| 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 4 3 | 7 4 I | 8 4 4 | 9 4 I | 10 4 5 | 11 4 I | 12 4 6 | 13 3 I | 14 3 7 | 15 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_93727.3_Instance_1 HL_93727.3_HL_5AOX_001_G11_C18 | G | G | U | G | G | C | U | C | ||||||||||||||
| HL_93727.3_Sequence_1 HL_93727.3_HL_5AOX_001_G11_C18 | G | G | U | G | G | C | U | C | true | 72 | 0 | 0 | 2.94 | |||||||||
| HL_93727.3_Instance_2 HL_93727.3_HL_1E8O_001_G110_C117 | G | G | U | G | G | C | G | C | ||||||||||||||
| HL_93727.3_Sequence_2 HL_93727.3_HL_1E8O_001_G110_C117 | G | G | U | G | G | C | G | C | true | 79 | 0 | 0 | 2.23 | |||||||||
| HL_93727.3_Instance_3 HL_93727.3_HL_5J7L_154_G712_C719 | G | G | U | A | A | C | A | C | ||||||||||||||
| HL_93727.3_Sequence_3 HL_93727.3_HL_5J7L_154_G712_C719 | G | G | U | A | A | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_93727.3_Instance_4 HL_93727.3_HL_3HHN_010_G92_C99 | G | U | U | A | A | A | A | C | ||||||||||||||
| HL_93727.3_Sequence_4 HL_93727.3_HL_3HHN_010_G92_C99 | G | U | U | A | A | A | A | C | true | 93 | 0 | 0 | 0.78 | |||||||||
| HL_93727.3_Instance_5 HL_93727.3_HL_4Y4O_124_G712_C719 | G | G | U | G | A | G | A | C | ||||||||||||||
| HL_93727.3_Sequence_5 HL_93727.3_HL_4Y4O_124_G712_C719 | G | G | U | G | A | G | A | C | true | 80 | 0 | 0 | 2.09 | |||||||||
| HL_93727.3_Instance_6 HL_93727.3_HL_1MMS_002_C1092_G1099 | C | G | U | A | A | C | A | G | ||||||||||||||
| HL_93727.3_Sequence_6 HL_93727.3_HL_1MMS_002_C_1092_G_1099 | C | G | U | A | A | C | A | G | true | 99 | 0 | 0 | 0.10 | |||||||||
| HL_93727.3_Instance_7 HL_93727.3_HL_5D8H_002_C1202_G1209 | C | G | U | A | A | C | A | G | ||||||||||||||
| HL_93727.3_Sequence_7 HL_93727.3_HL_5D8H_002_C_1202_G_1209 | C | G | U | A | A | C | A | G | true | 99 | 0 | 0 | 0.10 | |||||||||
| HL_93727.3_Instance_8 HL_93727.3_HL_1U9S_003_G181_C189 | G | G | U | A | A | G | A | G | C | |||||||||||||
| HL_93727.3_Sequence_8 HL_93727.3_HL_1U9S_003_G181_C189 | G | G | U | A | A | G | A | G | C | true | 77 | 0 | 0 | 2.47 | ||||||||
| HL_93727.3_Instance_9 HL_93727.3_HL_4LFB_006_G259_C267 | G | G | U | A | A | U | G | G | C | |||||||||||||
| HL_93727.3_Sequence_9 HL_93727.3_HL_4LFB_006_G259_C267 | G | G | U | A | A | U | G | G | C | true | 87 | 0 | 0 | 1.40 | ||||||||
| HL_93727.3_Instance_10 HL_93727.3_HL_6PRV_002_C1092_G1099 | C | G | U | A | A | U | A | G | ||||||||||||||
| HL_93727.3_Sequence_10 HL_93727.3_HL_6PRV_002_C_1092_G_1099 | C | G | U | A | A | U | A | G | true | 97 | 0 | 0 | 0.37 | |||||||||
| HL_93727.3_Instance_11 HL_93727.3_HL_5J7L_006_G259_C267 | G | G | U | A | A | C | G | G | C | |||||||||||||
| HL_93727.3_Sequence_11 HL_93727.3_HL_5J7L_006_G259_C267 | G | G | U | A | A | C | G | G | C | true | 89 | 0 | 0 | 1.13 | ||||||||
| HL_93727.3_Instance_12 HL_93727.3_HL_4WF9_004_A136_U143 | A | G | U | U | A | U | G | U | ||||||||||||||
| HL_93727.3_Sequence_12 HL_93727.3_HL_4WF9_004_A136_U143 | A | G | U | U | A | U | G | U | true | 72 | 0 | 0 | 2.91 | |||||||||
