| 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 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 3 I | 12 3 6 | 13 3 I | 14 3 7 | 15 3 I | 16 3 8 | 17 3 I | 18 3 9 | 19 3 I | 20 3 10 | 21 2 I | 22 2 11 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_35978.6_Instance_1 HL_35978.6_HL_4C4W_002_C11_G22 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_35978.6_Sequence_1 HL_35978.6_HL_4C4W_002_C11_G22 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_35978.6_Instance_2 HL_35978.6_HL_5FJ4_002_C11_G22 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_35978.6_Sequence_2 HL_35978.6_HL_5FJ4_002_C11_G22 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_35978.6_Instance_3 HL_35978.6_HL_1U6B_003_C1002_G1013 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_35978.6_Sequence_3 HL_35978.6_HL_1U6B_003_C_1002_G_1013 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_35978.6_Instance_4 HL_35978.6_HL_5DDP_002_C34_G45 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_35978.6_Sequence_4 HL_35978.6_HL_5DDP_002_C34_G45 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_35978.6_Instance_5 HL_35978.6_HL_3HHN_008_C1004_G1015 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_35978.6_Sequence_5 HL_35978.6_HL_3HHN_008_C_1004_G_1015 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_35978.6_Instance_6 HL_35978.6_HL_3CUL_002_C29_G40 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_35978.6_Sequence_6 HL_35978.6_HL_3CUL_002_C29_G40 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_35978.6_Instance_7 HL_35978.6_HL_6F4H_001_C6_G17 | C | A | U | U | G | C | A | C | C | U | C | G | ||||||||||||||||
| HL_35978.6_Sequence_7 HL_35978.6_HL_6F4H_001_C6_G17 | C | A | U | U | G | C | A | C | C | U | C | G | true | 82 | 0 | 0 | 3.98 | |||||||||||
| HL_35978.6_Instance_8 HL_35978.6_HL_3G9C_005_C17A_G17L | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_35978.6_Sequence_8 HL_35978.6_HL_3G9C_005_C17A_G17L | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_35978.6_Instance_9 HL_35978.6_HL_4PKD_001_C64_G75 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_35978.6_Sequence_9 HL_35978.6_HL_4PKD_001_C64_G75 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_35978.6_Instance_10 HL_35978.6_HL_5DDO_002_C34_G45 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_35978.6_Sequence_10 HL_35978.6_HL_5DDO_002_C34_G45 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_35978.6_Instance_11 HL_35978.6_HL_6F4G_001_U8_G20 | U | A | U | U | G | C | A | G | U | A | C | C | G | |||||||||||||||
| HL_35978.6_Sequence_11 HL_35978.6_HL_6F4G_001_U8_G20 | U | A | U | U | G | C | A | G | U | A | C | C | G | true | 64 | 0 | 0 | 8.05 | ||||||||||
| HL_35978.6_Instance_12 HL_35978.6_HL_3IWN_002_C57_G68 | C | A | U | U | G | C | A | C | U | C | C | G | ||||||||||||||||
| HL_35978.6_Sequence_12 HL_35978.6_HL_3IWN_002_C57_G68 | C | A | U | U | G | C | A | C | U | C | C | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 11 cWW 2 3 s35 2 11 s55 4 5 s55 6 7 s35 8 9 s35 9 10 s35JAR3D SCFG/MRF model for HL_35978.6:
Character Definition | A,C,G,U,* // Define characters here InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Initial node C11 - G22 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008814842,0.015337879,0.010236108,0.168782487,0.000000000],[0.039887656,0.010229656,0.275885847,0.012729598,0.000000000],[0.010362616,0.172347010,0.001995485,0.020703592,0.000000000],[0.174646453,0.012206329,0.056369083,0.009465356,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair C11 - G22 cWW HairpinNode | Num Bases [9] | Left Index [2] | Right Index [10] | Norm Constant [0.999999999999999] // Hairpin node A12:C21 Interaction | Interacting Bases [1,1] | Pair Probability [[0.892857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.035714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A12 Interaction | Interacting Bases [2,2] | Pair Probability [[0.035714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.035714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.892857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U13 Interaction | Interacting Bases [3,3] | Pair Probability [[0.035714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.035714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.892857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U14 Interaction | Interacting Bases [4,4] | Pair Probability [[0.035714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.035714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.892857143,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15 Interaction | Interacting Bases [5,5] | Pair Probability [[0.821428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.107142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A17 Interaction | Interacting Bases [6,6] | Pair Probability [[0.107142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.750000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.107142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C18 Interaction | Interacting Bases [7,7] | Pair Probability [[0.107142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.107142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U19 Interaction | Interacting Bases [8,8] | Pair Probability [[0.035714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.821428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.107142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C20 Interaction | Interacting Bases [9,9] | Pair Probability [[0.035714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.892857143,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C21 Insertion | Location [4] | Length Distribution [0.086444414,0.909560546,0.003805621,0.000189420] | Letter Distribution [0.038461538,0.884615385,0.038461538,0.038461538,0.000000000]// Insertion in Hairpin after nucleotide 5, position 4 Insertion | Location [6] | Length Distribution [0.829821046,0.169280730,0.000863677,0.000034547] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000]// Insertion in Hairpin after nucleotide 7, position 6Sequences of instances from HL_35978.6:
> HL_35978.6 HL_4C4W_002 C 11 G 22 CAUUGCACUCCG > HL_35978.6 HL_5FJ4_002 C 11 G 22 CAUUGCACUCCG > HL_35978.6 HL_1U6B_003 C 1002 G 1013 CAUUGCACUCCG > HL_35978.6 HL_5DDP_002 C 34 G 45 CAUUGCACUCCG > HL_35978.6 HL_3HHN_008 C 1004 G 1015 CAUUGCACUCCG > HL_35978.6 HL_3CUL_002 C 29 G 40 CAUUGCACUCCG > HL_35978.6 HL_6F4H_001 C 6 G 17 CAUUGCACCUCG > HL_35978.6 HL_3G9C_005 C 17A G 17L CAUUGCACUCCG > HL_35978.6 HL_4PKD_001 C 64 G 75 CAUUGCACUCCG > HL_35978.6 HL_5DDO_002 C 34 G 45 CAUUGCACUCCG > HL_35978.6 HL_6F4G_001 U 8 G 20 UAUUGCAGUACCG > HL_35978.6 HL_3IWN_002 C 57 G 68 CAUUGCACUCCG