Output of sir_graph (©)
mfold_util 4.6
Created Sun Jul 19 21:04:09 2015
Supplementary Figure 2 Secondary structures of nine lncRNAs containing precursors of known miRNAs shown in red shaded letters in P. tomentosa
U C
C
A
C
C
G
G
C
U
C
U
A
U
A
A
U
A
C
U
U
U
U
G
A
U
U
U
C
G
U
UU
U
U
C
A U
U
C
C
A
C
G U
G
G
C
U
A
A
C
U
C A
G
U
A
C
A
C
C
U
G
C
C
U
G
C
C
G
G
U
160
G
C
C
G
G
U
G
C
C
G
G
C
U
C
A
A
U
G
C
U
U
A
C
G
C
U
A
U
G
A
U
A
U
C
G
C
A
120
A
A
G
A
A
A
A
A
G
U
A
C
A
A
A
A
A
80
A
A
A
U
A
A
A
U
U
G
G
U
A
U
G
C
A
U
A
G
A
U
U
U
U
C
U
C
A
G
A
U A
A U
C
A U
A U
A U
A U
A U G
U A
A
A
C
U
U
G
U
C
U
C U
U
C
C
C
C
U
C
G
G
C U A
C
U
U U
C
A
U
U
A
A
U
A
A
A
360
A
U
A
U
U
A
C
U
U
U
U
C
C
G
C
U
A
A
A
U
C
U
A
A
40
U
G
A
A
U A
U
G
A A
C
A
U
C
A
U
U
G
A
A
U
A
C G
G C
G C
G C
A
A
3’
5’
A
A
U
A
C
U
A
C
G
C
A
C
A
A C U
A
C
G C U
A
C
320
G
A
C
A
A
C
U
A
C
280
C
C
U G
G
200
G
A
G
C
A
C
A
C
U
G
G
U
C
A
A
G
C
U
C
U
A
G
A
A
G
C
C
U
G
U
A
A
A
G
U
C
U
C
A
U
G
C
A
U
G
G
A
G
C
C
C
G
G
C
C C
C
G
A
G
U
C U U
G
U
C
G
A
A
C
U
G
G
U
A
U
U
dG = -84.57 [Initially -101.90] 15Jul19-21-04-01-5ee19bec93
TCONS_00021861
A
240
Output of sir_graph (©)
mfold_util 4.6
Created Sun Jul 19 21:12:42 2015
A U
C
A
A U
U A
A U
U A
60
G C
U
U
U
A
U
C
A
U
A U
C G
G C
G U
80
A U
G U
A U
C G
A C
C G
A U
C G
G C
A U
40
G C
U A
G C
U
A U
G C
A U
G C
A
A U
A U
100
G C
A U
C G
A U
G C
U A
C G
A
A
G C
20
A
U
A U
U
A U
A
C
G C
TCONS_00031860
G C
U A
5’
C G
U A
U U C
U
C
U
U
U
U
U
C
U
U
G
A U
G
U
A
U
A
G
C
C
U
G
U
A
G
A
G
C
G
A
A
C
G
U
U
240
U
C
G
A
U
C
G
G
C
A
G
C
C
G
G
G
A A
G A
U
3’
U
120
G
A
U
A
U
A
U
A
U
A
U
A
U
G
C
C
G
G
260
140
U
C
C
A
A
U
G
A
G
A
A
U
A
U G
U
A
G
U
G
220
U
U
C
G
C
G
U
U
U
A
U
G
U
C
A
U
A
U
160
C
U
G
C
U
A
A
U
G
C
A
U
A
U
G
U
G
U
U
C
C
200
A
C
U C
G
G
U
G
C
A
U
A
C
U
A
180
U
A
A
U
A
C
A
A
A
C
A
C
A
A
dG = -90.70 [Initially -88.30] 15Jul19-21-12-35-f4ca336326
A C
C
Output of sir_graph (©)
mfold_util 4.6
A
Created Sun Jul 19 21:14:59 2015
A U U
A
U
U
A
U
C
U
G
G
160
C A
A
A
U
G
U
U
C
G
C
U
G
U
U
C
U
A
C
U
U
G
U
A
U
C
C
A
C
G
A
G
A
U
C
U
G
C
A
C
G
U
G
C
A
C
G
200
C
G
A
G
U
U
A
A
C
U
C
G
G
G
G
G
U
C
A
A
A
U
U
U
A
U
A
A A
A
C
G
C
G
A
G
G
C
C
G
G
U
C
C U G
120
U
U
G
G
U
G
U
C
C
G
A
A A
G
U
U
C
A
G
G
C
A
C
G
U
G
C
G
A
U
U
C
A
U
G
U
A
A
A
240
U
G
G
C
G
U
G
A
C
U
C
G
G
A
C
U
C
U
G
G A
C
U
C
A
G
C U
U G
G
A
A
A
A
A
G
C
A
U
U
A
U
A
A
U
U
A
A
80
A
U
U
G
U
C
A
A
G
U
U
A
U
C
U