| HL_93727.3_Instance_13 HL_93727.3_HL_4V88_193_G330_C338 | G | A | U | A | G | U | G | G | C | |||||||||||||
| HL_93727.3_Sequence_13 HL_93727.3_HL_4V88_193_G330_C338 | G | A | U | A | G | U | G | G | C | true | 51 | 0 | 0 | 5.20 | ||||||||
| HL_93727.3_Instance_14 HL_93727.3_HL_7A0S_056_C2334_G2341 | C | U | G | A | C | A | C | G | ||||||||||||||
| HL_93727.3_Sequence_14 HL_93727.3_HL_7A0S_056_C_2334_G_2341 | C | U | G | A | C | A | C | G | true | 53 | 0 | 0 | 4.99 | |||||||||
| HL_93727.3_Instance_15 HL_93727.3_HL_4KQY_003_C94_G102 | C | U | C | G | A | A | C | A | G | |||||||||||||
| HL_93727.3_Sequence_15 HL_93727.3_HL_4KQY_003_C94_G102 | C | U | C | G | A | A | C | A | G | true | 49 | 0 | 0 | 5.36 | ||||||||
| HL_93727.3_Instance_16 HL_93727.3_HL_4KQY_006_C94_G102 | C | U | C | G | A | A | C | A | G | |||||||||||||
| HL_93727.3_Sequence_16 HL_93727.3_HL_4KQY_006_C94_G102 | C | U | C | G | A | A | C | A | G | true | 49 | 0 | 0 | 5.36 | ||||||||
| HL_93727.3_Instance_17 HL_93727.3_HL_6CZR_077_G255_C263 | G | G | U | A | A | U | G | G | C | |||||||||||||
| HL_93727.3_Sequence_17 HL_93727.3_HL_6CZR_077_G255_C263 | G | G | U | A | A | U | G | G | C | true | 87 | 0 | 0 | 1.40 | ||||||||
| HL_93727.3_Instance_18 HL_93727.3_HL_4WF9_053_C2382_G2389 | C | C | U | A | C | A | A | G | ||||||||||||||
| HL_93727.3_Sequence_18 HL_93727.3_HL_4WF9_053_C_2382_G_2389 | C | C | U | A | C | A | A | G | true | 80 | 0 | 0 | 2.16 | |||||||||
| HL_93727.3_Instance_19 HL_93727.3_HL_4Y4O_160_C2355_G2362 | C | C | U | G | C | A | A | G | ||||||||||||||
| HL_93727.3_Sequence_19 HL_93727.3_HL_4Y4O_160_C_2355_G_2362 | C | C | U | G | C | A | A | G | true | 71 | 0 | 0 | 3.03 | |||||||||
| HL_93727.3_Instance_20 HL_93727.3_HL_7A0S_029_C1103_G1110 | C | G | U | A | A | U | A | G | ||||||||||||||
| HL_93727.3_Sequence_20 HL_93727.3_HL_7A0S_029_C_1103_G_1110 | C | G | U | A | A | U | A | G | true | 97 | 0 | 0 | 0.37 | |||||||||
| HL_93727.3_Instance_21 HL_93727.3_HL_4WF9_041_G1761_C1768 | G | U | U | A | A | C | G | C | ||||||||||||||
| HL_93727.3_Sequence_21 HL_93727.3_HL_4WF9_041_G_1761_C_1768 | G | U | U | A | A | C | G | C | true | 79 | 0 | 0 | 2.20 | |||||||||
| HL_93727.3_Instance_22 HL_93727.3_HL_6UFM_004_G13_C20 | G | C | C | A | U | C | A | C | ||||||||||||||
| HL_93727.3_Sequence_22 HL_93727.3_HL_6UFM_004_G13_C20 | G | C | C | A | U | C | A | C | true | 58 | 0 | 0 | 4.41 |
1 2 s35 1 8 cWW 2 3 s35 2 7 tSH 2 8 s55 4 5 s35 5 6 s35 6 7 s35 7 8 s35 3 6 6BPhJAR3D SCFG/MRF model for HL_93727.3:
