| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 2 I | 4 3 2 | 5 3 I | 6 3 3 | 7 2 I | 8 2 4 | 9 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_48417.5_Instance_1 HL_48417.5,HL_6D12_002,C328_G334 | C | A | U | GUG | G | |||||||||
| HL_48417.5_Sequence_1 HL_48417.56D12_C328_G334 | C | A | U | G | UG | G | true | 80 | 0 | 0 | 1.93 | |||
| HL_48417.5_Instance_2 HL_48417.5,HL_5UD5_001,C13_G21 | C | A | U | GUA | G | |||||||||
| HL_48417.5_Sequence_2 HL_48417.55UD5_C13_G21 | C | A | U | G | UA | G | true | 77 | 0 | 0 | 2.19 | |||
| HL_48417.5_Instance_3 HL_48417.5,HL_6D12_001,C309_G315 | C | A | U | GUG | G | |||||||||
| HL_48417.5_Sequence_3 HL_48417.56D12_C309_G315 | C | A | U | G | UG | G | true | 80 | 0 | 0 | 1.93 | |||
| HL_48417.5_Instance_4 HL_48417.5,HL_7VTI_001,C15_G21 | C | G | A | UUU | G | |||||||||
| HL_48417.5_Sequence_4 HL_48417.57VTI_C15_G21 | C | G | A | U | UU | G | true | 67 | 0 | 0 | 3.09 | |||
| HL_48417.5_Instance_5 HL_48417.5,HL_2C4Q_001,G8_C13 | G | A | U | U | A | C | ||||||||
| HL_48417.5_Sequence_5 HL_48417.52C4Q_G8_C13 | G | A | U | UA | C | true | 89 | 0 | 0 | 1.08 | ||||
| HL_48417.5_Instance_6 HL_48417.5,HL_2IZN_001,G8_C13 | G | A | U | U | A | C | ||||||||
| HL_48417.5_Sequence_6 HL_48417.52IZN_G8_C13 | G | A | U | UA | C | true | 89 | 0 | 0 | 1.08 | ||||
| HL_48417.5_Instance_7 HL_48417.5,HL_5AMQ_001,U3_A9 | U | A | G | UGU | A | |||||||||
| HL_48417.5_Sequence_7 HL_48417.55AMQ_U3_A9 | U | A | G | UGU | A | true | 73 | 0 | 0 | 2.59 | ||||
| HL_48417.5_Instance_8 HL_48417.5,HL_5MSF_001,G7_C12 | G | A | U | C | A | C | ||||||||
| HL_48417.5_Sequence_8 HL_48417.55MSF_G7_C12 | G | A | U | C | A | C | true | 85 | 0 | 0 | 1.43 | |||
| HL_48417.5_Instance_9 HL_48417.5,HL_7MSF_001,C5_G10 | C | A | A | C | A | G | ||||||||
| HL_48417.5_Sequence_9 HL_48417.57MSF_C5_G10 | C | A | A | C | A | G | true | 78 | 0 | 0 | 2.09 | |||
| HL_48417.5_Instance_10 HL_48417.5,HL_4V9K_033,C13_G22 | C | A | G | UUGGUUA | G | |||||||||
| HL_48417.5_Sequence_10 HL_48417.54V9K_C13_G22 | C | A | G | UUGGUUA | G | true | 11 | 0 | 0 | 8.45 | ||||
| HL_48417.5_Instance_11 HL_48417.5,HL_1U1Y_001,G7_C12 | G | A | U | C | A | C | ||||||||
| HL_48417.5_Sequence_11 HL_48417.51U1Y_G7_C12 | G | A | U | C | A | C | true | 85 | 0 | 0 | 1.43 | |||
| HL_48417.5_Instance_12 HL_48417.5,HL_4LFB_004,C190B_G190G | C | C | U | UG | G | |||||||||
| HL_48417.5_Sequence_12 HL_48417.54LFB_C_190B_G_190G | C | C | U | UG | G | true | 79 | 0 | 0 | 2.04 | ||||
| HL_48417.5_Instance_13 HL_48417.5,HL_9BZC_001,G24_C30 | G | A | G | UUA | C | |||||||||
