| 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 5 I | 8 6 4 | 9 7 I | 10 8 5 | 11 9 I | 12 16 6 | 13 16 I | 14 17 7 | 15 17 I | 16 18 | 17 17 I | 18 17 8 | 19 16 I | 20 16 9 | 21 15 I | 22 14 10 | 23 13 I | 24 12 11 | 25 11 I | 26 10 12 | 27 3 I | 28 3 13 | 29 2 I | 30 2 14 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_88116.2_Instance_1 IL_88116.2,IL_8P9A_316,U2211_G2234 | U | C | A | A | A | G | U | A | A | C | C | A | A | G | ||||||||||||||||||||||
| IL_88116.2_Sequence_1 IL_88116.28P9A_U_2211_G_2234 | U | C | A | A | A | G | U | * | A | A | C | C | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_88116.2_Instance_2 IL_88116.2,IL_8CRE_093,U2189_G2212 | U | C | A | A | A | G | U | A | A | C | C | A | A | G | ||||||||||||||||||||||
| IL_88116.2_Sequence_2 IL_88116.28CRE_U_2189_G_2212 | U | C | A | A | A | G | U | * | A | A | C | C | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_88116.2_Instance_3 IL_88116.2,IL_4V9F_069,U1907_G1932 | U | G | A | A | C | A | C | G | A | C | G | A | A | G | ||||||||||||||||||||||
| IL_88116.2_Sequence_3 IL_88116.24V9F_U_1907_G_1932 | U | G | A | A | C | A | C | * | G | A | C | G | A | A | G | true | 93 | 0 | 0 | 1.41 |
1 2 s35 1 14 cWW 2 11 s33 2 13 tSH 3 4 s35 3 12 s55 4 5 s35 5 6 s35 6 7 s35 6 9 cWW 7 8 cWW 8 9 s35 9 10 s35 10 11 s35 12 13 s35 13 14 s35 13 2 6BRJAR3D SCFG/MRF model for IL_88116.2:
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 [14] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.011136961,0.013848204,0.014138980,0.036912705,0.000000000],[0.299600889,0.027679377,0.041942910,0.015878461,0.000000000],[0.014448515,0.036764849,0.003274049,0.014529563,0.000000000],[0.085355993,0.014536633,0.356531131,0.013420778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [14] // Basepair U2211 - G2234 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.146217981,0.053512369,0.001570915,0.007696513,0.000000000],[0.169325908,0.117962426,0.001570915,0.001570915,0.000000000],[0.148726299,0.001570915,0.009984515,0.052151474,0.000000000],[0.143160694,0.141836332,0.001570915,0.001570915,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [2] | Right Index [13] // Basepair C2212 - A2233 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [12] // Fixed node on left for 8P9A|1|AR|A|2213 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [12] // Fixed node on left for 8P9A|1|AR|A|2214 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [5] | Right Index [12] // Fixed node on left for 8P9A|1|AR|A|2215 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [6] | Right Index [12] // Fixed node on right for 8P9A|1|AR|A|2232 InitialNode | Left Length Distribution [1.000000000] | 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 [6] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.500000000,0.300000000,0.100000000,0.000000000] | Position [2] | Left Index [6] | Right Index [11] // Fixed node on right for 8P9A|1|AR|C|2231 InitialNode | Left Length Distribution [1.000000000] | 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 [6] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [6] | Right Index [10] // Fixed node on right for 8P9A|1|AR|C|2230 InitialNode | Left Length Distribution [1.000000000] | 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 [6] | Right Index [9] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.221476247,0.018609679,0.246057695,0.020536329,0.000000000],[0.015817087,0.010116944,0.021661006,0.038466736,0.000000000],[0.271029163,0.021707641,0.004357867,0.019927855,0.000000000],[0.020306283,0.037967298,0.017242677,0.014719491,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [6] | Right Index [9] // Basepair G2216 - A2229 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009112412,0.017228063,0.010161591,0.195229874,0.000000000],[0.021246469,0.009696958,0.208737087,0.011844029,0.000000000],[0.010214994,0.195415535,0.002039424,0.022961981,0.000000000],[0.220848146,0.011235231,0.044021864,0.010006340,0.000000000],[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 [7] | Right Index [8] // Basepair U2217 - A2228 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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_88116.2:
> IL_88116.2 8P9A U 2211 G 2234 UCAAAGU*AACCAAG > IL_88116.2 8CRE U 2189 G 2212 UCAAAGU*AACCAAG > IL_88116.2 4V9F U 1907 G 1932 UGAACAC*GACGAAG