGACCGTT	1	77	1	GTACGCGTAC	    0.499754	-26
       CAGGAAAACGGTCAACGTACGCG	1	90	0	GAAAACGGTC	    0.979985	-13
          **********

Masking position 6
Map Score:   8.06053

Number of sites scoring better than the average of aligned sites = 892
Number in coding regions = 244
Number in noncoding regions = 648
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

TGCCGCTAACAGCAAGTGAGTACGGGCGT 	1	10	0	AGCAAGTGAG	     0.90842	-93
CGTACCAAAAAGCACGTGCACGCGCTCTAT	1	62	0	AGCACGTGCA	    0.516253	-41
          **********

Masking position 4
Map Score:   0.0362425

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 1
Number in noncoding regions = 1
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:   -1.9652e-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:   -1.9652e-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:   -1.9652e-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