A
280
G
G
C
G
U
U
U
U
U
G
U
U
A
G
A
G
G
C
C
TCONS_00035853
G
U
A
U
C
A U
G
C
C
A
G
A A A
G
A
G
U
U
A
G
C
A U
A
U U
U
G
C
G
320
C
A
U
A
U U
U
G U
U
U
C
U
U G
U C
G A
A U
A G
C U
U
G
G
U
U
G
C
U
A
U A
G
C
A
A
U
C
C
A
U
U
C
A U U
G
G C
C G
40
C
440
C
U
U
U
C
U
C
G
U
C
C G
U A
A
G
U
A
G
C
C
U
A
A
U
A
G
C
A
C
G
3’
5’
U
C
U
U
C
C
U
A
U
U
U
C
dG = -135.68 [Initially -142.30] 15Jul19-21-14-48-2f1a4db7ed
C
G
U
A
A
U
G
A U
U
U
U
U
A
U
A
400
U
U
A
G
C
A
U
A
U
A
A
U
U
G
A
C
U C
C
G U U
G
U
A U A C
G
U
C
A
C
U
C G
C
U
U
A
A U
C G
U
360
G
G
C G
C
U
A
C
C
U
C
U
A
G C
U G
U
U
U
A
A
C
C
C
U
U
A
U
A
A
A
A
U A
Output of sir_graph (©)
mfold_util 4.6
Created Sun Jul 19 21:20:05 2015
C A A
A
A
U
A
G G
A
C
C
A
A U
A U
A
U
C
G
C A
C
A
A
A
A
U
A
C
A
A
U
A G
A
A U
G C
80
G
A
A
120
A A A
U A
U G
A
A C
A
C
G
A
U
U
A
U
A
C
G
C
A
C
G
G
G
U
C
A
A
A A A
A
C
G
A
A U
C G
A
A
A
A
A
A
C
G
A
G
G
A
A
A
A
A
40
A
U A
G C
G C
U A
A U
G A
C
G
C G
G C
A
G
U
C C
C
G
A
U
A
U
A
U
A
A
A
C
A
A
G
A
C G
U A
G C
A U
A U
U G
G
A
G
160
A
G
A
U
G
C
G
5’
A
3’
C G
U A
C G
U A
A A
C G
C G
C U
A U
C G
U A
A
A
G
C G
C G
U G
A U
360
A U
U A
U
C G
C G
C G
U
U
U
A
U
C
A
C
TCONS_00052315
C G
U A
C G
G C
A U
G C
G C
C
A
200
U
U
C
A
C
U
A
U
A
C
A U
G C
G C
U A
U A
A
U
C
A
A
A
U G
C G
C G
A A
A U
G C
A U
A
A
C
A
U
U
A
A
C
G
A
320
C
C G
C G
A
U
C
C
A
U A
A U
A A
U A
U A
C G
G C
A U
C C
G C
240
A U
U G
U A
C G
G A
A U
U A
A U
C G C
A
A
G
C
U
A
G C
G C
U G
G C
U A
C A
A A
G C
G C
A U
280
U A
A U
G C
A C
U U
A U
G C
U
G
U G
dG = -85.45 [Initially -96.80] 15Jul19-21-19-59-7eadb41071
Output of sir_graph (©)
mfold_util 4.6
Created Sun Jul 19 21:23:32 2015
U A U A
A
C
A
G
C
C
U
A
A
U
C
A
U
A
U
U
C
G
U
U
U
U
U
G
C
U
C
A
C
G
C
C
G
U
U
200
C
A
G
U
A
G
G
A
A
C
C
G
A
U
A
G
U
U
A
G
A
U
A
C
U
A
G
G
A
G
G
U
A
G
U
U
C
C
G
C
A
A
U
C
U U U U
A
C
C
C
U
G U G
U U
G C
U U
A A
C G
A A
A
U U
U
C
U
U
C
C
U
C
80
C
U
A
C
A
G
G
U
U
G
U
U
C
U
U
G
G
C
280
A
C
A
U
U
U
U
U
C
U
U
C
U
G
C
U
C
C
U
C
A
G
C
C
TCONS_00055114
A
G
G
C
A
U
C
C
U
360
U
A
G
C
A
U
A
A
C
G
U
A
U
A
G C
C
A
U
U
C
C
U
U
C
G
G
G
U
A U
U
U
U
G
U C
G
G C
G
A
C
C
C
C
G
G C U
G U
A G
U G
C A
U C
A C
A
G 320
A
U
C A
G
G U
C
U
G
U
C
C
G
A
U
U
120
G
A
U
A
U
G
A
A
U
C
160
A
G
U
A
A
A
U
G
C
G
C
A
U
U C
A
C
C G
U A
A U
U
U A
C U
C G
C
U
U
U
C
U
A
C
C
C
U
G
C
U
C
U
A
U
C
U A
C U A
U A U
C
U
C
A
A
A
U
C
A
U
A
A
A
A
U
U
U C
A A
G U
G
C
C
A
C
40
G
G
U
U A
U
A
U A
