| 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 5 2 | 5 5 I | 6 6 3 | 7 6 I | 8 6 4 | 9 6 I | 10 6 5 | 11 6 I | 12 6 6 | 13 6 I | 14 6 7 | 15 5 I | 16 5 8 | 17 4 I | 18 3 9 | 19 2 I | 20 2 10 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_67265.4_Instance_1 HL_67265.4_HL_4LFB_001_U12_G22 | U | U | U | G | A | U | C | C | U | G | G | |||||||||||||||
| HL_67265.4_Sequence_1 HL_67265.4_HL_4LFB_001_U12_G22 | U | U | U | G | A | U | C | C | U | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_67265.4_Instance_2 HL_67265.4_HL_5J7L_001_U12_G22 | U | U | U | G | A | U | C | A | U | G | G | |||||||||||||||
| HL_67265.4_Sequence_2 HL_67265.4_HL_5J7L_001_U12_G22 | U | U | U | G | A | U | C | A | U | G | G | true | 93 | 0 | 0 | 1.47 | ||||||||||
| HL_67265.4_Instance_3 HL_67265.4_HL_6CZR_072_U13_G23 | U | U | U | G | A | U | C | C | U | G | G | |||||||||||||||
| HL_67265.4_Sequence_3 HL_67265.4_HL_6CZR_072_U13_G23 | U | U | U | G | A | U | C | C | U | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_67265.4_Instance_4 HL_67265.4_HL_4V88_186_G7_C17 | G | U | U | G | A | U | C | C | U | G | C | |||||||||||||||
| HL_67265.4_Sequence_4 HL_67265.4_HL_4V88_186_G7_C17 | G | U | U | G | A | U | C | C | U | G | C | true | 100 | 0 | 0 | 0.04 | ||||||||||
| HL_67265.4_Instance_5 HL_67265.4_HL_4XWF_002_C50_G60 | C | G | C | C | C | G | C | C | U | G | G | |||||||||||||||
| HL_67265.4_Sequence_5 HL_67265.4_HL_4XWF_002_C50_G60 | C | G | C | C | C | G | C | C | U | G | G | true | 87 | 0 | 0 | 2.58 | ||||||||||
| HL_67265.4_Instance_6 HL_67265.4_HL_5X6B_002_G29_C39 | G | A | C | U | G | C | A | G | A | U | C | |||||||||||||||
| HL_67265.4_Sequence_6 HL_67265.4_HL_5X6B_002_G29_C39 | G | A | C | U | G | C | A | G | A | U | C | true | 47 | 0 | 0 | 10.55 | ||||||||||
| HL_67265.4_Instance_7 HL_67265.4_HL_4ZNP_002_C58_G68 | C | G | A | C | C | G | C | C | U | G | G | |||||||||||||||
| HL_67265.4_Sequence_7 HL_67265.4_HL_4ZNP_002_C58_G68 | C | G | A | C | C | G | C | C | U | G | G | true | 87 | 0 | 0 | 2.58 | ||||||||||
| HL_67265.4_Instance_8 HL_67265.4_HL_5BTP_004_C62_G72 | C | G | A | C | C | G | U | C | U | G | G | |||||||||||||||
| HL_67265.4_Sequence_8 HL_67265.4_HL_5BTP_004_C62_G72 | C | G | A | C | C | G | U | C | U | G | G | true | 80 | 0 | 0 | 4.05 |
1 2 s33 1 10 cWW 2 8 tHW 2 9 s55 2 10 s35 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35JAR3D SCFG/MRF model for HL_67265.4:
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 [10] // Initial node U12 - G22 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009658782,0.015795790,0.011556619,0.131140048,0.000000000],[0.118367062,0.015592795,0.164727178,0.013699441,0.000000000],[0.011681863,0.152918877,0.002404351,0.019826839,0.000000000],[0.148769631,0.013160068,0.159891367,0.010809289,0.000000000],[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 [10] // Basepair U12 - G22 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.050000000,0.050000000,0.750000000,0.150000000,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000001232656381] | Pair Probability [[0.046667391,0.290452158,0.003358559,0.033081247,0.000000000],[0.003358559,0.039191819,0.010509091,0.003358559,0.000000000],[0.029138771,0.003358559,0.021598119,0.104634874,0.000000000],[0.003358559,0.003358559,0.031682250,0.372892925,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.006170935,0.987349583,0.006170935,0.000308547] | Left Letter Distribution [0.250000000,0.250000000,0.050000000,0.450000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair U13 - U20 tHW HairpinNode | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G15:C19 Interaction | Interacting Bases [1,1] | Pair Probability [[0.050000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.350000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.450000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.150000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15 Interaction | Interacting Bases [2,2] | Pair Probability [[0.450000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.350000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.150000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.050000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A16 Interaction | Interacting Bases [3,3] | Pair Probability [[0.050000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.150000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.350000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.450000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U17 Interaction | Interacting Bases [4,4] | Pair Probability [[0.150000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.650000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.050000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.150000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C18 Interaction | Interacting Bases [5,5] | Pair Probability [[0.150000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.650000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.150000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.050000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C19Sequences of instances from HL_67265.4:
> HL_67265.4 HL_4LFB_001 U 12 G 22 UUUGAUCCUGG > HL_67265.4 HL_5J7L_001 U 12 G 22 UUUGAUCAUGG > HL_67265.4 HL_6CZR_072 U 13 G 23 UUUGAUCCUGG > HL_67265.4 HL_4V88_186 G 7 C 17 GUUGAUCCUGC > HL_67265.4 HL_4XWF_002 C 50 G 60 CGCCCGCCUGG > HL_67265.4 HL_5X6B_002 G 29 C 39 GACUGCAGAUC > HL_67265.4 HL_4ZNP_002 C 58 G 68 CGACCGCCUGG > HL_67265.4 HL_5BTP_004 C 62 G 72 CGACCGUCUGG