Output of sir_graph (©)
mfold_util 4.6
Created Sat Oct 22 09:51:41 2011
U
Supplementary material figure 1:
Predicted stem-loop structures of
novel miRNAs in Populus tomentosa.
Mature sequences are shown in
yellow; star sequences are shown in
green.
G A
G
A
U
U
U
U
40
U
G
G
A
U
50
G
U
A
C
U
U
U
U
Pto-M1
C G
A U
60
A U
U A
A U
G U
30
A U
A U
G C
G C
G C
G U
70
C A
G C
A U
20
G C
C
U A
G C
G C
G C
U A
80
G U
G C
G C
C C
U A
10
A U
U A
U G
G G
G U
90
A U
A U
G C
G C
5’
C G
3’
dG = -45.90 [Initially -45.90] 11Oct22-09-51-40
Output of sir_graph (©)
mfold_util 4.6
Created Sat Oct 22 09:53:24 2011
60
A U A C
U
G
C
A
A
A
C
U
U
A
A
A
U
C
C
U A
U
U A
Pto-M2
C G
G A
U A
U G
U A
U G
U A
40
G U
C G
U A
80
A
U
C
C
A
G C
C G
A U
G U
C G
C G
G C
U A
U G
C G
A U
G U
U G
A U
20
G U
G C
A U
100
A U
C G
C G
G C
A U
C A
G C
U A
A U
G U
U U
U U
A U
G C
A U
A U
5’
A U
3’
dG = -49.80 [Initially -49.30] 11Oct22-09-53-22
Output of sir_graph (©)
mfold_util 4.6
Created Sat Oct 22 09:54:43 2011
50
A A
U
G A U U U
U
C
U U A A A
A
A
A U
40
A U
G C
G C
Pto-M3
A U
30
A U
G C
A U
60
A U
C G
G C
U C
A U
U A
G C
20
A U
G C
C
A U
70
G C
G C
G C
U A
A U
G
A U
10
G C
G C
U A
80
U
C
U
U
U
C
U G
G C
A U
A U
3’
dG = -39.00 [Initially -38.50] 11Oct22-09-54-42
5’
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 03:55:16 2011
U G
A
40
U
G
U
U
A
U
Pto-M4a
A
A
A
G
U
A
30
U
G
U
A
U
A
A
G
C
U
20
A
G
U
U
A
U
A
A
G
C
10
U
C
C
C
U
A
U
U
U
U
5’
A
C
A
U
U
C
G
G
U
70
C
G
U
U
C
G
A
G
U
G
A
80
A
U
A
A
A
U
A
U
U
C
C
A
A
C
3’
dG = -36.70 [Initially -36.70] 11Sep02-03-55-15
60
U
U
C
U
A
U
G
G
A
50
A
Output of sir_graph (©)
mfold_util 4.6
Created Sat Oct 22 09:57:26 2011
G G U
U
U
A
A
G U
U A
40
50
A U
U G
Pto-M4b
A U
A U
A U
G C
U A
A U
U U
G C
30
60
U A
A C
U A
A U
A U
G C
C G
U G
A U
G C
20
70
U A
U A
A C
U G
A U
A U
G C
C G
U A
C G
10
80
C U
C G
U A
A U
U A
U A
U A
G C
U
5’
A
3’
dG = -40.30 [Initially -40.30] 11Oct22-09-57-24
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 03:59:10 2011
80
C
A C
A
C
G
U
A U
A
U
A
A
C
C
G
C
C
C
A
U
A
C
A U
G
C
A
A
U
A U C
C
A
U
C
G
A
A
A
U
U
A
U
C
A
100
G
A A C A
A
C
U
U
U
U
120
A
U
G
C
U
C
C
A
C
U
C
A
C
A
A
A
60
C
U
A
Pto-M5
U
C
U
U
C
U A
U
U
A140
A
G C
G C
A
A
U
U
U
A
A
A
U
A
U
U
A
A
A U
C
A U
C G
40
A U
U A
U A
C G
A A
A U
A U
A U
160
A U
C G
C G
A U
C G
A U
G C
G C
U A
A U
C G
A U
20
G C
U A
A U
G C
U A
A U
A U
A U
U
180
U
U
A
A
A
C
A
A
C
A
U
A
A
A
U
A
A
C
A
5’
A
A
3’
dG = -42.77 [Initially -46.20] 11Sep02-03-59-07
Output of sir_graph (©)
mfold_util 4.6
G
U
5’
Created Fri Sep 2 04:02:32 2011
C
A
U
C
G
G
U
3’
100
C
C
Pto-M6
U
A
C
G
U
C
A
G
G
U
U
A
A
U
A
U
U
A
C
G C
20
U
U
A
C
A
A
G
U
U
U
A
C
A
U
G
C
G
A
G
80
C
U
A
G
A
C
C
U
G
G
G
C
C
C
A
G
A
A 40
A
G
C
U
U
G
A
U
C
U
U
A
A
U
C
dG = -38.60 [Initially -39.10] 11Sep02-04-02-31
A
A
U
C C
U
U
G
A
U
G
U
A
U
A
60
U
C
Output of sir_graph (©)
mfold_util 4.6
Created Sat Oct 22 10:17:08 2011
C
30
A
C G C
40
A
A
A
G
A
A
U
U
C
U A A
A U C
C
U A G
A
U U C
G
A
C G
G C
70
60
U
U
U
G
C
A
G
A G
C C
A
G C
20
A
G
C G
Pto-M7
50
C
C
U
U A
A U
80
C G
G C
G C
U A
U A
A A
C G
C G
10
U A
U G
90
C A
G U
A U
A U
C G
G C
G C
5’
G C
3’
dG = -37.79 [Initially -39.70] 11Oct22-10-17-06
C
U
G
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:11:08 2011
