Figure S1 Mature and precursor sequences and the predicted stem-loop structures of novel miRNAs from P.beijingensis. The mature miRNAs are in green ,and the miRNA*s are in red. Output of sir_graph (©) mfold_util 4.6 Created Thu Jul 14 21:31:04 2011 G C A A A A A C A A 80 G A A A C C C U A C U U A A A A U G C 60 U A A U C G G A A A C C C U C U C 100 A C U A A G U A A U A C A U U A C G U A U A G U Pbe-SR1 A A G U 40 G C G C U A C G U A A U A U 120 G C G C U A G C U A G C U A A U U A G C A U C G A U 20 A U G C U A C G C G C G G C 140 C G U A U A G C A U G C A U G U G G A A A U U 5’ U 3’ dG = -69.90 Pbe-miR1 Output of sir_graph (©) mfold_util 4.6 Created Thu Sep 1 10:01:18 2011 U G G 3’ U G C A U A A G U A Pbe-SR2a A G G 100 G C A U A U G C G C A U U A U A U A U A A U G G C A U A U G C A A U A A A C U U G C U G C U A A U C C U U G A A U G C 80 20 40 GA U A A A G A U A U U A 60 U A A A A A A A A A A U A A dG = -42.00 Pbe-SR2a C U C A U U C G U U U G U C A 5’ Output of sir_graph (©) mfold_util 4.6 Created Thu Sep 1 09:56:32 2011 U G C U G A U A U U G U A A 60 U U U A U G C G C A U G 40 C A U G U G C A U G U A C A U G C G C U A A U A U A U Pbe-SR2b A U U A 80 C G C G U A 20 U A C G U C G C G U A U A A U C G U A U A G U U A U C G U C G A U C G 100 G U 5’ dG = -53.50 Pbe-SR2b G C 3’ Output of sir_graph (©) mfold_util 4.6 Created Thu Jul 14 23:41:40 2011 50 U G C G A C A U G C C G C G A U A U G C 40 C G 60 C G A U U C G U C G C G C A A U G C 30 Pbe-SR3 U A 70 U A U A A U G C A U A U A U G C U A 20 C G 80 U A U A U A A U A U U A U A U A U A 10 U G U A A G A C C G C 90 U C G A A A 5’ U A A 3’ dG = -50.00 pbe-miR3 Output of sir_graph (©) mfold_util 4.6 Created Thu Jul 14 23:43:28 2011 U U U G G C A U A C U G U G C 60 U A U A U A U U U U U U A 80 G U G A G C A U A C G A U A U A C C G C G C G A U A A C G 40 U G U A U A U A 100 G C Pbe-SR4 U A A U C G U A C G C G C G C G C G A U A U A G G C A U C G 20 A U G C U A U A 120 U G G C U A A U U A U A U A U A G G C G A A A U U U A 5’ C G U 3’ dG = -55.10 pbe-miR4 Output of sir_graph (©) mfold_util 4.6 Created Thu Jul 14 23:45:35 2011 120 U U U U A U U C C U A A U U A A U U A U A A G U G U A U A U A G C U U U U U A U A U 140 U 100 G U A U A U G A U U A U A U U U G A U U U U U U U U 80 U U A C G U U U U U A C G U A G U G U G G C 160 U G A U U G U A C A U G C U G U G U U C A C U A 180 A U U A 60 U U G G U G U G U U G G C U A G Pbe-SR5 A A U A A U C A U A A U U A A U A U G G A U 200 A U C G U A A A C 220 U A C G 40 U A G U A U C G G U G C U A A U C G U A C G U A A U C G C A C G 240 G C U A C G 20 C U A C G C G U A U A A U A U G C G C A U U A A G U C U C G U G C A U A U C 5’ dG = -73.80 pbe-miR5 C G A A C U U G C U A C G C G 260 3’ Output of sir_graph (©) mfold_util 4.6 Created Thu Jul 14 23:50:09 2011 A C U A G C A 60 A A C A G G G C A U Pbe-SR6 A U G C U G C U A U G C A U 40 U A C G G C A U A U U A U A U A 80 G C G A G C C G U A U A G C A U G C A G U A U G 20 G C U U C G U A U A C G U A U C U G 100 G U A G U A G C C G U A U C U U U A A C A C 5’ dG = -41.90 Pbe-miR6 3’ Output of sir_graph (©) mfold_util 4.6 Created Thu Jul 14 23:51:41 2011 C A U A G U A U U 60 C G C G G C U A U A A U U U A A U Pbe-SR7 G C U U 40 G C G C A U C U U C C G C G U A U A 80 U A