| 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 2 2 | 5 3 I | 6 4 3 | 7 4 I | 8 4 4 | 9 3 I | 10 2 5 | 11 2 I | 12 2 6 | 13 2 I | 14 2 7 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_88205.2_Instance_1 HL_88205.2,HL_8P9A_132,A876_U885 | A | C | G | U | G | C | A | AA | U | |||||||||||
| HL_88205.2_Sequence_1 HL_88205.28P9A_A876_U885 | A | C | G | U | G | C | A | AA | U | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_88205.2_Instance_2 HL_88205.2,HL_8CRE_019,A872_U881 | A | C | G | U | G | C | A | AA | U | |||||||||||
| HL_88205.2_Sequence_2 HL_88205.28CRE_A872_U881 | A | C | G | U | G | C | A | AA | U | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_88205.2_Instance_3 HL_88205.2,HL_4V9F_024,U837_A846 | U | C | C | U | A | C | A | AU | A | |||||||||||
| HL_88205.2_Sequence_3 HL_88205.24V9F_U837_A846 | U | C | C | U | A | C | A | AU | A | true | 74 | 0 | 0 | 3.85 | ||||||
| HL_88205.2_Instance_4 HL_88205.2,HL_9DFE_021,G744_C753 | G | G | A | U | G | C | A | AA | C | |||||||||||
| HL_88205.2_Sequence_4 HL_88205.29DFE_G744_C753 | G | G | A | U | G | C | A | AA | C | true | 97 | 0 | 0 | 0.52 | ||||||
| HL_88205.2_Instance_5 HL_88205.2,HL_7A0S_022,U757_A766 | U | G | C | U | G | A | A | AC | A | |||||||||||
| HL_88205.2_Sequence_5 HL_88205.27A0S_U757_A766 | U | G | C | U | G | A | A | AC | A | true | 85 | 0 | 0 | 2.30 | ||||||
| HL_88205.2_Instance_6 HL_88205.2,HL_4WF9_023,C789_G798 | C | G | U | U | G | A | A | AA | G | |||||||||||
| HL_88205.2_Sequence_6 HL_88205.24WF9_C789_G798 | C | G | U | U | G | A | A | AA | G | true | 97 | 0 | 0 | 0.38 | ||||||
| HL_88205.2_Instance_7 HL_88205.2,HL_5J7L_155,U744_A753 | U | G | U | U | G | A | A | AA | A | |||||||||||
| HL_88205.2_Sequence_7 HL_88205.25J7L_U744_A753 | U | G | U | U | G | A | A | AA | A | true | 99 | 0 | 0 | 0.18 |
1 2 s35 1 7 cWW 2 3 s35 2 4 s33 2 6 tSW 2 7 s55 4 6 s33 5 6 s35 5 7 cWS 6 7 s55 6 2 7BR 4 3 2BRJAR3D SCFG/MRF model for HL_88205.2:
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 [7] // Initial node ClusterNode | Deletion Probability [0.000000000000000077834144636918971208239992618431520099098200] | Num Left Bases [2] | Num Right Bases [3] | Left Index [1] | Right Index [7] | Norm Constant [0.250977124753292] // Cluster node 8P9A|1|AR|A|876:8P9A|1|AR|C|877 and 8P9A|1|AR|C|881:8P9A|1|AR|U|885 Interaction | Interacting Bases [2,4] | Pair Probability [[0.156393807,0.153327837,0.001913240,0.009327635,0.000000000],[0.213188418,0.008588135,0.001913240,0.007713853,0.000000000],[0.237914047,0.001913240,0.001913240,0.006245988,0.000000000],[0.167885785,0.008476387,0.014022145,0.009263002,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|C|877 - 8P9A|1|AR|A|882 tSW Interaction | Interacting Bases [1,5] | Pair Probability [[0.008843513,0.018252218,0.009751492,0.208978640,0.000000000],[0.018866880,0.009248518,0.198812373,0.011020769,0.000000000],[0.009754135,0.198467838,0.001960210,0.030750014,0.000000000],[0.219431451,0.010929189,0.034881686,0.010051076,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|876 - 8P9A|1|AR|U|885 cWW Interaction | Interacting Bases [3,5] | Pair Probability [[0.117219757,0.094553977,0.106037736,0.095431809,0.000000000],[0.153777412,0.153338228,0.002337805,0.164536746,0.000000000],[0.022423066,0.002337805,0.026365274,0.010167450,0.000000000],[0.012477862,0.017945698,0.009389952,0.011659423,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|C|881 - 8P9A|1|AR|U|885 cWS Insertion | Location [4] | Length Distribution [0.000000000,0.007039775,0.985568462,0.007039775,0.000351989] | Letter Distribution [0.781250000,0.093750000,0.031250000,0.093750000,0.000000000]// Insertion after nucleotide 6, position 4 in cluster node InitialNode | 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 [3] | Right Index [4] // New Initial node after Cluster HairpinNode | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G878:G880 Interaction | Interacting Bases [1,1] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G878 Interaction | Interacting Bases [2,2] | Pair Probability [[0.148648649,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.013513514,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.824324324,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G880 Insertion | Location [1] | Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1Sequences of instances from HL_88205.2:
> HL_88205.2 8P9A A 876 U 885 ACGUGCAAAU > HL_88205.2 8CRE A 872 U 881 ACGUGCAAAU > HL_88205.2 4V9F U 837 A 846 UCCUACAAUA > HL_88205.2 9DFE G 744 C 753 GGAUGCAAAC > HL_88205.2 7A0S U 757 A 766 UGCUGAAACA > HL_88205.2 4WF9 C 789 G 798 CGUUGAAAAG > HL_88205.2 5J7L U 744 A 753 UGUUGAAAAA