A C
G
A
A U
60
C G
G
U A
Pto-M8
A U
A C
A U
G C
U U
A C
C G
U A
U A
U A
G C
G C
A
G C
80
G C
40
A
A
C
U
U
U
G
U
U
C G
C G
C G
U
U
U
U
C
G C
U A
C G
C G
G C
U
U G
C G
A U
G C
100
U
A U
20
G C
G C
A U
A U
C G
C G
G C
A U
U A
A
G C
G U
U U
U G
U A
G C
U A
U G
C G
U
5’
120
C
3’
dG = -57.20 [Initially -57.20] 11Sep02-04-11-07
Output of sir_graph (©)
mfold_util 4.6
Created Sat Oct 22 10:21:33 2011
C
U G G
C
C
C
C
A
U
50
U
G
A
U A
40
G U
A
U
G U
Pto-M9a
C U
C G
C G
U A
A
30
60
U
G C
U
U A
A
U
C G
G C
C U
U A
A
U
G C
20
70
G C
G C
A
U
A
U
A
U
C G
C G
U A
A
U
C U
10
80
G C
G C
A
U
G C
G C
A
U
G U
A
U
U G
5’
C G
3’
dG = -49.80 [Initially -49.80] 11Oct22-10-21-32
Output of sir_graph (©)
mfold_util 4.6
Created Sat Oct 22 10:28:14 2011
C
U
C
C
C
G C
50
U A
Pto-M9b
C
U
G
U
A
U A
40
G U
A U
A U
C U
C G
C G
60
U A
A U
30
G C
U
U A
A U
C G
G C
C U
U A
A U
70
G C
20
G C
G C
A U
A U
A U
C G
C G
U A
A U
80
C U
10
G C
G C
A U
G C
G C
A U
G U
A U
5’
U G
90
C G
3’
dG = -49.70 [Initially -49.70] 11Oct22-10-28-13
Output of sir_graph (©)
mfold_util 4.6
G
Created Fri Sep 2 04:13:50 2011
C U C
C
A
A
A
Pto-M10a
U
U
U
A
A
60
G
C
C
A
G
U
U
A
U
G
U
C
A
40
G
A
U
G A
U
C
A
G
G
A
U
C
U
A
G
A
U
C
G
A
C
C
U
G
C
A
80
U
G
C
A
U
G
A
A
U
C A
U
C
U
G
20
U
A
C
A
U
G
G
A
U
C
C
A
A
G
A
U
A
A
A
G
A
A
C
G
C
G
5’
U
A
G
G
3’
dG = -51.60 [Initially -51.60] 11Sep02-04-13-49
A
G
U
U
C
U
C
100
A
C
Output of sir_graph (©)
mfold_util 4.6
G
Created Fri Sep 2 04:14:58 2011
C U C
C
A
A
A
U
U
U
A
G
A
Pto-M10b
60
C
C
A
G
U
U
U
A
U
G
C
A
40
A
G
U
U
C G
G
U
C
A
G
G
A
G
A
A A
C
U
A
G
C
C
G
U
A
C
G
80
U
A
C
G
U
A
A
U
C A
U
C
G
20
U
A
U
A
C
G
U
A
G
C
U
A
C
G
A
A
U
A
G
A
U
G
C
U
A
A
C
G
C
G
5’
A
U
G
G
3’
dG = -49.00 [Initially -49.00] 11Sep02-04-14-57
A
G
U
C
100
A
C
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:15:57 2011
A G
60
U
G
G
A
A U
A U
Pto-M11
C G
U G
G C
U A
U A
C C
G C
A U
A C
G U
G C
A U
U A
80
C A
U C
A U
40
C G
C G
G C
U A
A U
A G
G A
U G
C G
C G
C G
U A
C G
G U
G C
U A
C C
100
C G
G C
U A
C G
20
U G
G C
G C
C
A
A
U
A
A
G C
A U
A
A
A
G C
U A
C
C G
U A
U
U
G C
120
G U
C G
U
C
5’
C
U
3’
dG = -56.10 [Initially -56.10] 11Sep02-04-15-55
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:16:58 2011
C G G
60
A
C
U
C
A
C
U
Pto-M12
G C
G C
U U
G C
G C
G U
G U
U U
U A
G C
A U
G C
U G
80
U A A
A
G
G
C
U
U
G C
G C
A U
40
A U
U A
U A
U
U
C
A
A
A U
U
U
C
U
G
A
100
C G
A G
C G
U A
U A
A U
G C
A U
A U
C G
U A
20
A U
C G
G A
A U
C G
G C
G U
C G
G C
120
U A
A U
G C
C G
C G
G C
A
G
A
U
A
U
A
5’
U
3’
dG = -57.20 [Initially -57.20] 11Sep02-04-16-57
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:18:35 2011
A A
A
A
A
G
C
U
C
U
Pto-M13a
C
C
A
A U U
U
140
A
U
C
U
U C
G
G
G
G
A
G
G
160
G
G
U
A U
U G U G C
A U
A U
U
A U
U G
120
U
U
A
U G
G
U G U G
U A
U A
U A
C G
180
U A
U A
U G
U A
G C
U A
U A
C G
U A
U A
G C
C
A
U
G
C
A
U
100
C G U
G C
200
A U
G U
U G
A
A
A U
G C
U A
C G
A U
C
U
U
A
A U
C G
G C
U G
G C
G U
80
C
G
U C
U
U
U A
G
A A
U G A U
U U
G
U
A U
G
U
A
U
U
220
U A
C
G
G
U
G
U
U
G
A
U A
60
A U
C G
C G
C A
G U
C G
U G
C G
U A
G U
A C
C G
C G
240
G C
40
C A
U G
C G
C G
C G
U A
G C
U A
U A
U A
U A
U A
A U
C G
G
G C
U A
A U
U A
260
U A
20
C G
U A
C G
U
U A
U
U G
U
C G
A U
U A
C C
C A
C G