G C U C G G C G C A U G C A U U A G C 20 G G A C U G A G U C C U G U A A A C 100 U G C A C G G C U A G C A G U U A A A C C 5’ U 3’ dG = -43.50 pbe-miR7 Output of sir_graph (©) mfold_util 4.6 Created Thu Jul 14 23:53:08 2011 G A G G U G C G U A 40 G U Pbe-SR8 50 A A A U C U A U A G A A C G U A U 30 60 G U U C G A U U G A G C U C A A A U C U 20 70 G U G U U C U A G A C C A A A U A 10 U A U A 80 C A A G G U A U 3’ G U U C A C 5’ dG = -34.40 pbe-miR8 Output of sir_graph (©) mfold_util 4.6 Created Thu Jul 14 23:54:22 2011 C G A U C G U A U A 40 G U 50 U A C G A U C G C G Pbe-SR9a U A C G U A U C 30 U A 60 A U C G U G U A U A C G A U C G G C 20 U A 70 C G U A U A C G U A U A C G U A U A 10 C G 80 C A U A C G U U U A U C G 5’ U C G 3’ dG = -51.60 Pbe-miR9a Output of sir_graph (©) mfold_util 4.6 C A Created Thu Jul 14 23:56:00 2011 G U G A C U U 40 50 A U Pbe-SR9b A G G U U C G A G C G A C U A C 60 A U A A 30 U U G A G C A C A U G U U C G A A G 20 70 C C G U A C A U G U A C A U G U A C G U 10 80 A U A U A U A U A C A A U C U G C C U 5’ dG = -48.10 Pbe-miR9b 3’ Output of sir_graph (©) mfold_util 4.6 C A Created Thu Jul 14 23:57:30 2011 G U G A C Pbe-SR9c C U 40 50 A U A A G U U A C A G C A C G U A C A G 30 60 C U U U G A G C A C A U G U U C G A A U 20 70 C C G U A C A U G U A C A U G U A C G U 10 80 A U A C A U G U A C A A U A U A C C U 5’ dG = -50.10 Pbe-mi9c 3’ Output of sir_graph (©) mfold_util 4.6 C Created Thu Jul 14 23:59:23 2011 U G U U A C C 60 A C U C Pbe-SR9d C U G G U U A C C G A A U C U 40 A G G U U C A A G C A C G U A C C U A G U U G A 80 G C A C A U G U U C G A C C A U 20 G U A C A U G U A C A U G U A C A U G U A C A U 100 A U A C A A U C U G C U U 5’ dG = -51.90 Pbe-mi9d 3’ Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:00:55 2011 U C C A A C A C U A 80 A U C G C A U U A U U U G U A U U A A U A U 100 A U A U C G U A U A G U U A U 60 U U U U U G A U U U U U G U A G U A U C G U U A 120 C G U G U A A U C G C U U A U A U A 40 C G A U Pbe-SR10 U G A U U A U A A U A U A C U A A U 140 C G U A U A U A C G A U U A A U C A C G 20 U A C G C G C G U A U A A A C G A U C G 160 U A U A U A A U A U G U U A C G 3’ U 5’ dG = -54.80 Pbe-miR10 Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:02:31 2011 G A A U C G A A U A U G C 60 G A U A A G C G C A C G 80 G C G C A U A U G G G A G C G U G U C G A A U 40 U G U A U G U A U G C Pbe-SR11 A U G C A U A U U A A U C G G C 100 G U A A U A U A U 20 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 120 C U G C U 5’ G 3’ dG = -54.80 Pbe-miR11 A Output of sir_graph (©) mfold_util 4.6 Created Mon Sep 5 10:26:30 2011 G A G C U A A U 80 C G G C G C U A C G A A U G C G A A A U U 60 A A G U A U C G U A U U G A U G C G U A G C U A A U 100 U G U U A U A U C G 40 U C A U U A U U G C A U A U C G C G U A Pbe-SR12 G U C G C A A U G C 120 U A A U C G A U A U U G 20 C G G C U A U A U C G C U A A U C G U U U G A U G A U U U G 140 A U C G C G 5’ A U 3’ dG = -53.60 11Sep05-10-26-29 Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:06:52 2011 U U A U A 30 A U A U G C 40 U A G C Pbe-SR13a A U G C A U G C G C U A G C 20 A U 50 C G A U A U G C U A G C A U A U U A 10 U A 60 C G A U C G C G U A G C U A C G 5’ A U G 3’ dG = -55.20 