| 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 5 I | 12 6 | 13 5 I | 14 4 6 | 15 3 I | 16 3 7 | 17 2 I | 18 2 8 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_36516.3_Instance_1 IL_36516.3,IL_7EL1_001,A42_U31 | A | A | U | C | U | A | C | U | ||||||||||||||||
| IL_36516.3_Sequence_1 IL_36516.37EL1_A42_U31 | A | A | U | C | U | * | A | C | U | true | 99 | 0 | 0 | 0.13 | ||||||||||
| IL_36516.3_Instance_2 IL_36516.3,IL_7ENI_001,A42_U31 | A | A | U | C | U | A | C | U | ||||||||||||||||
| IL_36516.3_Sequence_2 IL_36516.37ENI_A42_U31 | A | A | U | C | U | * | A | C | U | true | 99 | 0 | 0 | 0.13 | ||||||||||
| IL_36516.3_Instance_3 IL_36516.3,IL_6M0X_001,A38_U31 | A | A | G | C | U | A | C | U | ||||||||||||||||
| IL_36516.3_Sequence_3 IL_36516.36M0X_A38_U31 | A | A | G | C | U | * | A | C | U | true | 93 | 0 | 0 | 0.65 | ||||||||||
| IL_36516.3_Instance_4 IL_36516.3,IL_6DME_002,G15_C39 | G | G | A | U | C | G | A | C | ||||||||||||||||
| IL_36516.3_Sequence_4 IL_36516.36DME_G15_C39 | G | G | A | U | C | * | G | A | C | true | 96 | 0 | 0 | 0.39 | ||||||||||
| IL_36516.3_Instance_5 IL_36516.3,IL_6CK5_002,G16_C44 | G | G | U | U | C | G | A | C | ||||||||||||||||
| IL_36516.3_Sequence_5 IL_36516.36CK5_G16_C44 | G | G | U | U | C | * | G | A | C | true | 94 | 0 | 0 | 0.57 | ||||||||||
| IL_36516.3_Instance_6 IL_36516.3,IL_4PDB_001,C9_G30 | C | A | G | U | G | C | A | G | ||||||||||||||||
| IL_36516.3_Sequence_6 IL_36516.34PDB_C9_G30 | C | A | G | U | G | * | C | A | G | true | 90 | 0 | 0 | 0.91 | ||||||||||
| IL_36516.3_Instance_7 IL_36516.3,IL_8P9A_315,G2206_C2237 | G | A | A | U | G | C | G | C | ||||||||||||||||
| IL_36516.3_Sequence_7 IL_36516.38P9A_G_2206_C_2237 | G | A | A | U | G | * | C | G | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 8 cWW 2 3 s35 2 7 cWW 3 5 cSH 4 5 s35 5 6 cWW 6 7 s35 7 8 s35JAR3D SCFG/MRF model for IL_36516.3:
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 [8] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009067845,0.019603119,0.010071826,0.220747538,0.000000000],[0.016903319,0.009136162,0.200075347,0.011537189,0.000000000],[0.010030419,0.221402449,0.001972052,0.035870644,0.000000000],[0.188702726,0.011947758,0.022632251,0.010299353,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair A42 - U31 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.116080178,0.176285660,0.146810382,0.024758432,0.000000000],[0.013168086,0.010233170,0.021665544,0.023830889,0.000000000],[0.143331769,0.023806144,0.003457474,0.137030898,0.000000000],[0.021580629,0.024141361,0.014060792,0.099758592,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair A43 - C30 cWW ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [3] | Right Index [6] | Norm Constant [0.252410397920198] // Cluster node 7EL1|1|B|U|44:7EL1|1|B|U|46 and 7EL1|1|B|A|29:7EL1|1|B|A|29 Interaction | Interacting Bases [3,4] | Pair Probability [[0.008939441,0.017346894,0.010053653,0.189181225,0.000000000],[0.019185212,0.009261737,0.211381604,0.011886470,0.000000000],[0.010061557,0.210351303,0.001973383,0.023097129,0.000000000],[0.220529544,0.011612576,0.035454589,0.009683680,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7EL1|1|B|U|46 - 7EL1|1|B|A|29 cWW Interaction | Interacting Bases [1,3] | Pair Probability [[0.063569176,0.098738364,0.143590998,0.069048957,0.000000000],[0.059501789,0.068138337,0.001998079,0.029008056,0.000000000],[0.027691089,0.001998079,0.081238651,0.077145551,0.000000000],[0.064690024,0.083122071,0.001998079,0.128522701,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7EL1|1|B|U|44 - 7EL1|1|B|U|46 cSH Interaction | Interacting Bases [2,2] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.388888889,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7EL1|1|B|C|45 InitialNode | Left Length Distribution [0.992332775,0.007314709,0.000352516] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.992332775,0.007314709,0.000352516] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from IL_36516.3:
> IL_36516.3 7EL1 A 42 U 31 AAUCU*ACU > IL_36516.3 7ENI A 42 U 31 AAUCU*ACU > IL_36516.3 6M0X A 38 U 31 AAGCU*ACU > IL_36516.3 6DME G 15 C 39 GGAUC*GAC > IL_36516.3 6CK5 G 16 C 44 GGUUC*GAC > IL_36516.3 4PDB C 9 G 30 CAGUG*CAG > IL_36516.3 8P9A G 2206 C 2237 GAAUG*CGC