A U
3’
U
C
C
A U
5’
dG = -105.03 [Initially -106.40] 11Sep02-04-18-33
Output of sir_graph (©)
mfold_util 4.6
Created Sat Oct 22 10:31:17 2011
60
C C
A
A
G
A
A
A
U
A
A U
G C
A U
G
G C
Pto-M13b
A U
C G
G C
G U
A A
G C
G C
G C
40
U
U
G
A
C
A
U
C
U
U
U
80
G U
G U
A U
G C
A U
G C
A U
A U
U A
A U
C
G
A
G C
U G
A U
20
A U
A U
A U
A U
C G
100
A U
G C
G U
G C
G U
A C
C G
G C
G C
C G
U G
A U
G C
G U
5’
G C
3’
dG = -57.50 [Initially -57.50] 11Oct22-10-31-16
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:20:55 2011
G A
U
A
U A
Pto-M14
C G
60
G A
A U
U A
C G
G A
A C
U A
C G
G C
A
C
G
A
A
G U
C G
80
A U
U A
G U
U U
A U
40
C
A
G C
A U
A U
A U
C G
U A
U A
A G
C G
A U
C G
U A
G
U A
100
A
A U
G C
A U
A U
C G
U A
20
A U
C G
U A
A U
C G
G C
A U
C G
G C
U A
G U
G C
A A
C G
120
G C
C
U
A
U
U
U
G
5’
A
3’
dG = -54.50 [Initially -54.50] 11Sep02-04-20-54
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:22:12 2011
A
A C
G
A
A
U
A
A
A
U
U
A
U
A
U
80
A
U
G
U
A
Pto-M15
A
A
G
60
A
G
U
U
A
A
U
G
C
A
G
U
G
U
A
G
U
A
C
U
G
A
A
U
U
A
A
A
C
100
A
U
A G C
C
A U
G C
A U
A U
40
C G
A U
U U
A U
C G
G
U
U
A
U
C G
G C
C
U A
C G
C G
120
G C
U A
U
C G
A U
G C
U
A U
20
G C
G C
A U
A U
C G
C G
G C
A U
U A
A
G
C
U
A
G
U
U G
140
U A
G C
U A
U G
C G
U
5’
C
3’
dG = -51.13 [Initially -54.30] 11Sep02-04-22-11
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:24:00 2011
A G
60
U
G
G
A
A U
A U
C G
Pto-M16
U G
G C
U A
U A
C C
G C
A U
A U
G U
G C
A U
U A
80
C U
U U
A U
40
C G
C G
G C
U A
A U
A G
G A
U G
C G
C G
C G
U A
C G
G U
G C
U G
C A
C G
100
G C
U A
C G
20
C G
G C
G C
U A
A
A U
A U
A
G
A
A
C
A
A
A
A
G C
U A
C G
U
G C
120
G U
U
U
U
A
C
C
A
5’
3’
dG = -61.50 [Initially -61.50] 11Sep02-04-23-59
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:24:50 2011
A C U
C
U
A
C
U
U
U G
G C
U A
60
G U
Pto-M17
C G
A U
U
A
G
40
G C A
U
C
U
A
U
A
U
A
C
G
A
U
A
U
C
G
U
A
G
C
C
G
C
G
U
A
U
A
C
G
C
C
U
U
A
G
C
U
A
U
A
G
G
C
A
A
C
U
G
A
C
U
U
U
C
G
A
C
100
U
C
C
A
G
A
A
G
U
20
A
G
A
G
A
5’
A
A
A
3’
dG = -56.78 [Initially -59.30] 11Sep02-04-24-48
A
C G U
A
G
C
80
G U
C
G
A
C
C
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:26:09 2011
G
A
A
C
C
C G
40
Pto-M18
U A
U A
C
50
A
C
C
A
G
G
30
G
U
C
A
C
U
U
C
A
C
20
G
A
G
U
U
C
C
C
U
U
10
G
A
G
A
U
C
C
C
5’
70
U
G
U
U
U
G
G
80
A
A
C
U
C
C
G
G
G
G
U
C
U
U
G
G
G
C
A
A
G
A
90
U
G
A
C
U
3’
dG = -42.50 [Initially -44.30] 11Sep02-04-26-08
C
C
C
U
U
G U
G A
A
C U
U
A U
U
60
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:27:28 2011
60
A A
G
G
A A
G
A
G
U
A
C
G
G
A
U
G
Pto-M19
A
G
A
A
A U
G C
G U
G A
A C
U G
G C
G C
G C
80
G C
A U
40
C
U
C
A
U
G
U
U
U
A U
G U
A U
G C
A U
G C
A U
A U
U A
A U
C G
G C
G
U A
A U
20
100
A U
A U
A U
A U
C G
A U
G C
G C
G C
A U
A C
C G
G C
G C
C A
C G
A U
G C
C
5’
U
3’
dG = -57.50 [Initially -57.50] 11Sep02-04-27-27
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:28:36 2011
3’
G
U
U
80
C
Pto-M20
C
A
C
5’
G
A
G
C
U
U
G
A
U
C
A
A
A
G
C G
10
U A
U G
70
G U
G C
G C
U A
G U
C G
G C
20
G U
G C
A
60
U
G C
C
C
A
U
G C
U
G U
C G
30
U A
U
C
50
U A
G U
G C
U G
C G
U
U
U
U
C
C
U C G
40
dG = -28.30 [Initially -28.30] 11Sep02-04-28-35
Output of sir_graph (©)
mfold_util 4.6
Created Sat Oct 22 10:39:22 2011
C
U C
U
U
G
G
G
U
U
A
A
U
U
