Output of sir_graph (©) mfold_util 4.6 Created Thu Aug 20 22:16:19 2015 Supplementary Figure 3 Secondary structures of five lncRNAs containing precursors of novel miRNAs shown in red shaded letters in P. tomentosa U C C U U U U C U U U G C 60 C A C C U C C A A C C C A U U G 80 A U C U U C U A U U C C C A U C U U U U 100 A U G C U C A C C C G U U C G C A A C G C C U A C 120 C U U U U C C U G A U A A A A A G 40 A A G U A A A A A A A A A CU C U U U U U U U U U U G U A 3’ C A A G A G C G U U U U C G A A A G U U G C U A U G U C G G C A G G U A C C 240 A U C U U U 160 U U A C C A U C A U A U U U A G U U A U G 220 G C A U A U 180 A U U C A U G C A U C U U G C G C G C U U A G C A U U C C U G U U U U 140 U A 5’ C U G 20C U U A C U C C U A U U U U U U A U U C C U A C C U 200 dG = -34.52 [Initially -43.10] 15Aug20-22-16-16-9ae23ac21b TCONS_00008696 Output of sir_graph (©) mfold_util 4.6 Created Thu Aug 20 22:14:52 2015 G A G G C G 40 G A U U A U G G A A A A U G C U C G G A U 60 U G G U U C A A U G U U U G A C G C U G AU G U U G G U C A A U G A A 80 A U A G A A A A C G U G C C G 20 A A U A U C G U G C G 100 U A U U G A A A A A A A A A U C AA G G G A 5’ C G U G G 3’ U G G U TCONS_00069374 U A A G C G G U A C G 120 G G U G G C G U U A G C G C U A U U U A 180 U G C G A U G A U U U G A U C G U G A U C G C G 140 G U G G U G 160 G A U U A G G A U A G G C G A G G A A dG = -51.47 [Initially -56.10] 15Aug20-22-14-50-c059203c67 Output of sir_graph (©) mfold_util 4.6 Created Thu Aug 20 22:18:25 2015 200 U A A A C A A A C A U G C U G A G U U A U A A U U G C G C G A U G G U A U G A U A A U A U U A U A C U A U U G G C C G U G A U A C G C U G G 160 A G C G U G G U G C G U U G A U A C A A C A A G A A G G C A U 240 A A A A A G A A U C A U G U 120 A G G A A G C C A A U G A A G C G A G G G A A A A C CA A G A U A G A G A U G C G U A C A U G C U A A U A A U U U G A C A A G A A G TCONS_00013609 G U A A U A U U G U U A U U A C 80 U G 280 G A A A C U A A A U A C C G A A A G C A G A U A A G A G A A G G G U C G U G U G C C G A C A G U A G A A C C A A A A A G A U A C U C U U A G A U G G G U U A A A A C G U A A U A U A U 320 U C 5’ U G A G U A A A A G U G A G C G C G A C A C A U 40 U A C G A G U 3’ A U U A C G U A C C G A G C A G A C C G A U G C A U 400 G U U A G C C G A A G C C G A U A U A U C C C G A U A U C G U U U A C G G C G A C G U A U U 360 G C A U U A C G U U A A U U U dG = -90.56 [Initially -105.80] 15Aug20-22-18-20-a99f9abc72 G U U Output of sir_graph (©) mfold_util 4.7 Created Thu Feb 4 03:48:58 2016 C A A U U A C G A U A U C G A A U A U U A U A U G C U A U A A U A U C A U A U A C G 320 U U 360 U A U G C A U U A U A C G 280 G C U A U A U C A A C C G U A A U U U C G G C G U C C U U A U A U U A C U C G C U A U U C A U U G C U C G U A U C A G G G A A G C C A C U U G A G U U G U A A G A A A G C A U G U A C G U A U C C C A U U C A A U A G C C U A A U 240 A C A 400 A U C G G U A U C G C G U G C C A C A U C G CUUUA A U U A 480 C U U A U A G U U U C A C U U A C U UU A A U C C U A U A C U C U U C A U C U U A G A C U U A U A U A G A U C U G C A A G G G C G A C A 440 U C G U A U A U C A C U A A A A U U U A C U C U U C A G A G A A G A C G G U U G C U U C G G 520 U U A C 200 A U A G C C G G U U U A G U A U C G U A A U A U 160 C U A C G A G C AA C C G U C G C U G G G G U G A U C U C A U AG C U U U A U C C C C C U C U U U C C A A A G G U A G C G G C G C U C A A U A A A U C A U C U U G U A U A U G C U A A U C G C G 120 U A A U U C A C 560 U A U A G U C C C A U G U A A U A U C C G U A U C G U 600 A C U A G U G U A U A C G C U A U C G C A U A C G U U U U G U C A U G U G C U G A U G C U U U C U C G C G U C U U C U C C C A U A C U C U G G C U C G U G C U UU A U C U U A C A C C U U U U A U C U A U A G G 80 G G A A C U A U A A U C C G C G U U A G C U A U C U G U U G U A 40 U A G C U A U A C G A U A U A A 640 G U G C U U U U C G U A C C G C A U A U 5’ C G 3’ dG = -144.35 [Initially -167.40] 16Feb04-03-48-53 TCONS_00026533 Output of sir_graph (©) mfold_util 4.6 G Created Thu Aug 20 22:21:43 2015 A A A U 100 C G U G G G A U A U G U A A G U A C G A U A U A U A U C U G A 120 A 80 U C G A A C AG A G C G A U C G A A A G G G U G G U U C U A C TCONS_00039013 A 60 C G G A U A G A G C G G U A G G G G U C G U A U A A U U G 140 G A C U G C U C U C A U U G C G G U G A G A G U A C G G C A A C A 40 C G U U G A U C U A C G200 U A G G G AG C A U GGGA GU A U U A 220 C G G G C G U G U G G G G U U A U C U 3’ 20 A C G C C G 5’ U G G C U C G C G G C A G G G Note: Sequences shown in green shaded letters are predicted mature miRNAs. Only one mature miRNA is shown for each corresponding lncRNA. dG = -73.67 [Initially -80.10] 15Aug20-22-21-41-8b447b9494 160 U U C U A A G A 180 A G A G C C U C G G G U A A A
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