AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_tpal_bbur_300.orf -o113_tpal_bbur_300.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

CGCCCGTACTCACTTGCTGTTAGCGGCAGA	1	12	1	CACTTGCTGT	    0.989556	-91
CGGCAGATGCCGCTTTCGATGGAGGGGATA	1	35	1	CGCTTTCGAT	     0.99439	-68
AGCACGTGCACGCGCTCTATCCCCTCCATC	1	52	0	CGCGCTCTAT	    0.994018	-51
AGAGCGCGTGCACGTGCTTTTTGGTACGCG	1	64	1	CACGTGCTTT	    0.992575	-39
CTTTTTGGTACGCGTACGTTGACCGTTTTC	1	80	1	CGCGTACGTT	    0.968431	-23
          **********

Masking position 10
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

        ACGCCCGTACTCACTTGCTGTT	1	3	1	GCCCGTACTC	    0.988915	-100
AAGCGGCATCTGCCGCTAACAGCAAGTGAG	1	20	0	TGCCGCTAAC	     0.97799	-83
TAGCGGCAGATGCCGCTTTCGATGGAGGGG	1	32	1	TGCCGCTTTC	    0.994739	-71
AAAAGCACGTGCACGCGCTCTATCCCCTCC	1	55	0	GCACGCGCTC	    0.689462	-48
GTGCTTTTTGGTACGCGTACGTTGACCGTT	1	77	1	GTACGCGTAC	    0.499759	-26
CGCGTACGTTGACCGTTTTCCTG       	1	90	1	GACCGTTTTC	    0.980048	-13
          **********

Masking position 5
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

GCCGCTAACAGCAAGTGAGTACGGGCGT  	1	9	0	GCAAGTGAGT	    0.993218	-94
TAGAGCGCGTGCACGTGCTTTTTGGTACGC	1	63	1	GCACGTGCTT	     0.99665	-40
GCTTTTTGGTACGCGTACGTTGACCGTTTT	1	79	1	ACGCGTACGT	    0.867618	-24
          **********

Masking position 6
Map Score:   1.15296

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 5
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


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