C
40
G
C
A U
U
U
60
G
A
U
A
U
G
A
U
G
Pto-M21
U
A
U
C
U
G
U
C G U 80
A
G
C G
C
G C
U
C G
A
A
C
U
G C
A U
U A
A U
G C
G C
G A
A U
G C
20
G C
A U
C G
U A
C G
G U
A U
A U
100
U U
U A
G C
U U
C G
U G
A U
A U
G C
A U
A U
5’
G C
3’
dG = -49.24 [Initially -51.10] 11Oct22-10-39-21
Output of sir_graph (©)
mfold_util 4.6
Created Sat Oct 22 10:43:18 2011
G
A
U G
G
A
A
50
A
C G
Pto-M22a
A U
C
A
40
A
U A
U A
U A
A U
G C
60
C
G
A
A
C
A U
30
G C
A
A U
G C
C A
C G
U A
A U
70
A U
C G
U A
20
U G
G C
G C
A G
G C
U G
G C
80
G C
U A
U A
10
G U
U A
A U
G C
C A
G C
A U
90
A U
A U
5’
G U
3’
dG = -37.20 [Initially -36.70] 11Oct22-10-43-17
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:33:54 2011
A G
A
A
U
G
A
60
U A
G U
Pto-M22b
C
A U
C G
A U
U A
U A
U A
A
U
A
A
G
G C
80
C G
A
A U
G C
A U
A
G C
C A
C G
40
U A
A U
A U
C G
U A
U G
G C
G C
A G
G C
U G
G C
100
G C
U A
U A
G U
U A
A U
G C
C A
20
G C
A U
A U
A U
G C
C A G
A U
G
G
A U
A U
A U U
A U
C G
120
G C
G U
A U
G U
3’
G
A
A
G
U C
5’
dG = -48.50 [Initially -48.50] 11Sep02-04-33-52
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:34:40 2011
A
G A C
C
A
60
A
A
Pto-M23
A
G
U
A
A
G U
G C
A
U
C G
G C
G C
A
A
G C
G C
40
G C
U
U
G
A
C
A
U
C
U
U
U
G U
G C
A
80
U
G C
A
U
G C
A
U
A
U
U A
A
U
C G
G
G C
U G
20
A
U
A
U
A
U
A
U
A
U
C G
A
U
G C
A
U
100
G C
G U
A
C
C G
G C
G C
C G
U G
A
U
G C
G
5’
A
3’
dG = -61.60 [Initially -61.60] 11Sep02-04-34-39
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:35:37 2011
G C A
A
A
C
U
G U
U A
40
50
C G
Pto-M24a
U A
U A
U
A
U A
G U
U A
A U
C G
30
U A
U A
60
C A
A U
C G
G C
G C
U A
A U
C G
20
U A
U A
70
G C
U A
A
G C
C G
U A
A U
G C
G U
10
U C
80
A U
A U
A U
U A
A U
U G
C G
G
5’
G
3’
dG = -41.70 [Initially -41.70] 11Sep02-04-35-36
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:36:32 2011
U U C
A
A
A
A
50
C G
Pto-M24b
G U
G U
U A
G C
40
U A
C G
U G
U G
C
U
G
60
U
A
G
U A
A U
C G
30
U A
U A
C A
A U
70
C G
G C
G C
U A
A U
C G
20
U A
U A
G C
80
U A
A
G C
C G
U A
A U
G C
G U
10
U C
A U
A U
90
A U
C A
A U
U G
C G
G
5’
G
3’
dG = -42.90 [Initially -42.90] 11Sep02-04-36-31
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:37:16 2011
C G U
A
A
A U
60
A U
A U
Pto-M25
A U
A U
A U
U G
U G
U A
A U
U
A
U
U
A U
A U
A U
80
C G
G U
U
U
A
G
U
U
U
A U
40
A U
A U
A U
A U
U G
C U
G U
U A
A U
A U
A U
A U
G U
U G
100
C G
G
U A
A U
A U
C
A U
20
G U
A U
G C
U G
U A
U A
U A
C
U
U
A
U
A U
A U
A U
U A
U
U
U
C
A
5’
A
120
3’
dG = -20.80 [Initially -20.80] 11Sep02-04-37-15
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:38:09 2011
50
U
G A A
Pto-M26
A
A
A
G
A
C
A
G U A
U
U
A
U
C
U
A
G
A
C
40
60
C
U U
U
U
U
A
C
A
C
G
U
G
C
U
30
70
A
G
U
C
G
A
A
C
A
U
G
U
U
C
G
A
U
C
U
A
20
80
U
G
G
G
G
U
G
C
G
U
G
C
A
C
A
U
C
U
C
A
10
90
U
G
C
G
U
A
G
U
U
G
C
C
U
C
C
A
C
U
G
5’
dG = -42.40 [Initially -42.40] 11Sep02-04-38-08
G
3’
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:39:02 2011
U A
U
U
G
C
G A
U U
C
U
U
60
U
C A
U
A
40
Pto-M27a
U
G
G
G
G
A
U
A
C
50
A
U
G
A
A
G
C
A
C
70
C
A
A A
U
G
G
A
G
C
30
A
U
A
U
G
U
80
A
C
U
U
G
A
C
G U
A
G
C
G
20 G
G C
G
U
C
G
A
C
U
90
C
U
A
G
U
U
U
G
A
G
10
A
C
U
A
G
A
U
C
C
A
G
G
A
G
U
5’
dG = -25.60 [Initially -25.60] 11Sep02-04-39-00
3’
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:39:56 2011
