AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i243_tpal_bbur_300.orf -o243_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	RTP00740	47	AE000520
#2	RTP00743	169	AE000520

Motif number 1

GCCTCGAGCGCGAGGTGCAGCCGAGGCGCC	1	12	1	CGAGGTGCAG	    0.997711	-36
GAGGTGCAGCCGAGGCGCCGCTGCCACTGG	1	23	1	CGAGGCGCCG	    0.996407	-25
     CTGCGCCAGTGGCAGCGGCGCCTCG	1	33	0	CCAGTGGCAG	    0.996392	-15
CGTGTACATACCAGATGCCGTCGCGGGAGG	2	55	0	CCAGATGCCG	    0.995004	-115
GAAGGCACTTTTAGTCGCAGATGATCCCGT	2	118	1	TTAGTCGCAG	    0.972755	-52
          **********

Masking position 3
Map Score:   8.37355

Number of sites scoring better than the average of aligned sites = 200
Number in coding regions = 55
Number in noncoding regions = 145
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

AGCGGCGCCTCGGCTGCACCTCGCGCTCGA	1	15	0	CGGCTGCACC	    0.998615	-33
GCGCCAGTGGCAGCGGCGCCTCGGCTGCAC	1	26	0	CAGCGGCGCC	    0.998717	-22
TGTCCTCCCGCGACGGCATCTGGTATGTAC	2	52	1	CGACGGCATC	    0.980122	-118
GAAACGGGATCATCTGCGACTAAAAGTGCC	2	121	0	CATCTGCGAC	    0.978576	-49
TTTCAAATACCAGATTCACCGAAACGGGAT	2	141	0	CAGATTCACC	    0.960824	-29
          **********

Masking position 7
Map Score:   5.73636

Number of sites scoring better than the average of aligned sites = 642
Number in coding regions = 178
Number in noncoding regions = 464
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

GTAAAGCGCTTCTTTTCCCGGAAATCCCGG	2	14	0	TCTTTTCCCG	    0.993087	-156
GAAAAGAAGCGCTTTACCTATCACCTGTCC	2	27	1	GCTTTACCTA	    0.901939	-143
CGGCATCTGGTATGTACACGATTACGTAGT	2	65	1	TATGTACACG	    0.931804	-105
CCTTCATCATTCTGTTCCCAAATTCTCAAC	2	93	0	TCTGTTCCCA	    0.992177	-77
TTTAGTCGCAGATGATCCCGTTTCGGTGAA	2	127	1	GATGATCCCG	    0.979165	-43
          **********

Masking position 3
Map Score:   2.54217

Number of sites scoring better than the average of aligned sites = 1085
Number in coding regions = 335
Number in noncoding regions = 750
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

          GTACCGGGATTTCCGGGAAA	2	1	1	GTACCGGGAT	    0.944663	-169
GTCGCGGGAGGACAGGTGATAGGTAAAGCG	2	36	0	GACAGGTGAT	    0.968944	-134
ACCAGATGCCGTCGCGGGAGGACAGGTGAT	2	46	0	GTCGCGGGAG	     0.93049	-124
CAGATTCACCGAAACGGGATCATCTGCGAC	2	131	0	GAAACGGGAT	    0.994539	-39
          **********

Masking position 9
Map Score:   2.43126

Number of sites scoring better than the average of aligned sites = 114
Number in coding regions = 38
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   2.93755e-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:   2.93755e-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 7

          **********

No masking
Map Score:   2.93755e-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