Pbe-miR13a Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:11:05 2011 U U A U A 30 Pbe-SR13b A U A U G C 40 U A G C A U G C A U G C G C U A G C 20 A U 50 C G A U A U G C U A G C A U A U U A 10 U A 60 C G A U C G C G U A G C U A C G 5’ A U G 3’ dG = -55.20 Pbe-miR13b Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:16:34 2011 C G A U C G U A 50 U A G C U A 40 C G A U C A Pbe-SR13c C G U A C G A A A U 60 G C 30 U A G C A U G C A U G C G C U A G U 70 A U 20 C G A U A U G C C G U A G C A U 80 A U U G 10 C G U A C U C U A U G A G U C A 3’ 5’ dG = -38.00 Pbe-miR13c Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:19:14 2011 U U A A A U 30 G U U A G C A U 40 G C Pbe-SR13d A U G C G U U A G C 20 A U C G A U A U 50 G C U A G C A U A U U A 10 U A C G A U C G 60 G C U A A C U A C G 5’ A U G 3’ dG = -44.50 Pbe-miR13d Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:21:31 2011 U U A U A 30 A U A U G C 40 U A G C A Pbe-SR13e U G C A U G C G C U A G C 20 A U 50 C G A U A U G C U A G C A U A U U A 10 U A 60 C G A U C G C G U A G C U A C G 5’ A U G 3’ dG = -55.20 Pbe-miR13e Output of sir_graph (©) mfold_util 4.6 Created Mon Sep 5 10:24:23 2011 C C U A A G U A U U U A A U A U C C G U U A U 60 U G C U A 40 G U A A A C A C G G C G C C G A U A C C G A U C G U G 80 C G U A Pbe-SR14 U A A U C G U A 20 U A C G C U A A U A U U A G U C G U A C G U A C C G U C G 100 A U C G G U U 5’ A 3’ dG = -42.80 11Sep05-10-24-21 Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:30:03 2011 A A A U C A U G C 60 A A G G U U G C G U A C A A C G A U 80 C G A U G C U A U U U A A U A A A U U A U A U A A U 40 A U C G C G C G U A C G 100 G C U U Pbe-SR15 A U C G U A U A U A A U U A A U C G G C U A C G A U 20 A U G C G C G C G C C G 120 C G A U U A C G C G A U C G U A A U C G C G U A 5’ C G C 3’ dG = -86.50 Pbe-miR15 Output of sir_graph (©) mfold_util 4.6 A U C C Created Mon Sep 5 10:21:00 2011 U U U C A U 20 C G A 100G U C C G U A C C G U A G A U G U A U A C U U A U C A G U A G G G U A U C 3’ A A G U A C U U A A G U C C A G 40 U U 80 G U U C A A G U U C U A U G G A C C U U U A G G U U G U G C U C A A U Pbe-SR16 5’ G G 60 dG = -43.50 11Sep05-10-20-59 A U Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:36:23 2011 A C U A A U U A U A A A A 60 U C A U A U A A A U G C A A A A A A U G C U A A A A A U A U A G C U A U A U U U A A U U A 40 U A U A U A Pbe-SR17 100 U G U A A U A U U G U A C G U A U A A U C G U A C G A C G U U A U G 20 G U G C U A 120 G C G C U A G C U A U A C G C A G U A U A G U A U A C G A U A 5’ C 3’ dG = -41.10 Pbe-miR17 80 Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:38:20 2011 A A A U A A 120 U A C G U A A U C C U U U C A A A C C A U A C U C G A U A U 100 A U C G U A A G 140 C A A U A U A U U A C C G A A U A U U A A C G C G C U G U A 80 C U U U G U G U A U A U 160 A U C G A C G U A C G U A C G U A U A U A A A G U A U A C C 60 A U C G A U A U C C 180 A U A U C U C U G C G U U U G C G C A U A U A U Pbe-SR18 A U C G U A 40 U A A C C A U G C 200 G C A U A U A U A G C A U C A U A A U C G G C G C G U A U U A 20 C G U A U A A U A U 220 A U A U U A U G G C A U U G G G U U A U A A U A A 5’ G U G 3’ dG = -68.70 Pbe-miR18 Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:39:45 2011 A A U A A U C A U U C U C G U U