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 [8] // Initial node G11 - C18 from junction BasepairNode | Deletion Probability [0.0000045283410407] | Pair Probability [[0.008053456,0.015930260,0.009181313,0.175754462,0.000000000],[0.015397884,0.008038891,0.245211997,0.011168415,0.000000000],[0.009166555,0.270570173,0.001745108,0.022254230,0.000000000],[0.166956691,0.011251217,0.020730033,0.008589315,0.000000000],[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 [0.680425536,0.318740281,0.000798138,0.000036045] | Right Letter Distribution [0.277777778,0.055555556,0.611111111,0.055555556,0.000000000] | Left Index [1] | Right Index [8] // Basepair G11 - C18 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.065340768,0.060719131,0.015625149,0.106197426,0.000000000],[0.103735802,0.060596947,0.001890102,0.001890102,0.000000000],[0.140329191,0.001890102,0.158604543,0.078639827,0.000000000],[0.084541987,0.102483673,0.015625149,0.001890102,0.000000000],[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 [2] | Right Index [7] // Basepair G12 - U17 tSH HairpinNode | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U13:C16 Interaction | Interacting Bases [1,1] | Pair Probability [[0.003205128,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.137820513,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.048076923,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.810897436,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U13 Interaction | Interacting Bases [2,2] | Pair Probability [[0.645833333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.020833333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.270833333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G14 Interaction | Interacting Bases [3,3] | Pair Probability [[0.645833333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.145833333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.145833333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15 Interaction | Interacting Bases [4,4] | Pair Probability [[0.270833333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.354166667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.104166667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.270833333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C16Sequences of instances from HL_93727.3:
> HL_93727.3 HL_5AOX_001 G 11 C 18 GGUGGCUC > HL_93727.3 HL_1E8O_001 G 110 C 117 GGUGGCGC > HL_93727.3 HL_5J7L_154 G 712 C 719 GGUAACAC > HL_93727.3 HL_3HHN_010 G 92 C 99 GUUAAAAC > HL_93727.3 HL_4Y4O_124 G 712 C 719 GGUGAGAC > HL_93727.3 HL_1MMS_002 C 1092 G 1099 CGUAACAG > HL_93727.3 HL_5D8H_002 C 1202 G 1209 CGUAACAG > HL_93727.3 HL_1U9S_003 G 181 C 189 GGUAAGAGC > HL_93727.3 HL_4LFB_006 G 259 C 267 GGUAAUGGC > HL_93727.3 HL_6PRV_002 C 1092 G 1099 CGUAAUAG > HL_93727.3 HL_5J7L_006 G 259 C 267 GGUAACGGC > HL_93727.3 HL_4WF9_004 A 136 U 143 AGUUAUGU > HL_93727.3 HL_4V88_193 G 330 C 338 GAUAGUGGC > HL_93727.3 HL_7A0S_056 C 2334 G 2341 CUGACACG > HL_93727.3 HL_4KQY_003 C 94 G 102 CUCGAACAG > HL_93727.3 HL_4KQY_006 C 94 G 102 CUCGAACAG > HL_93727.3 HL_6CZR_077 G 255 C 263 GGUAAUGGC > HL_93727.3 HL_4WF9_053 C 2382 G 2389 CCUACAAG > HL_93727.3 HL_4Y4O_160 C 2355 G 2362 CCUGCAAG > HL_93727.3 HL_7A0S_029 C 1103 G 1110 CGUAAUAG > HL_93727.3 HL_4WF9_041 G 1761 C 1768 GUUAACGC > HL_93727.3 HL_6UFM_004 G 13 C 20 GCCAUCAC