A A
U
U
U A
C G
G U
Pto-M27b
60
G U
G
G U
G
A
C
U
A
G
C
40
U
U
A
U
C
U
G
A
U
C
A
G
A
A
A
C
A G C
A U
C G
U G
U A
U A
C G
U A
A U
80
C G
G
U A
C G
20
G
G
C G
C G
A U
U G
U C
G C
U A
G U
G U
G A
A A
A U
C G
A U
G C
U A
5’
U G
100
A
3’
dG = -23.39 [Initially -27.60] 11Sep02-04-39-55
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:40:58 2011
80
C
U
A
G C
A U
G C
Pto-M28
U A
G C
A
U
C
C
A
G C
G C
A U
A U
A U
C G
U A
G
G C
U A
U G
G U
60
100
U A
U A
C G
A U
C G
A U
C G
U A
G C
G A
G C
U A
G C
A U
G C
U G
A G
C G
A U
G A
40
120
U A
G C
A C
U G
A U
A U
U G
C A
A U
C G
U A
G C
G C
A U
A U
G U
A U
A U
A U
A A
20
140
C G
A U
C G
A U
G U
U G
A U
A U
C G
U G
U G
A U
G U
G U
U G
A U
A
G
U
A
G
5’
U
3’
dG = -77.00 [Initially -77.00] 11Sep02-04-40-57
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:41:49 2011
C
A
40
A
G
U
C G
Pto-M29
G C
U A
C G
A
U
G C
50
G C
U A
G C
U A
30
C G
A
U
U A
U A
U A
U A
60
G C
U A
G C
A
20
U
C G
U A
A
U
G C
A
C
C G
A
U
A
U
A
U
10
A
U
C
G U
70
U
A
G
U
U
A
U
U
U
A
U
C
5’
A
U
3’
80
U
dG = -48.70 [Initially -48.70] 11Sep02-04-41-48
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:42:35 2011
A
G
5’
A
U
C
Pto-M30
U
A
A
3’
G
U
U
C
10
A
U
C
G
A
A
G
G C
G
C
A
U
90
U
A
G
C
U
C
C
G
20
U
A
A
U
C
G
C
G
A
U
U
A
80
G
G
C
G
C
G
C
G
30
C
G
U
A
U
A
G
C
A
U
A
U
70
U
A
G
C
C
G
C
G
40
A
U
U
A
U
A
C
G
U
60
A
U
C
U
A
C
G
dG = -60.00 [Initially -60.00] 11Sep02-04-42-33
G
G
A
U
C
U A
G
50
U
U
U
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:43:28 2011
A C
U
G
A
G
U A
C G
Pto-M31
A
C G
C G
G C
U A
60
80
U G
U G
A A
G C
G C
G C
U U
U C
U A
A U
A U
C
G
A
C
C
U G
C G
C G
U
U
U
U
U
G C
100
U A
40
C G
C G
G C
U
U A
C G
A U
G C
C
A U
G C
G C
A U
A U
C G
C G
G C
A U
U A
20
G
G
U
U
G
120
A U
U G
U A
G C
U
U A
C G
U G
G C
A U
G C
A U
A U
U C
A U
A U
A U
5’
G
A
U
A C
3’
dG = -63.00 [Initially -63.00] 11Sep02-04-43-27
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:45:33 2011
U C
U
U
G
G
A
U
C
A
C G
80
Pto-M32
U A
A U
A
A
A
A
C
A
C G
A U
A A
A U
C G
100
A U
C G
C G
U
C G
A A
G C A U U
A
U A
G
60
U G
A
U A G
U
U A
U A
120
U A
G C
U
U
U
U A
U A
G U
U A
U A
U G
G C
C U
G U
U A
U G
U G
U A
40
C G
U G
A U
C G
U
U
140
G C
U A
C G
C G
A U
C G
G C
U A
U A
U G
A U
C G
G C
U A
20
C
C
C G
U G
A U
U G
160
U A
U A
U
G
3’
G
U
U
A
G
5’
U
U
G
A
U
A A C
C
dG = -56.20 [Initially -56.20] 11Sep02-04-45-29
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:46:46 2011
3’
U
U
U
G
Pto-M33
A
100
G
C
U
A
C
U
U
C
G
A
U
C
G
A
U
C
A
A
U
A
U
C
G
G
C
A
U
G
C
G
C
A
C
A
U
G
U
U
U
C
U
G
G
C
U
A
A
U
A
U
A
C
C
C
A
U
U
C
A
G
C
A
G
80
20
A
A
40
A
C
A
U
U
U
C
A
G
C
A
C
U
A
G
U
C
A
C
U
A
A
60
A
A
A
C A
A
dG = -32.10 [Initially -32.10] 11Sep02-04-46-45
U
U
A
G
C
A
G
A
C
A
A
5’
Output of sir_graph (©)
mfold_util 4.6
A
A
Created Fri Sep 2 04:47:33 2011
U U
U
A
G
40
Pto-M34
U
A
50
G
U
C
U
G
U
C
A
A
A
U
C
U
A
G
A
U
U
U
60
U
A
G
A
30
C
C
A
G
A
U
G
U
U
C
U
A
C
A
U
G
70
A
A
U
U
20
G
A
A
C
C
U
C
G
A
G
U
U
U
A
A
A
80
G
U
U
C
10
U
A
G
A
U
C
C
A
3’
U
G
C
A
G
G
5’
dG = -62.60 [Initially -62.60] 11Sep02-04-47-32
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:49:16 2011
80
A
A U
U
A
C
U
A
A
U
G
A
C
A
A U
U
U
G
Pto-M35
60
U
U
C
C
U
C
A
U
U
U
A
G
U
A
A
100
U
U
G
A