| HL_48417.5_Sequence_13 HL_48417.59BZC_G24_C30 | G | A | G | UUA | C | true | 71 | 0 | 0 | 2.76 | ||||
| HL_48417.5_Instance_14 HL_48417.5,HL_3SKI_003,A67_U72 | A | C | C | UA | U | |||||||||
| HL_48417.5_Sequence_14 HL_48417.53SKI_A67_U72 | A | C | C | UA | U | true | 69 | 0 | 0 | 2.94 | ||||
| HL_48417.5_Instance_15 HL_48417.5,HL_8CRE_202,C448_G454 | C | G | A | C | AC | G | ||||||||
| HL_48417.5_Sequence_15 HL_48417.58CRE_C448_G454 | C | G | A | C | AC | G | true | 32 | 0 | 0 | 6.48 | |||
| HL_48417.5_Instance_16 HL_48417.5,HL_3SKL_007,A66_U71 | A | C | C | UA | U | |||||||||
| HL_48417.5_Sequence_16 HL_48417.53SKL_A66_U71 | A | C | C | UA | U | true | 69 | 0 | 0 | 2.94 | ||||
| HL_48417.5_Instance_17 HL_48417.5,HL_6XH2_001,C30_G34 | C | U | G | G | G | |||||||||
| HL_48417.5_Sequence_17 HL_48417.56XH2_C30_G34 | C | U | G | G | G | true | 79 | 0 | 0 | 2.03 | ||||
| HL_48417.5_Instance_18 HL_48417.5,HL_6DTD_001,C16_G22 | C | U | UU | U | U | G | ||||||||
| HL_48417.5_Sequence_18 HL_48417.56DTD_C16_G22 | C | U | U | U | UU | G | true | 75 | 0 | 0 | 2.34 | |||
| HL_48417.5_Instance_19 HL_48417.5,HL_2Y9H_004,C11_G16 | C | G | C | GU | G | |||||||||
| HL_48417.5_Sequence_19 HL_48417.52Y9H_C11_G16 | C | G | C | GU | G | true | 79 | 0 | 0 | 2.00 | ||||
| HL_48417.5_Instance_20 HL_48417.5,HL_1H4S_002,U32_A38 | U | U | C | GGG | A | |||||||||
| HL_48417.5_Sequence_20 HL_48417.51H4S_U32_A38 | U | U | C | GGG | A | true | 51 | 0 | 0 | 4.68 | ||||
| HL_48417.5_Instance_21 HL_48417.5,HL_5E7K_218,C13_G22 | C | A | G | UUGGUA | G | |||||||||
| HL_48417.5_Sequence_21 HL_48417.55E7K_C13_G22 | C | A | G | UUGGUA | G | true | 19 | 0 | 0 | 7.68 | ||||
| HL_48417.5_Instance_22 HL_48417.5,HL_5E08_001,C6_G11 | C | A | U | A | G | G | ||||||||
| HL_48417.5_Sequence_22 HL_48417.55E08_C6_G11 | C | A | U | AG | G | true | 87 | 0 | 0 | 1.23 | ||||
| HL_48417.5_Instance_23 HL_48417.5,HL_8CRE_220,C1344_G1349 | C | A | U | UU | G | |||||||||
| HL_48417.5_Sequence_23 HL_48417.58CRE_C_1344_G_1349 | C | A | U | UU | G | true | 100 | 0 | 0 | 0.00 | ||||
| HL_48417.5_Instance_24 HL_48417.5,HL_8P9A_207,C777_G783 | C | G | U | A | UU | G | ||||||||
| HL_48417.5_Sequence_24 HL_48417.58P9A_C777_G783 | C | G | U | AUU | G | true | 68 | 0 | 0 | 3.08 | ||||
| HL_48417.5_Instance_25 HL_48417.5,HL_8P9A_201,U450_A456 | U | A | A | U | UC | A | ||||||||
| HL_48417.5_Sequence_25 HL_48417.58P9A_U450_A456 | U | A | A | U | UC | A | true | 51 | 0 | 0 | 4.65 | |||
| HL_48417.5_Instance_26 HL_48417.5,HL_8UO6_007,A77_U83 | A | A | U | U | AU | U | ||||||||