A
A
C
C
A
G
U
U
3’
C
A
A
G
400
A
U
C
U
U A
A
A
5’
A U
U
U
A
A
C G
G
A
A
U
C G
G C
G C
C
U
C
U
U
U
U
A
C
U
G
U U U
240
U
U
C
G
U
A
U
G
A
A
A
dG = -111.48 [Initially -119.80] 15Jul19-21-23-25-7e998f9d8b
Output of sir_graph (©)
mfold_util 4.6
Created Sun Jul 19 21:25:36 2015
C U
A
G
G
A
U
U
A
G
A
G
A
U
A
G
C
U
A
120
A
U
A
G
C
100
C
C
G
G
G
C
G
U
A
G
C
U
G
C
C
G
G
G
A
A
G
A
U
U
C
C
G
A
U
U
A
A
U
140
G
A
C
G
U
A
80
C
G
A
U
G
C
C
C
A
U
G
C
C
G
U
A
C
A
G
A
U
A
A
U
C
U
A
A
U
G
G
60
A
U
U
A
C
160
C
C
C
A
G
C
A
A
A
G
U
G
C
A
U
TCONS_00061454
G
A
C
G
U
A
A
U
C
U
A
A
A
A
U
A
U
A
G
C
C
U
40
180
G
A
C
U
A
A
U
C
C
U
A
A
U
C
G
C
G
C
A
U
G
C
C
G
G
A C
C
U
A
U
C
C
200
A U
U A
C
A
U A
U U
G C
G C
A U
A U
20
C
A
C
A
C
U
A U
G C
A
U
C
A
A
A
A U
G C
U A
C G
G C
G U
220
A U
A U
G A
G
A
A
A
A
U
A
C
A
C
5’
G
A
3’
U
C
C
C G
C G
A U
A
A
U
A
G C
240
dG = -71.60 [Initially -71.60] 15Jul19-21-25-31-74d28e7b85
Output of sir_graph (©)
mfold_util 4.6
Created Sun Jul 19 21:27:16 2015
G
C U
U
C G
G C
U A
C
A
A
C
U
A
C
C
G
U A
U A
C G
A
U A
U A
G C
80
G
U
A
U A
A U
A U
A
A
120
A
C
U A
A U
U G
U
U
U
G
A
A G
G
G
A
A
C
A
U A AU
A
U
G A
A
A
U
A
G C
C
A
A
U
A
160
A
U
A
A C
G
A
G
A
G
C
C
A
C
A
A
G
U
A
A
A
U G
A U
A C
C C
A A
U U
G G
G A
A
3’
C
A
U
U
A
U
G
40
C
U A U A G
G U A U UUA
A
U
U
U U
U U U
360
C U U C
U G A G
U C A
A A A U
A
C A
C
A
A C U U
G A A U
C
U U U G
G U
G A C
C
A
U U A
C U G
C
U
A U
U
A
A
C
C
U
A
A
G
U
A
A
A
C
G
C
G
C
U
A
U
A
C
5’
A
U
A
C
C
G
G
A
A
C
G
G
C
A
C
G
C
G
C
A
U
G
C
G
320
U
A
U
G
C
G
C
A
U
G
C
G
C
G
200
G
G
U
C
C
G
G
U
A
G
G
C
G
C
C
TCONS_00061456
U
A
G
C
U
A
A
A
G
A
C
A
U
A
C
G
A
A
U
A
G
C
A
U
C
G
A
U
G
C
A
U
U
C
A
G
C
U
A
U
A
A
U
G
C
A
U
G
C
A
U
G
C
C
G
280
A
U
C
G
U
240
A
A
A
G
C
U
A
C
U
G
A
G
U
A
G
C
G
U
G
A
A
U
U
A
G
C
C
G
A
U
U
A
dG = -101.68 [Initially -112.90] 15Jul19-21-27-09-5659665d9e
G
A
G
C C U
Output of sir_graph (©)
mfold_util 4.6
Created Sun Jul 19 21:29:33 2015
G A G
G
U
160
U
U
A
A
C
G
U
A
A
A
G
U
A
G
U
A
G
A
C
A
C
140
G
A
G
A
G
A
U
A
G
A
A
G
A
U G
U
120
G
U
U
A
G
C
100
A
U
U
U
U
U U
A A
U G
U U
U U
U G
A U
U G
A C
U U
G C
A U
A G
G
60
U
A
U
U A U C UC
G
A
U
C
40
A
C
U
U
G
C
U U
U
C
200
U
G
U
C
U
C
U
U
G
A C
C
TCONS_00066551
220
C
U
C
U
A
U
U
G
C
U
A
240
A
U
C
C
U
C
U
G A
A
U
C
G
U
U
G
U
C
G
C
G
A
A
A
A
C
C G
U
G C
A U
A U
A
20
G C
G C
U A
U
U
A
U
C
A
C G
U G
U G
A U
A U
G C
5’
G
C
U
A
G
U
U
C
G
U
U
C
A
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U
A
U U 80
U
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G
U
180
U
C
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A
A
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C
C
C
U
C
C
G
A
G
U
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A
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A
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U
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U A
A
A
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A
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G
G
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C
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U
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3’
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A C
dG = -82.27 [Initially -89.00] 15Jul19-21-29-28-76ef61cf70
C
Output of sir_graph (©)
mfold_util 4.6
Created Sun Jul 19 21:33:38 2015
A
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A A A G
A
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200
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40
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320
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160
G A
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G G G C AAC
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5’
G G A A
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A A G U C U
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880
920
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3’
A
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360
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120
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240
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440
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480
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840
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TCONS_00069227
520
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760
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800
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640
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720
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680
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dG = -197.32 [Initially -231.30] 15Jul19-21-33-20-57b9282a05