| 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 4 I | 10 5 5 | 11 6 I | 12 7 6 | 13 8 I | 14 9 7 | 15 10 I | 16 11 8 | 17 12 I | 18 13 9 | 19 13 I | 20 14 | 21 13 I | 22 13 10 | 23 4 I | 24 3 11 | 25 3 I | 26 3 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_22854.4_Instance_1 IL_22854.4,IL_5J7L_386,G1666_C1994 | G | G | A | A | C | U | A | G | G | C | U | G | U | C | ||||||||||||||||||||||
| IL_22854.4_Sequence_1 IL_22854.45J7L_G_1666_C_1994 | G | G | A | A | C | U | A | G | G | * | C | U | G | U | C | true | 94 | 0 | 0 | 1.30 | ||||||||||||||||
| IL_22854.4_Instance_2 IL_22854.4,IL_4WF9_117,G1710_C2021 | G | G | A | A | C | U | C | G | G | C | U | G | U | C | ||||||||||||||||||||||
| IL_22854.4_Sequence_2 IL_22854.44WF9_G_1710_C_2021 | G | G | A | A | C | U | C | G | G | * | C | U | G | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_22854.4_Instance_3 IL_22854.4,IL_9DFE_066,G1666_C1994 | G | G | A | A | C | U | C | U | G | C | U | G | U | C | ||||||||||||||||||||||
| IL_22854.4_Sequence_3 IL_22854.49DFE_G_1666_C_1994 | G | G | A | A | C | U | C | U | G | * | C | U | G | U | C | true | 96 | 0 | 0 | 0.79 | ||||||||||||||||
| IL_22854.4_Instance_4 IL_22854.4,IL_4V9F_111,G1744_C2035 | G | G | A | A | U | U | C | G | G | C | U | G | U | C | ||||||||||||||||||||||
| IL_22854.4_Sequence_4 IL_22854.44V9F_G_1744_C_2035 | G | G | A | A | U | U | C | G | G | * | C | U | G | U | C | true | 93 | 0 | 0 | 1.34 | ||||||||||||||||
| IL_22854.4_Instance_5 IL_22854.4,IL_7A0S_109,G1683_C1977 | G | G | A | A | C | U | U | U | G | C | U | G | U | C | ||||||||||||||||||||||
| IL_22854.4_Sequence_5 IL_22854.47A0S_G_1683_C_1977 | G | G | A | A | C | U | U | U | G | * | C | U | G | U | C | true | 90 | 0 | 0 | 2.09 | ||||||||||||||||
| IL_22854.4_Instance_6 IL_22854.4,IL_8CRE_082,G1894_C2315 | G | G | A | A | G | U | C | G | G | C | U | G | U | C | ||||||||||||||||||||||
| IL_22854.4_Sequence_6 IL_22854.48CRE_G_1894_C_2315 | G | G | A | A | G | U | C | G | G | * | C | U | G | U | C | true | 97 | 0 | 0 | 0.68 | ||||||||||||||||
| IL_22854.4_Instance_7 IL_22854.4,IL_8P9A_305,G1898_C2337 | G | G | A | A | G | U | C | G | G | C | U | G | U | C | ||||||||||||||||||||||
| IL_22854.4_Sequence_7 IL_22854.48P9A_G_1898_C_2337 | G | G | A | A | G | U | C | G | G | * | C | U | G | U | C | true | 97 | 0 | 0 | 0.68 |
1 2 s35 1 4 s35 1 14 cWW 2 11 s33 2 13 tSH 3 5 perp 3 9 s35 3 11 tHW 3 13 s55 4 13 cWW 4 14 s55 5 6 s35 5 13 perp 7 8 s35 9 10 cWW 10 11 s35 12 14 s53 13 14 s35 5 4 7BPh 6 5 7BPh 6 9 6BPh 2 12 6BPh 14 12 7BRJAR3D SCFG/MRF model for IL_22854.4:
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 [0.0000244705618206] | Pair Probability [[0.004570114,0.047589562,0.005204141,0.094523114,0.000000000],[0.008027530,0.022407281,0.095324053,0.006237038,0.000000000],[0.005146346,0.555894766,0.000980948,0.012566650,0.000000000],[0.093313400,0.032367215,0.011015235,0.004832607,0.000000000],[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 [14] // Basepair G1666 - C1994 cWW ClusterNode | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [3] | Num Right Bases [3] | Left Index [2] | Right Index [13] | Norm Constant [0.275811635852425] // Cluster node 5J7L|1|DA|G|1667:5J7L|1|DA|A|1669 and 5J7L|1|DA|U|1991:5J7L|1|DA|U|1993 Interaction | Interacting Bases [2,4] | Pair Probability [[0.017898242,0.039832166,0.003960910,0.461511524,0.000000000],[0.003960910,0.319173624,0.009494562,0.003960910,0.000000000],[0.018590254,0.003960910,0.030122383,0.022980723,0.000000000],[0.003960910,0.003960910,0.017616762,0.039014302,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1668 - 5J7L|1|DA|U|1991 tHW Interaction | Interacting Bases [1,6] | Pair Probability [[0.013077402,0.016509270,0.000599176,0.003636415,0.000000000],[0.007585540,0.007458860,0.000599176,0.000599176,0.000000000],[0.355990514,0.004194232,0.030052293,0.484843713,0.000000000],[0.049742739,0.023913142,0.000599176,0.000599176,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|1667 - 5J7L|1|DA|U|1993 tSH Interaction | Interacting Bases [3,6] | Pair Probability [[0.008849144,0.020982013,0.009451078,0.259997638,0.000000000],[0.016699564,0.009132583,0.185092798,0.009874781,0.000000000],[0.009432681,0.187492341,0.001945771,0.050727154,0.000000000],[0.186863639,0.010512826,0.021937258,0.011008732,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1669 - 5J7L|1|DA|U|1993 cWW Interaction | Interacting Bases [5,5] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.833333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 5J7L|1|DA|G|1992 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 [5] | Right Index [10] // Initial node 5J7L|1|DA|C|1670 - 5J7L|1|DA|C|1990 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.009803922,0.558823529,0.284313725,0.147058824,0.000000000] | Position [1] | Left Index [5] | Right Index [10] // Fixed node on left for 5J7L|1|DA|C|1670 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 [1.000000000] | 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 [0.001449275,0.001449275,0.001449275,0.995652174,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left for 5J7L|1|DA|U|1671 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.611111111,0.055555556,0.166666667,0.000000000] | Position [1] | Left Index [7] | Right Index [10] // Fixed node on left for 5J7L|1|DA|A|1672 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.611111111,0.277777778,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 5J7L|1|DA|G|1673 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009278847,0.019324516,0.010566130,0.191913241,0.000000000],[0.016298546,0.009098841,0.193539411,0.012663253,0.000000000],[0.010448787,0.264585590,0.001991650,0.025514464,0.000000000],[0.189457119,0.013143234,0.022364576,0.009811793,0.000000000],[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 [9] | Right Index [10] // Basepair G1674 - C1990 cWW HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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_22854.4:
> IL_22854.4 5J7L G 1666 C 1994 GGAACUAGG*CUGUC > IL_22854.4 4WF9 G 1710 C 2021 GGAACUCGG*CUGUC > IL_22854.4 9DFE G 1666 C 1994 GGAACUCUG*CUGUC > IL_22854.4 4V9F G 1744 C 2035 GGAAUUCGG*CUGUC > IL_22854.4 7A0S G 1683 C 1977 GGAACUUUG*CUGUC > IL_22854.4 8CRE G 1894 C 2315 GGAAGUCGG*CUGUC > IL_22854.4 8P9A G 1898 C 2337 GGAAGUCGG*CUGUC