| HL_48417.5_Sequence_26 HL_48417.58UO6_A77_U83 | A | A | U | U | AU | U | true | 79 | 0 | 0 | 1.97 |
1 2 s35 1 4 cWW 2 3 s35 2 4 s55JAR3D SCFG/MRF model for HL_48417.5:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [4] // Initial node BasepairNode | Deletion Probability [0.0000000001209991] | Pair Probability [[0.007680168,0.014837498,0.008697580,0.185395242,0.000000000],[0.015826807,0.007835289,0.284788526,0.010507956,0.000000000],[0.008735922,0.203585037,0.001682842,0.022249541,0.000000000],[0.186198875,0.010351038,0.023282983,0.008344694,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000589392,0.307147120,0.345899671,0.268866083,0.000548872,0.000099460,0.038384181,0.038384181,0.000077358,0.000003684] | Right Letter Distribution [0.217741935,0.040322581,0.282258065,0.459677419,0.000000000] | Left Index [1] | Right Index [4] // Basepair C328 - G334 cWW HairpinNode | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A329:U330 Interaction | Interacting Bases [1,1] | Pair Probability [[0.589285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.160714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A329 Interaction | Interacting Bases [2,2] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.303571429,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.196428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.375000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U330 Insertion | Location [1] | Length Distribution [0.576030918,0.384708997,0.039145763,0.000110633,0.000003688] | Letter Distribution [0.250000000,0.035714286,0.035714286,0.678571429,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1Sequences of instances from HL_48417.5:
> HL_48417.5 6D12 C 328 G 334 CAUGUGG > HL_48417.5 5UD5 C 13 G 21 CAUGUAG > HL_48417.5 6D12 C 309 G 315 CAUGUGG > HL_48417.5 7VTI C 15 G 21 CGAUUUG > HL_48417.5 2C4Q G 8 C 13 GAUUAC > HL_48417.5 2IZN G 8 C 13 GAUUAC > HL_48417.5 5AMQ U 3 A 9 UAGUGUA > HL_48417.5 5MSF G 7 C 12 GAUCAC > HL_48417.5 7MSF C 5 G 10 CAACAG > HL_48417.5 4V9K C 13 G 22 CAGUUGGUUAG > HL_48417.5 1U1Y G 7 C 12 GAUCAC > HL_48417.5 4LFB C 190B G 190G CCUUGG > HL_48417.5 9BZC G 24 C 30 GAGUUAC > HL_48417.5 3SKI A 67 U 72 ACCUAU > HL_48417.5 8CRE C 448 G 454 CGACACG > HL_48417.5 3SKL A 66 U 71 ACCUAU > HL_48417.5 6XH2 C 30 G 34 CUGGG > HL_48417.5 6DTD C 16 G 22 CUUUUUG > HL_48417.5 2Y9H C 11 G 16 CGCGUG > HL_48417.5 1H4S U 32 A 38 UUCGGGA > HL_48417.5 5E7K C 13 G 22 CAGUUGGUAG > HL_48417.5 5E08 C 6 G 11 CAUAGG > HL_48417.5 8CRE C 1344 G 1349 CAUUUG > HL_48417.5 8P9A C 777 G 783 CGUAUUG > HL_48417.5 8P9A U 450 A 456 UAAUUCA > HL_48417.5 8UO6 A 77 U 83 AAUUAUU