| 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_22447.1_Instance_1 HL_22447.1_HL_4TUW_002_U13_A18 | U | U | U | U | C | A | ||||||||
| HL_22447.1_Sequence_1 HL_22447.1_HL_4TUW_002_U13_A18 | U | U | U | U | C | A | true | 100 | 0 | 0 | 0.00 | |||
| HL_22447.1_Instance_2 HL_22447.1_HL_4QOZ_001_U11_A16 | U | U | U | U | C | A | ||||||||
| HL_22447.1_Sequence_2 HL_22447.1_HL_4QOZ_001_U11_A16 | U | U | U | U | C | A | true | 100 | 0 | 0 | 0.00 | |||
| HL_22447.1_Instance_3 HL_22447.1_HL_2PJP_001_G22_C25 | G | G | U | C | ||||||||||
| HL_22447.1_Sequence_3 HL_22447.1_HL_2PJP_001_G22_C25 | G | G | U | C | true | 97 | 0 | 0 | 0.30 | |||||
| HL_22447.1_Instance_4 HL_22447.1_HL_2UWM_002_G22_C25 | G | G | U | C | ||||||||||
| HL_22447.1_Sequence_4 HL_22447.1_HL_2UWM_002_G22_C25 | G | G | U | C | true | 97 | 0 | 0 | 0.30 | |||||
| HL_22447.1_Instance_5 HL_22447.1_HL_4ILM_002_U8_A14 | U | A | C | U | A | U | A | |||||||
| HL_22447.1_Sequence_5 HL_22447.1_HL_4ILM_002_U8_A14 | U | A | C | U | A | U | A | true | 82 | 0 | 0 | 1.74 | ||
| HL_22447.1_Instance_6 HL_22447.1_HL_4ILL_001_U8_A14 | U | A | C | U | A | U | A | |||||||
| HL_22447.1_Sequence_6 HL_22447.1_HL_4ILL_001_U8_A14 | U | A | C | U | A | U | A | true | 82 | 0 | 0 | 1.74 |
1 3 s35 1 4 cWW 2 3 s53 3 4 s55JAR3D SCFG/MRF model for HL_22447.1:
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 [4] // Initial node U13 - A18 from junction BasepairNode | Deletion Probability [0.0000001163511744] | Pair Probability [[0.008917739,0.017757404,0.009912684,0.190516459,0.000000000],[0.019625506,0.009368672,0.191487360,0.011346314,0.000000000],[0.009885600,0.210630944,0.001981552,0.023370273,0.000000000],[0.232624561,0.011077789,0.041714145,0.009783000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.661815186,0.335026775,0.003020733,0.000137306] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [0.334109270,0.660002739,0.005614131,0.000273860] | Right Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Left Index [1] | Right Index [4] // Basepair U13 - A18 cWW HairpinNode | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U14:U16 Interaction | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U14 Interaction | Interacting Bases [2,2] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U16 Insertion | Location [1] | Length Distribution [0.334109270,0.660002739,0.005614131,0.000273860] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1Sequences of instances from HL_22447.1:
> HL_22447.1 HL_4TUW_002 U 13 A 18 UUUUCA > HL_22447.1 HL_4QOZ_001 U 11 A 16 UUUUCA > HL_22447.1 HL_2PJP_001 G 22 C 25 GGUC > HL_22447.1 HL_2UWM_002 G 22 C 25 GGUC > HL_22447.1 HL_4ILM_002 U 8 A 14 UACUAUA > HL_22447.1 HL_4ILL_001 U 8 A 14 UACUAUA