C
U
U A U U
G
C
U
G
120
C
U
C
U
G
C
U
C
U
U
C
U
U
U
A
C
U
U
A
U
A
U
C
C
C
U
A
C
U A A
G
U
U
A
A
G C
C A
A U
C G
A U
140
G U
C U
G C
A U
G
A
40
A
A U
A U
G C
G C
A C
U A
G C
G A
C A
G U
G C
A U
A U
A U
160
C G
A U
G C
A U
A C
A U
A U
20
G C
A U
C G
A U
U
G C
G C
G U
C G
U A
C
U A
G C
U G
C G
180
A U
G A
U A
G C
5’
G C
G
3’
dG = -55.72 [Initially -59.40] 11Sep02-04-49-14
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:50:24 2011
G
G
U A U G
A U A C
C G
30
Pto-M36
G
U
U
C
U
G C
G U
C G
C G
50
A
A
A U
C G
C G
U G
C G
G U
20
U U
A G
60
G C
G C
U
C
A U
C G
C G
10
A U
C
C G
C
A
U
U
U
U
G
A
C
U
70
C
C
C
A
C
5’
3’
dG = -23.80 [Initially -23.80] 11Sep02-04-50-23
40
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:51:17 2011
U C
A
U
A
A
G C
Pto-M37
50
G C
U A
U A
40
G U
A U
G U
C G
U A
A U
A U
60
A U
A U
C G
30
U A
A U
A U
G C
A U
A U
A U
70
A U
U A
A U
20
C G
G C
G C
U
G C
U A
A U
U A
80
U A
10
U
U
C
U
A
A
U A
U A
A U
G C
U A
U A
U
5’
90
C
3’
dG = -47.60 [Initially -47.60] 11Sep02-04-51-16
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:52:08 2011
G
A U U
G
A
A
G
A
Pto-M38a
A
A
A
A
G
G
A
C
A
A
A
80
G
C G
C G
60
A U
G
A
G
C
A
U
U
A
C
A
G C
A U
G G
U G
G
G C
U A
A U
C G
U G
U A
100
G U
G C
40
C
A U
A U
C G
U A
U A
C
G
U
U
C G
A U
U A
U A
C G
U A
A
U A
A U
A U
C G
120
C G
U A
C G
20
C G
U G
U A
U A
A G
A U
U A
U A
U A
G C
G C
U C
A U
U A
A U
U A
A
A
A
G
U
5’
140
U
3’
dG = -45.90 [Initially -45.90] 11Sep02-04-52-07
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:52:58 2011
G
A U U
G
A
A
G
A
Pto-M38b
A
A
A
A
G
G
A
C
A
A
A
80
G
C G
C G
60
A U
G
A
G
C
A
U
U
A
C
A
G C
A U
G G
U G
G
G C
U A
A U
C G
U G
U A
100
G U
G C
40
C
A U
A U
C G
U A
U A
C
G
U
U
C G
A U
U A
U A
C G
U A
A
U A
A U
A U
C G
120
C G
U A
C G
20
C G
U G
U A
U A
A G
A U
U A
U A
U A
G C
G C
U C
A U
U A
A U
U A
A
A
A
G
U
5’
140
U
3’
dG = -45.90 [Initially -45.90] 11Sep02-04-52-57
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:53:49 2011
50
A
U A U
C
C
C
G
C
A
C
C
G
U
A
U
A
Pto-M39
40
60
U
G
C
A
A
U
G
A
G
C
U
G
U
U
U A
C G
G C
30
U A
A U
C G
70
G C
A U
G C
U A
U A
C G
U A
20
A U
G C
U G
80
C G
A U
G C
U A
A U
G C
U G
10
U A
C G
G C
90
U A
A U
U G
U A
A U
C G
5’
G C
U
3’
dG = -62.40 [Initially -62.40] 11Sep02-04-53-48
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:55:48 2011
40
G
A A
U
U
A
Pto-M40
U
G
U
U AU
U
A
U A
U
A
G U
80
U
A
U
A
U A
A
U A
U
U A
A
G U
A
U
A U
U
A
G
C
U A
U
A
A
U A
U A
C
U
G
G
A
U A
C
U A
C
U A
C G
G C
U A
A U
G C
20
C G
U A
U A
A U
A U
U A
100
U A
A U
G G
U G
A U
A U
A U
A U
U U
G U
U A
U A
U
5’
U
3’
dG = -38.40 [Initially -38.40] 11Sep02-04-55-47
60
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 04:56:32 2011
80
G
A U G
U
G
G
U
G
U
C A
A
A
U
A
U
U U G
A
A
A
A
A
U
U
Pto-M41
A
U
C
U
G
100
G
G
U
G
G
U
A
U
U C U
G
C
U
A
U
U
G
G
G
G
A
U
G
U
120
A
C
C
U
A
G
U
G
A
A
G
U G
60
G U
U G
U A
G U
U A
A A
A A
U G
U A
G C
G C
U
A
140
U
A
A
U
U
A
U
A U
A U
G U
A U
40
A U
C G
A U
U A
U A
C G
U U
A U
A U
A U
A U
C G
160
C G
A U
C G
A U
G C
G C
U A
A U
20
C G
A U
G C
U A
A U
G C
U A
A U
A U
A U
180
A
A
A
U
U
U
U
G
U
G
A
U
U
U
U
5’
U
U
A
3’
dG = -64.50 [Initially -64.00] 11Sep02-04-56-30
Output of sir_graph (©)
mfold_util 4.6
A
A
5’
Created Fri Sep 2 04:58:04 2011
