| 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 2 I | 6 2 3 | 7 2 I | 8 2 4 | 9 2 I | 10 2 5 | 11 2 I | 12 2 6 | 13 2 I | 14 2 7 | 15 3 I | 16 4 8 | 17 4 I | 18 5 | 19 4 I | 20 4 9 | 21 3 I | 22 2 10 | 23 2 I | 24 2 11 | 25 2 I | 26 2 12 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_24134.1_Instance_1 IL_24134.1,IL_2VPL_001,C33_G13 | C | G | A | G | A | A | A | C | G | G | A | G | ||||||||||||||||||||
| IL_24134.1_Sequence_1 IL_24134.12VPL_C33_G13 | C | G | A | G | A | A | A | C | * | G | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_24134.1_Instance_2 IL_24134.1,IL_2HW8_001,C22_G13 | C | G | C | G | A | A | A | C | G | G | A | G | ||||||||||||||||||||
| IL_24134.1_Sequence_2 IL_24134.12HW8_C22_G13 | C | G | C | G | A | A | A | C | * | G | G | A | G | true | 97 | 0 | 0 | 0.51 | ||||||||||||||
| IL_24134.1_Instance_3 IL_24134.1,IL_1U63_003,C33_G13 | C | G | A | G | A | A | A | C | G | G | A | G | ||||||||||||||||||||
| IL_24134.1_Sequence_3 IL_24134.11U63_C33_G13 | C | G | A | G | A | A | A | C | * | G | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 7 cSS 1 12 cWW 2 3 s35 2 12 s55 5 6 s35 7 8 s35 7 10 tHS 7 11 s55 7 12 tSS 8 9 cWW 8 10 s55 9 10 s35 10 11 s35 10 6 6BPh 8 7 7BPh 7 10 6BRJAR3D SCFG/MRF model for IL_24134.1:
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 [12] // Initial node ClusterNode | Deletion Probability [0.000000000000000000000009765625000000002403123293600734118083] | Num Left Bases [7] | Num Right Bases [3] | Left Index [1] | Right Index [12] | Norm Constant [0.016689729955295] // Cluster node 2VPL|1|B|C|33:2VPL|1|B|A|39 and 2VPL|1|B|G|11:2VPL|1|B|G|13 Interaction | Interacting Bases [7,8] | Pair Probability [[0.043273743,0.043595236,0.392756919,0.048305054,0.000000000],[0.045811089,0.045705009,0.003636307,0.045458262,0.000000000],[0.000519472,0.000519472,0.017776750,0.000519472,0.000000000],[0.002448275,0.000519472,0.308635994,0.000519472,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 2VPL|1|B|A|39 - 2VPL|1|B|G|11 tHS Interaction | Interacting Bases [1,10] | 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]] // Cluster Interaction 2VPL|1|B|C|33 - 2VPL|1|B|G|13 cWW Interaction | Interacting Bases [7,10] | Pair Probability [[0.216554087,0.216035898,0.251361434,0.204874167,0.000000000],[0.000959476,0.000959476,0.009942319,0.000959476,0.000000000],[0.007523181,0.000959476,0.007835896,0.078197207,0.000000000],[0.000959476,0.000959476,0.000959476,0.000959476,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 2VPL|1|B|A|39 - 2VPL|1|B|G|13 tSS Interaction | Interacting Bases [1,7] | Pair Probability [[0.112153950,0.050138957,0.048840398,0.050633177,0.000000000],[0.200684444,0.051159484,0.002378257,0.045528061,0.000000000],[0.118920782,0.002341774,0.004594934,0.054390939,0.000000000],[0.113322594,0.049131132,0.048844775,0.046936343,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 2VPL|1|B|C|33 - 2VPL|1|B|A|39 cSS Interaction | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 2VPL|1|B|G|34 Interaction | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 2VPL|1|B|A|35 Interaction | Interacting Bases [4,4] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 2VPL|1|B|G|36 Interaction | Interacting Bases [5,5] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 2VPL|1|B|A|37 Interaction | Interacting Bases [6,6] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 2VPL|1|B|A|38 Interaction | Interacting Bases [9,9] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 2VPL|1|B|A|12 InitialNode | 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 [8] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003708089,0.006649494,0.004262905,0.077294868,0.000000000],[0.055188220,0.026436068,0.597914779,0.037535311,0.000000000],[0.004310778,0.078960365,0.000812555,0.009124318,0.000000000],[0.078296919,0.005166364,0.010409412,0.003929554,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [8] | Right Index [9] // Basepair C40 - G10 cWW HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | 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_24134.1:
> IL_24134.1 2VPL C 33 G 13 CGAGAAAC*GGAG > IL_24134.1 2HW8 C 22 G 13 CGCGAAAC*GGAG > IL_24134.1 1U63 C 33 G 13 CGAGAAAC*GGAG