| 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 4 I | 14 4 7 | 15 4 I | 16 4 8 | 17 3 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_55436.1_Instance_1 HL_55436.1,HL_2JLT_001,G5_C14 | G | G | U | C | C | C | A | G | A | C | ||||||||||||||||
| HL_55436.1_Sequence_1 HL_55436.12JLT_G5_C14 | G | G | U | C | C | C | A | G | A | C | true | 95 | 0 | 0 | 0.78 | |||||||||||
| HL_55436.1_Instance_2 HL_55436.1,HL_6VMY_005,U333_A342 | U | C | U | G | C | G | A | G | G | A | ||||||||||||||||
| HL_55436.1_Sequence_2 HL_55436.16VMY_U333_A342 | U | C | U | G | C | G | A | G | G | A | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_55436.1_Instance_3 HL_55436.1,HL_3SUX_001,A38_U47 | A | C | G | G | G | G | A | G | U | U | ||||||||||||||||
| HL_55436.1_Sequence_3 HL_55436.13SUX_A38_U47 | A | C | G | G | G | G | A | G | U | U | true | 99 | 0 | 0 | 0.08 | |||||||||||
| HL_55436.1_Instance_4 HL_55436.1,HL_1F27_001,U7_A16 | U | C | A | G | A | G | G | A | C | A | ||||||||||||||||
| HL_55436.1_Sequence_4 HL_55436.11F27_U7_A16 | U | C | A | G | A | G | G | A | C | A | true | 83 | 0 | 0 | 2.85 |
1 2 s35 1 10 cWW 2 9 cWW 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35JAR3D SCFG/MRF model for HL_55436.1:
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 [10] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009093027,0.018970985,0.010008411,0.205298032,0.000000000],[0.019297510,0.009510635,0.193985360,0.011213292,0.000000000],[0.009982975,0.204428655,0.002015219,0.030912385,0.000000000],[0.216271682,0.011172138,0.037529771,0.010309924,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G5 - C14 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.017566882,0.013101557,0.174772177,0.016271931,0.000000000],[0.013907879,0.063614789,0.072867991,0.196093928,0.000000000],[0.191834520,0.019050234,0.003278597,0.014360677,0.000000000],[0.016832726,0.160212705,0.015195176,0.011038230,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair G6 - A13 cWW HairpinNode | Num Bases [6] | Left Index [3] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node U7:G12 Interaction | Interacting Bases [1,1] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U7 Interaction | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.583333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C8 Interaction | Interacting Bases [3,3] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C9 Interaction | Interacting Bases [4,4] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.583333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C10 Interaction | Interacting Bases [5,5] | Pair Probability [[0.583333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A11 Interaction | Interacting Bases [6,6] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.583333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G12Sequences of instances from HL_55436.1:
> HL_55436.1 2JLT G 5 C 14 GGUCCCAGAC > HL_55436.1 6VMY U 333 A 342 UCUGCGAGGA > HL_55436.1 3SUX A 38 U 47 ACGGGGAGUU > HL_55436.1 1F27 U 7 A 16 UCAGAGGACA