U
C
C
Pto-M42
U
G
A
3’
C
C
10
C
G
U
U
G
A
G
C
80
C
U
U
G
C
A
C
G
G
A
C
U
G
A
C
20
G G
A
U
U
70
G
A
C
C
C
G
A
G
A
U
C
U
30
U
G
A
A
A
U
G
A
60
A
C
A
U
A
U
C
U
U
U
U
C G
A U
40
G C
U G
U A
50
C G
U
U
G G
dG = -43.10 [Initially -43.20] 11Sep02-04-58-03
Output of sir_graph (©)
mfold_util 4.6
U
Created Fri Sep 2 04:58:47 2011
C A U
G
A
A
A
A
40
U
Pto-M43
50
A
U
U
U
A
U
U
U
A
U
A
C
G
C
G
U
A
60
U
A
C
G
30
U
A
U
A
G
C
C
G
A
G
U
A
A
U
C
G
U
A
G G
20
70
C
U
A
C
G
C
G
C
G
A
U
U
C
U
A
A
80
C
G
C
G
A
U
C
G
5’
U
A
G
3’
dG = -40.40 [Initially -40.40] 11Sep02-04-58-46
C
A
A
G
U
A
A
A
U
A
G
10
G
A
90
A
C
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:00:03 2011
U C
A
G
U
G
C
C
C
Pto-M44
C
G
G
80
U
U
A
G
U
G
U
C
U
G
G
U
U
G
A
U
C
100
U
G
C
G
G
U
G
G
A
G
C
C
G
G
U
A
A
C U
U
C
C
U
U
G
G
G
G
A
U
A
60
A
G
A
A
U
U
G
U
A
G
G
A
C
C
U
A
A
40
G C
U G
120
G G
U A
C G
C G
G U
G U
U
A U
A
G
G C
U G
C G
G G
A U
C G
G U
G
U A
G C
G
G U
140
C G
20
C G
A
U
C G
A C
U A
G C
G C
C G
A
A
G
A
A
G
U A
C G
G C
U
C
U
A
G
A
G
5’
G
3’
dG = -58.20 [Initially -60.80] 11Sep02-05-00-02
A
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:01:08 2011
3’
100
U
A
A
U G U
G
A
U
C
U
U
A
A
U
A
U
C
G
A
U
G
C
A
U
G
C
U
A
C
A
A
G
G
C
U
A
U
A
U
C
G
G
C
U
A
U
A
A
U
A
U
C
G
U
A
A
U
G
C
C
U
U
20
C
A
A
U
U
G
U
U
A
80
40
A
G
A
U
C
U
60
A
G
A
U
U
U
C
A
A
G
A
A
A
U
U G
dG = -44.20 [Initially -44.20] 11Sep02-05-01-07
C
U
A
A
C
Pto-M45
U
U G
G
5’
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:01:50 2011
G C
C
A
U A
U A
Pto-M46
G C
A
U
C
A
G C
U A
G U
100
120
G C
A U
A U
A U
C G
A G
C A
G C
C G
C G
G C
A U
G U
C G
A U
C A
A U
U G
C A
G C
80
140
G C
G C
U A
G C
A U
G U
G C
C G
A
U
C
C
A
A
U A
A U
A C
C G
A U
A U
U A
C A
A U
60
160
C G
U A
G C
G C
A U
A U
A U
G C
A U
A U
C G
C G
A U
C G
A U
A U
C G
G U
A U
C A
40
180
C G
U A
G C
A U
G C
A U
A U
A A
A U
A U
U G
A U
G C
U A
U A
C G
U A
A U
G C
A U
20
200
A U
A U
A C
A C
C G
U A
A U
C G
C A
A U
U A
A U
A U
C G
A U
A U
A U
G U
5’
A U
G
3’
dG = -120.70 [Initially -120.70] 11Sep02-05-01-49
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:02:30 2011
U U
C
U
U
U
U
C
A U
A U
Pto-M47
A U
A U
A U
U
U
C
A
U
U
U
A
U
U
A U U
G U
200
U A
160
A
A
U U U U
G U
U A
G U
U
U
U
UU
A
U A
U
U
U
A U
U
U
U
A
U U
U A
CU A
U U A
U A
A U
G G
U G
U A
C G
A U
G
C G
U A
A
A
C
A U
A U
U
A
C G
A A
U A
A U
120
U
A
A U
G C
A U
G C
U A
A U
C G
A U
G
A
C
A
A
U
C
C
240
C G
G C
U A
G
A
U
U
A
A
G
A
A
A
U
A
A U
U A
C G
C U
A U
A U
A U
C
G
A
U A
A U
C G
U A
U G
U A
U A
A U
U A
A U
80
A U
A U
U G
A
G
U
G
A
A
U
C
A
U
U
A
U
C
A
G
U A
280
A U
U A
C G
U A
A U
U
A
C G
C G
U A
C G
U A
U A
A U
U A
U G
G C
G U
A U
U
U A
G U
U A
U U
C
A
U A
G C
U G
40
U
C G
C G
U A
G A
U A
U A
U A
A U
A U
C U
C G
320
C G
U A
C A
G U
U A
U A
G U
A U
U A
C G
U A
G C
A U
A U
C G
A U
U A
A
G
A
C
C
C
U A
A U
U A
C U
U A
A
U
A U
C G
C
5’
C
3’
dG = -102.60 [Initially -102.60] 11Sep02-05-02-28
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:03:17 2011
Pto-M48
A
C
G
A
C
U
G
U
U
A
G
C
U
A
U
G
A
G
C
U
5’
C
G
A
C
A
C
A
U
G
G
A
G
C
C
A
U
U
50
G
G
10
U
G
G
U
A
A
20
60
G
G
G
U
U
3’
dG = -24.40 [Initially -24.40] 11Sep02-05-03-16
U U G
U
30
C
G
U
U
C
A
U
A
U
G
C
A
40
U
U G
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:04:24 2011
