AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i138_tpal_bbur_100.orf -o138_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

Purged sequences:
RTP00364	197	AE000520

Input sequences:
#1	RTP00365	197	AE000520

Motif number 1

ACGCATAGACGTGAATCGCTCAACATCCTGTACGTCCC	1	26	1	GGACCCCACC	    0.994104	-172
TCAACATCCTGTACGTCCCCTCCCTCCCTTTGGAGAAC	1	45	1	GAGCCTCTCC	    0.998044	-153
CCCTCCCTTTGGAGAACACGTTTCACCCGCTCTTTTAA	1	66	1	GAACCTCACC	    0.971153	-132
CGCGCTGAAGGTATATCTTTTGGCTTCATTAAAAGAGC	1	94	0	GAACTTCTCA	    0.982893	-104
TATACCTTCAGCGCGGCATCTTTCACCAACCAAATGGC	1	117	1	GGGCTTCACA	    0.986727	-81
CAACCAAATGGCCAGGCGCGACCCTACCACGCAGGAAG	1	143	1	GCGCCACTCC	     0.92242	-55
TACCACGCAGGAAGAACGCATCGCAAGACAGAGCTGCC	1	167	1	GAACCTCAGA	    0.981528	-31
          * * * * * *  ** **

Masking position 7
Map Score:   6.44681

Number of sites scoring better than the average of aligned sites = 349
Number in coding regions = 92
Number in noncoding regions = 257
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

      CATATCTTCAGCGTCACGCATAGA	1	5	1	TCTTCAGCGT	    0.963359	-193
CGTGAATCGCTCAACATCCTGTACGTCCCC	1	35	1	TCAACATCCT	    0.899623	-163
CTGTACGTCCCCTCCCTCCCTTTGGAGAAC	1	53	1	CCTCCCTCCC	    0.991265	-145
AGAACACGTTTCACCCGCTCTTTTAATGAA	1	78	1	TCACCCGCTC	    0.976149	-120
AAAAGATATACCTTCAGCGCGGCATCTTTC	1	111	1	CCTTCAGCGC	     0.98947	-87
GCGGCATCTTTCACCAACCAAATGGCCAGG	1	129	1	TCACCAACCA	    0.919689	-69
CAGGCGCGACCCTACCACGCAGGAAGAACG	1	155	1	CCTACCACGC	    0.980531	-43
          **********

Masking position 5
Map Score:   5.32251

Number of sites scoring better than the average of aligned sites = 1922
Number in coding regions = 530
Number in noncoding regions = 1392
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 3

          **********

No masking
Map Score:   8.05918e-14

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:   8.05918e-14

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:   8.05918e-14

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