| 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_36684.4_Instance_1 HL_36684.4,HL_5IB8_208,G30_C40 | G | A | C | U | U | U | U | A | A | U | C | |||||||||||||||||
| HL_36684.4_Sequence_1 HL_36684.45IB8_G30_C40 | G | A | C | U | U | U | U | A | A | U | C | true | 84 | 0 | 0 | 2.68 | ||||||||||||
| HL_36684.4_Instance_2 HL_36684.4,HL_7K16_002,G27_C37 | G | C | U | U | G | A | G | A | A | C | C | |||||||||||||||||
| HL_36684.4_Sequence_2 HL_36684.47K16_G27_C37 | G | C | U | U | G | A | G | A | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| HL_36684.4_Instance_3 HL_36684.4,HL_4V7M_039,G29_C39 | G | A | U | U | G | U | G | A | U | U | C | |||||||||||||||||
| HL_36684.4_Sequence_3 HL_36684.44V7M_G29_C39 | G | A | U | U | G | U | G | A | U | U | C | true | 97 | 0 | 0 | 0.59 | ||||||||||||
| HL_36684.4_Instance_4 HL_36684.4,HL_4UYK_001,G21_C31 | G | G | U | U | C | G | G | C | G | U | C | |||||||||||||||||
| HL_36684.4_Sequence_4 HL_36684.44UYK_G21_C31 | G | G | U | U | C | G | G | C | G | U | C | true | 80 | 0 | 0 | 3.50 | ||||||||||||
| HL_36684.4_Instance_5 HL_36684.4,HL_6GSL_238,G31_C41 | G | G | C | U | A | C | G | A | A | C | C | |||||||||||||||||
| HL_36684.4_Sequence_5 HL_36684.46GSL_G31_C41 | G | G | C | U | A | C | G | A | A | C | C | true | 84 | 0 | 0 | 2.73 | ||||||||||||
| HL_36684.4_Instance_6 HL_36684.4,HL_6GSK_218,C30_G40 | C | C | U | U | G | G | U | A | A | G | G | |||||||||||||||||
| HL_36684.4_Sequence_6 HL_36684.46GSK_C30_G40 | C | C | U | U | G | G | U | A | A | G | G | true | 95 | 0 | 0 | 0.92 | ||||||||||||
| HL_36684.4_Instance_7 HL_36684.4,HL_4WSM_225,C31_G41 | C | C | U | U | G | A | G | G | U | G | G | |||||||||||||||||
| HL_36684.4_Sequence_7 HL_36684.44WSM_C31_G41 | C | C | U | U | G | A | G | G | U | G | G | true | 88 | 0 | 0 | 2.02 |
1 2 s35 1 11 cWW 2 3 s35 2 11 s55 3 4 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35 10 11 s35 4 7 6BPhJAR3D SCFG/MRF model for HL_36684.4:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009225160,0.018461010,0.010533281,0.191223781,0.000000000],[0.017164362,0.009144562,0.213851238,0.012801243,0.000000000],[0.010482999,0.244299236,0.001991779,0.024615947,0.000000000],[0.190171317,0.013006918,0.023266199,0.009760966,0.000000000],[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 G30 - C40 cWW HairpinNode | Num Bases [9] | Left Index [2] | Right Index [10] | Norm Constant [1.000000000000000] // Hairpin node A31:U39 Interaction | Interacting Bases [1,1] | Pair Probability [[0.277777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.388888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.277777778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A31 Interaction | Interacting Bases [2,2] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.277777778,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.611111111,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C32 Interaction | Interacting Bases [3,3] | Pair Probability [[0.009803922,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.009803922,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009803922,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.970588235,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U33 Interaction | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U34 Interaction | Interacting Bases [5,5] | Pair Probability [[0.277777778,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.277777778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U35 Interaction | Interacting Bases [6,6] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.611111111,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U36 Interaction | Interacting Bases [7,7] | Pair Probability [[0.611111111,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A37 Interaction | Interacting Bases [8,8] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A38 Interaction | Interacting Bases [9,9] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.277777778,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.277777778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.388888889,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U39Sequences of instances from HL_36684.4:
> HL_36684.4 5IB8 G 30 C 40 GACUUUUAAUC > HL_36684.4 7K16 G 27 C 37 GCUUGAGAACC > HL_36684.4 4V7M G 29 C 39 GAUUGUGAUUC > HL_36684.4 4UYK G 21 C 31 GGUUCGGCGUC > HL_36684.4 6GSL G 31 C 41 GGCUACGAACC > HL_36684.4 6GSK C 30 G 40 CCUUGGUAAGG > HL_36684.4 4WSM C 31 G 41 CCUUGAGGUGG