U
G
U
G
U
A
U
C
G
Pto-M49
U
A
A
U
G C
G
A
U
A
G
U
U
40
C
G
A
U
U
U
C
U
U
U
C
60
G
U
U
U
A
C
G
G
A
G
A
80
C
G
G
U A G
U
A
A
G
A
C
C
G
U
C G
U A
U G
U A
U A
G U
U G
A
C G
100
U A
G C
A U
20
U A
U U
U A
A U
U A
U U
A U
G U
U
U
G
G
U
C G
G
G
A
U
U A
U G
A U
120
G U
U A
3’
G
5’
dG = -25.23 [Initially -27.40] 11Sep02-05-04-23
U
A
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:05:10 2011
A U
U
C
A
G
U
C
U
60
Pto-M50
U
C G
A U
U U
U A
U
U
U A
U A
A U
U A
A U
C G
G
A
G
A
A
80
A U
C G
A U
A U
40
C G
G C
U
G
G
U
A
U A
U A
C U
C G
G C
A U
U A
G C
A U
C G
100
G U
A U
C U
A C
A U
C G
20
C A
U G
U A
A U
U G
G C
A U
G C
U A
A U
A U
A U
C G
U A
C G
120
G C
U A
U A
5’
C G
U
3’
dG = -51.10 [Initially -51.10] 11Sep02-05-05-08
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:05:52 2011
C
Pto-M51
U U G
U
U
U
U
A
C
U
60
G
G
U
U U
40
C
C
U
G
U
U
C U
U
C
U
U
A
G
C
G
A
U
U
U
A
U
A
U
U
G U
U
U A
U A
C G
80
U A
U A
C G
U A
G C
U A
U A
U A
U A
U A
20
U A
U A
U A
A U
U A
U A
U A
U A
U A
C G
100
U A
C G
U A
C G
U A
C C
C G
C G
A
C G
5’
C G
A
3’
dG = -38.95 [Initially -41.70] 11Sep02-05-05-51
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:07:31 2011
40
U
Pto-M52
U U C
U
U
G
G
U
U
U
U
U
G
C
A
30
C
A U
A U
A U
50
G C
U C
A U
G C
G C
U A
A C
20
U A
A U
A U
60
G C
C G
C G
A U
G C
U A
U A
10
G U
U G
A U
70
A U
G C
U C
U A
C G
A U
5’
C G
A
3’
dG = -32.50 [Initially -32.50] 11Sep02-05-07-30
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:08:06 2011
U A
G
U
A
C
G
C
G
U
20
A
C
G
A
U
U
G
Pto-M53a
C
C
G
U
U
U
U
U
A
G
C
A
A
A
40
U
A
A
U
A
A
U
G
C
G
U
A
3’
C
G
G
C
U
A
5’
A
G
G
U
A
A
U
A
UA
UGU U
A
U
A
U
120
U
G
A
U
U
A
U
A
C
U
60
G
A
U
A
U
U
A
C
G
G
U
A
U
G
U
G
C
G
U
G
A
U
U
G
100
U
G
A
A
A
A
U
G
U
U
U
U
C
A U
U
A
U
A
C
A
G
G
C
80
A
G
A G
dG = -33.00 [Initially -32.80] 11Sep02-05-08-05
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:08:59 2011
140
A U A G A
A
A
A
G
U
A
A
A
U
A
A
A
A
A
A
A
U
Pto-M53b
A
A
A
A
G
U
A
A
G
C
A
A
A
A
A
120
U A
A U
G C
G
G G
A
G
160
A U
U A
U A
A U
A U
U G
G
G
U
G
G
A
100
U
U
C
C
U U
G
U
A
A
U
A
180
U A
G C
G C
G C
G U
A A
G U
U A
A U
A
G
U
G
U
A U
A U
A U
U
U G
A A
U A
G C
G U
200
G A
U A
G C
A U
80
A
A A
G
U
U C
G
A
A
A
G G C U U
C C G A A
A
U
60
G
A
G
U
U
CG
A
G U
A U
A U
A U
A U
G C
G C
A U
U A
40
A
A
A
A
U
U
A
A
A
G
220
G U A
A
A
A
C
C
G
U
C
U U A
U A
G C
U A
A U
A U
U A
U
A
G C
U G
20
U G
A U
G U
A U
240
G U
G C
G C
G C
U G
G
A
A
G
A
A
U
A
U
C
A
U
A
U
A
U
U
U
5’
C
U
3’
dG = -47.73 [Initially -51.34] 11Sep02-05-08-57
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:10:19 2011
G U
U
Pto-M54a
G
U A
G U
U A
U A
A U
40
C
A
U
G
A
C
C
U
A
C
C
A
30
U
C
A
C
C
A
G
C
A
A
20
A
G
A
A
C
A
G
A
C
U
10
U
G
U
A
G
U
A
C
U
G
5’
G
U
A
G
U
A
G
U
U
U
C
80
U
U
U
G
A
A
C
A
U
C
G
A
U
U
90
A
U
G
G
A
A
C
A
3’
dG = -51.60 [Initially -51.60] 11Sep02-05-10-18
70
U
G
G
A
U
G
G
C
60
C
50
Output of sir_graph (©)
mfold_util 4.6
Created Fri Sep 2 05:11:26 2011
G U
Pto-M54b
U
G
U A
G U
U A
U A
A U
40
C
A
U
G
A
C
C
U
A
C
C
A
30
U
C
A
C
C
A
G
C
A
A
20
A
G
A
A
C
A
G
A
C
U
10
U
G
U
A
G
U
A
C
U
G
5’
G
U
A
G
U
A
G
U
U
U
C
80
U
U
U
G
A
A
C
A
U
C
G
A
U
U
90
A
U
G
G
A
A
C
A
3’
dG = -51.60 [Initially -51.60] 11Sep02-05-11-25
70
U
G
G
A
U
G
G
C
60
C
50