| 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_53987.3_Instance_1 HL_53987.3_HL_4M6D_004_C32_G36 | C | U | U | A | G | |||||||||
| HL_53987.3_Sequence_1 HL_53987.3_HL_4M6D_004_C32_G36 | C | U | U | A | G | true | 100 | 0 | 0 | 0.00 | ||||
| HL_53987.3_Instance_2 HL_53987.3_HL_4M4O_001_C32_G36 | C | U | U | A | G | |||||||||
| HL_53987.3_Sequence_2 HL_53987.3_HL_4M4O_001_C32_G36 | C | U | U | A | G | true | 100 | 0 | 0 | 0.00 | ||||
| HL_53987.3_Instance_3 HL_53987.3_HL_4V88_190_C230_G235 | C | U | UC | G | G | |||||||||
| HL_53987.3_Sequence_3 HL_53987.3_HL_4V88_190_C230_G235 | C | U | UC | G | G | true | 78 | 0 | 0 | 2.06 |
1 2 s35 1 4 cWW 2 3 cWS 3 4 s35JAR3D SCFG/MRF model for HL_53987.3:
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 [4] // Initial node C32 - G36 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair C32 - G36 cWW HairpinNode | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U33:A35 Interaction | Interacting Bases [1,2] | Pair Probability [[0.007861111,0.007975876,0.007642854,0.008260816,0.000000000],[0.014262644,0.013529871,0.003070167,0.014596640,0.000000000],[0.010173082,0.002201965,0.009282757,0.007903972,0.000000000],[0.239613933,0.198615943,0.238666258,0.216342112,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U33 - A35 cWS Insertion | Location [1] | Length Distribution [0.010744024,0.650013430,0.333064733,0.005909213,0.000268601] | Letter Distribution [0.083333333,0.250000000,0.083333333,0.583333333,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1Sequences of instances from HL_53987.3:
> HL_53987.3 HL_4M6D_004 C 32 G 36 CUUAG > HL_53987.3 HL_4M4O_001 C 32 G 36 CUUAG > HL_53987.3 HL_4V88_190 C 230 G 235 CUUCGG