A U 80 A U A U A U U C 60 A U C G U C U A A U G A U A U A A U U U G A U A U A G C U A C G 40 100 U G AU U U U U C U G A U U U U A A U C G Pbe-SR19 G U U A A U A U U A C U A U G C A U 20 A U C G C G A U 120 A U U A A U U A U A A U U A A U U U C G U A U A U C U C A 5’ U 3’ dG = -33.40 Pbe-miR19 Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:41:47 2011 C U G U U G A A A C A G C A U U U A U A A 80 U U G C G U 60 C A U A G C A U G C G C G C U A C C U A U A U A C G U A 40 C C U G A U U 100 U A A U U U G C G G G C A U U A A U U A A C Pbe-SR20 G C G C G C U A G C U A A U U A 20 U A 120 A U A U U A C G U A C G G C A U G U C G C G U A C G G C A U G C G U 5’ A A 3’ dG = -67.50 Pbe-miR20 Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:43:01 2011 U A C G C G U C U 40 C G G U 50 U U U A U A C G A C G A U A C G 30 U A A U 60 G C C G Pbe-SR21 U A U A A U A U A U C G 20 C U C G 70 G C A U A U C G U A C G U 10 C A A C U C G A 80 A G C A U A U G C A U A 5’ A 3’ dG = -31.90 Pbe-miR21 Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:45:00 2011 U U A U U A 40 A U U U Pbe-SR22 50 A A A U U C C A G U A U A U A A U 30 C A U G 60 A C C C C G C G G U G A G C A U 20 G C A U 70 U A U A A A G C U A U G C A U G C A U U 10 G 80 A A C G G C C G A C C G U A A 5’ dG = -20.80 Pbe-miR22 G 3’ Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:46:16 2011 3’ A G C A Pbe-SR23 A G U G U U G A U A G C U A U C G U A C G G C U A A G C G A C U 60 U G A U U C A A C G U A U 20 U C 70 30 G U A U A U A A A U G U A 40 G U U 50 C G C A U U U G C G A G C 80 U G A U A U C U dG = -35.70 Pbe-miR23 10 G C U U U C 90 5’ Output of sir_graph (©) mfold_util 4.6 Created Mon Sep 5 10:02:47 2011 C A C A A A A A C U U U U A G A U A A 80 C C G A 100 G U A G U U C C A U C A A U G A A 120 U A G A A A A U A G U G C A U U A U C C C U U U A U C G G C A A A 60 U A U U U A U A U A A U A U A 140 U C G C A G C U A G C U A Pbe-SR24 C G C G C A U A C G 40 C G U A G C U A U A A A A U U A A U 160 U A U A U A A U A U A G C A C G C G A U A U C G 20 G C U A A U C G G C U A A U C G 180 U A U A G C A U A U C G U A U A U A A U 5’ U A 3’ dG = -72.30 11Sep05-10-02-46 Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:48:59 2011 60 U A U A C G A C A A C U U A A A C U C U U A U A C G G A U A U G U A U G U A G U 40 C G 80 U A Pbe-SR25 C A A U G C 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 G U G C 20 A U A U 100 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 U 5’ A U A U A U C 3’ dG = -45.90 Pbe-miR25 Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:50:03 2011 60 C A G G A Pbe-SR26 G C G C C C U G U A G C G C U A A U U U G U A G A G U C A C 80 G C C C C C U G C 40 G C U U U A C C C G G G G C C C G G G U G U U C U A G G U U C A C G 20 100 U G U A G A G C C C U G A A U C A G U U U A U A G G G C U U U G C A C G A C G 5’ dG = -56.30 Pbe-miR26 3’ Output of sir_graph (©) mfold_util 4.6 Created Fri Jul 15 00:51:11 2011 A G A G U A U A U C U Pbe-SR27 A C U U G U C A U U A C U U U A U C G C G G C U A U A G A U C A G U G C U G C A C G G C U A C G C G G C G C U A A U U A 5’ A A G G U G A G C C A 80 G C 20 G 100 A G A A C 3’ dG = -56.60 Pbe-miR27 C A A G C G 40 G C A U A G G U G 60 G
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