| 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 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_01008.4_Instance_1 HL_01008.4_HL_5MSF_001_G7_C12 | G | A | U | C | A | C | ||||||||||
| HL_01008.4_Sequence_1 HL_01008.4_HL_5MSF_001_G7_C12 | G | A | U | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_01008.4_Instance_2 HL_01008.4_HL_5MSF_005_G7_C12 | G | A | U | C | A | C | ||||||||||
| HL_01008.4_Sequence_2 HL_01008.4_HL_5MSF_005_G7_C12 | G | A | U | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_01008.4_Instance_3 HL_01008.4_HL_1U1Y_005_G7_C12 | G | A | U | C | A | C | ||||||||||
| HL_01008.4_Sequence_3 HL_01008.4_HL_1U1Y_005_G7_C12 | G | A | U | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_01008.4_Instance_4 HL_01008.4_HL_1U1Y_001_G7_C12 | G | A | U | C | A | C | ||||||||||
| HL_01008.4_Sequence_4 HL_01008.4_HL_1U1Y_001_G7_C12 | G | A | U | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_01008.4_Instance_5 HL_01008.4_HL_2IZN_005_G8_C13 | G | A | U | U | A | C | ||||||||||
| HL_01008.4_Sequence_5 HL_01008.4_HL_2IZN_005_G8_C13 | G | A | U | U | A | C | true | 88 | 0 | 0 | 1.23 | |||||
| HL_01008.4_Instance_6 HL_01008.4_HL_2IZN_001_G8_C13 | G | A | U | U | A | C | ||||||||||
| HL_01008.4_Sequence_6 HL_01008.4_HL_2IZN_001_G8_C13 | G | A | U | U | A | C | true | 88 | 0 | 0 | 1.23 | |||||
| HL_01008.4_Instance_7 HL_01008.4_HL_7MSF_005_C5_G10 | C | A | A | C | A | G | ||||||||||
| HL_01008.4_Sequence_7 HL_01008.4_HL_7MSF_005_C5_G10 | C | A | A | C | A | G | true | 93 | 0 | 0 | 0.74 | |||||
| HL_01008.4_Instance_8 HL_01008.4_HL_7MSF_001_C5_G10 | C | A | A | C | A | G | ||||||||||
| HL_01008.4_Sequence_8 HL_01008.4_HL_7MSF_001_C5_G10 | C | A | A | C | A | G | true | 93 | 0 | 0 | 0.74 | |||||
| HL_01008.4_Instance_9 HL_01008.4_HL_6CZR_102_C1430_G1435 | C | U | A | C | G | G | ||||||||||
| HL_01008.4_Sequence_9 HL_01008.4_HL_6CZR_102_C_1430_G_1435 | C | U | A | C | G | G | true | 59 | 0 | 0 | 4.21 |
1 2 s35 1 5 cWW 2 4 s35 2 5 s55 4 3 7BPhJAR3D SCFG/MRF model for HL_01008.4:
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 [5] // Initial node G7 - C12 from junction BasepairNode | Deletion Probability [0.0000001233099223] | Pair Probability [[0.009047108,0.017980999,0.010334636,0.187602286,0.000000000],[0.016991075,0.008984252,0.219366759,0.012588934,0.000000000],[0.010296248,0.248730076,0.001955254,0.024017273,0.000000000],[0.186798784,0.012745957,0.022986810,0.009573550,0.000000000],[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 [0.005492996,0.988739357,0.005492996,0.000274650] | Right Letter Distribution [0.772727273,0.045454545,0.136363636,0.045454545,0.000000000] | Left Index [1] | Right Index [5] // Basepair G7 - C12 cWW HairpinNode | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A8:C10 Interaction | Interacting Bases [1,1] | Pair Probability [[0.772727273,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.136363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A8 Interaction | Interacting Bases [2,2] | Pair Probability [[0.318181818,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.590909091,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U9 Interaction | Interacting Bases [3,3] | Pair Probability [[0.007692308,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.761538462,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.007692308,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.223076923,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C10Sequences of instances from HL_01008.4:
> HL_01008.4 HL_5MSF_001 G 7 C 12 GAUCAC > HL_01008.4 HL_5MSF_005 G 7 C 12 GAUCAC > HL_01008.4 HL_1U1Y_005 G 7 C 12 GAUCAC > HL_01008.4 HL_1U1Y_001 G 7 C 12 GAUCAC > HL_01008.4 HL_2IZN_005 G 8 C 13 GAUUAC > HL_01008.4 HL_2IZN_001 G 8 C 13 GAUUAC > HL_01008.4 HL_7MSF_005 C 5 G 10 CAACAG > HL_01008.4 HL_7MSF_001 C 5 G 10 CAACAG > HL_01008.4 HL_6CZR_102 C 1430 G 1435 CUACGG