| 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 5 2 | 5 5 I | 6 5 3 | 7 5 I | 8 5 4 | 9 5 I | 10 5 5 | 11 5 I | 12 5 6 | 13 5 I | 14 5 7 | 15 5 I | 16 5 8 | 17 5 I | 18 5 9 | 19 6 I | 20 7 10 | 21 7 I | 22 8 11 | 23 8 I | 24 9 12 | 25 9 I | 26 10 | 27 9 I | 28 9 13 | 29 8 I | 30 8 14 | 31 7 I | 32 7 15 | 33 6 I | 34 5 16 | 35 5 I | 36 5 17 | 37 5 I | 38 5 18 | 39 5 I | 40 5 19 | 41 5 I | 42 5 20 | 43 4 I | 44 3 21 | 45 2 I | 46 2 22 | 47 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_64858.3_Instance_1 IL_64858.3,IL_8K85_002,A40_U14 | A | G | U | A | G | U | G | U | G | U | G | G | G | C | G | A | C | G | G | U | C | G | G | G | U | |||||||||||||||||||||||||||
| IL_64858.3_Sequence_1 IL_64858.38K85_A40_U14 | A | G | U | A | G | U | G | U | G | U | G | G | G | C | * | G | A | C | G | G | U | C | G | G | G | U | true | 98 | 0 | 0 | 0.59 | |||||||||||||||||||||
| IL_64858.3_Instance_2 IL_64858.3,IL_8K85_011,A40_U14 | A | G | U | A | G | U | G | U | G | U | G | G | G | C | G | A | C | G | G | U | C | G | G | G | U | |||||||||||||||||||||||||||
| IL_64858.3_Sequence_2 IL_64858.38K85_A40_U14 | A | G | U | A | G | U | G | U | G | U | G | G | G | C | * | G | A | C | G | G | U | C | G | G | G | U | true | 98 | 0 | 0 | 0.59 | |||||||||||||||||||||
| IL_64858.3_Instance_3 IL_64858.3,IL_8K7W_002,A34_U13 | A | G | U | A | G | A | G | U | G | U | G | G | G | C | G | A | C | G | G | U | C | G | G | G | U | |||||||||||||||||||||||||||
| IL_64858.3_Sequence_3 IL_64858.38K7W_A34_U13 | A | G | U | A | G | A | G | U | G | U | G | G | G | C | * | G | A | C | G | G | U | C | G | G | G | U | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||||
| IL_64858.3_Instance_4 IL_64858.3,IL_4TS2_010,A64_U32 | A | G | U | A | G | A | G | U | G | U | G | A | G | C | G | A | A | G | G | A | C | G | G | G | U | |||||||||||||||||||||||||||
| IL_64858.3_Sequence_4 IL_64858.34TS2_A64_U32 | A | G | U | A | G | A | G | U | G | U | G | A | G | C | * | G | A | A | G | G | A | C | G | G | G | U | true | 99 | 0 | 0 | 0.13 | |||||||||||||||||||||
| IL_64858.3_Instance_5 IL_64858.3,IL_7L0Z_005,A45_U22 | A | G | U | A | G | A | G | U | G | U | G | G | G | C | G | A | G | G | G | U | C | G | G | G | U | |||||||||||||||||||||||||||
| IL_64858.3_Sequence_5 IL_64858.37L0Z_A45_U22 | A | G | U | A | G | A | G | U | G | U | G | G | G | C | * | G | A | G | G | G | U | C | G | G | G | U | true | 94 | 0 | 0 | 1.61 | |||||||||||||||||||||
| IL_64858.3_Instance_6 IL_64858.3,IL_4KZD_007,A53_U29 | A | G | U | A | G | A | G | U | G | U | G | A | G | C | G | A | A | G | G | A | C | G | G | G | U | |||||||||||||||||||||||||||
| IL_64858.3_Sequence_6 IL_64858.34KZD_A53_U29 | A | G | U | A | G | A | G | U | G | U | G | A | G | C | * | G | A | A | G | G | A | C | G | G | G | U | true | 99 | 0 | 0 | 0.13 |
1 22 cWW 2 4 s53 2 6 cHW 2 16 s53 2 17 cWH 3 4 s55 3 8 tSW 3 15 s33 3 16 s55 4 6 s35 4 7 cHW 4 8 s55 4 16 cWH 6 7 s53 6 20 cHW 6 21 s35 7 9 s55 7 19 cHW 7 20 s35 9 10 s35 9 18 cWW 9 19 s55 10 11 s35 10 15 cWW 10 18 s55 11 12 s35 11 14 cWW 12 13 cWW 13 14 s35 14 15 s35 16 17 s35 16 18 s53 16 19 cWH 17 19 s53 17 20 cWH 18 19 s35 19 20 s35 20 21 s35 21 22 s35 8 4 7BPh 6 5 2BR 7 6 2BR 2 16 2BR 3 16 7BRJAR3D SCFG/MRF model for IL_64858.3:
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 [22] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008932627,0.021179957,0.009540239,0.253016483,0.000000000],[0.016857107,0.009218740,0.186838956,0.009967940,0.000000000],[0.009521668,0.189261136,0.001964127,0.051205712,0.000000000],[0.188626503,0.010612004,0.022144213,0.011112588,0.000000000],[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 [22] // Basepair A40 - U14 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000] | Position [2] | Left Index [2] | Right Index [21] // Fixed node on right for 8K85|1|B|U|49 InitialNode | Left Length Distribution [1.000000000] | 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 [20] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000000000000000000000150613574911793666666304] | Num Left Bases [8] | Num Right Bases [5] | Left Index [2] | Right Index [20] | Norm Constant [0.042106869219010] // Cluster node 8K85|1|B|G|41:8K85|1|B|G|50 and 8K85|1|A|G|7:8K85|1|A|G|12 Interaction | Interacting Bases [3,9] | Pair Probability [[0.004732165,0.004732165,0.048667733,0.040090134,0.000000000],[0.004732165,0.050159009,0.004732165,0.017067191,0.000000000],[0.196762814,0.004732165,0.529820255,0.004732165,0.000000000],[0.016355421,0.004732165,0.014803301,0.053148989,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|44 - 8K85|1|A|G|7 cWH Interaction | Interacting Bases [1,10] | Pair Probability [[0.001219366,0.001219366,0.012540512,0.010330270,0.000000000],[0.001219366,0.012924778,0.001219366,0.004397807,0.000000000],[0.253505381,0.006096829,0.666286682,0.006096829,0.000000000],[0.004214401,0.001219366,0.003814457,0.013695225,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|41 - 8K85|1|A|G|8 cWH Interaction | Interacting Bases [8,11] | Pair Probability [[0.009366383,0.019506822,0.010665810,0.193723744,0.000000000],[0.016452306,0.009184679,0.195365254,0.012782718,0.000000000],[0.010547361,0.257647718,0.002010439,0.025755166,0.000000000],[0.191244451,0.013267227,0.022575563,0.009904357,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|50 - 8K85|1|A|C|10 cWW Interaction | Interacting Bases [6,12] | Pair Probability [[0.001435895,0.001435895,0.059704349,0.004962776,0.000000000],[0.001435895,0.015219903,0.001435895,0.001435895,0.000000000],[0.073837003,0.007179477,0.774551476,0.022459058,0.000000000],[0.012164673,0.005178750,0.001435895,0.016127162,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|48 - 8K85|1|A|G|11 cHW Interaction | Interacting Bases [5,13] | Pair Probability [[0.001435895,0.001435895,0.059704349,0.004962776,0.000000000],[0.001435895,0.015219903,0.001435895,0.001435895,0.000000000],[0.073837003,0.007179477,0.774551476,0.022459058,0.000000000],[0.012164673,0.005178750,0.001435895,0.016127162,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|46 - 8K85|1|A|G|12 cHW Interaction | Interacting Bases [1,5] | Pair Probability [[0.000333199,0.000333199,0.069271890,0.001151611,0.000000000],[0.000333199,0.003531774,0.001665996,0.000333199,0.000000000],[0.017133857,0.001665996,0.889601625,0.005211618,0.000000000],[0.002822809,0.001201728,0.001665996,0.003742304,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|41 - 8K85|1|B|G|46 cHW Interaction | Interacting Bases [3,6] | Pair Probability [[0.001219366,0.001219366,0.253505381,0.004214401,0.000000000],[0.001219366,0.012924778,0.006096829,0.001219366,0.000000000],[0.012540512,0.001219366,0.666286682,0.003814457,0.000000000],[0.010330270,0.004397807,0.006096829,0.013695225,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|G|44 - 8K85|1|B|G|48 cHW Interaction | Interacting Bases [2,7] | Pair Probability [[0.000942582,0.000813813,0.000168455,0.113049415,0.000000000],[0.000822289,0.001011382,0.000168455,0.094866045,0.000000000],[0.000808931,0.000168455,0.000168455,0.005814680,0.000000000],[0.003926562,0.009840102,0.035471773,0.731958608,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|B|U|42 - 8K85|1|B|U|49 tSW Interaction | Interacting Bases [9,12] | Pair Probability [[0.004732165,0.004732165,0.048667733,0.040090134,0.000000000],[0.004732165,0.050159009,0.004732165,0.017067191,0.000000000],[0.196762814,0.004732165,0.529820255,0.004732165,0.000000000],[0.016355421,0.004732165,0.014803301,0.053148989,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|A|G|7 - 8K85|1|A|G|11 cWH Interaction | Interacting Bases [10,13] | Pair Probability [[0.004732165,0.004732165,0.048667733,0.040090134,0.000000000],[0.004732165,0.050159009,0.004732165,0.017067191,0.000000000],[0.196762814,0.004732165,0.529820255,0.004732165,0.000000000],[0.016355421,0.004732165,0.014803301,0.053148989,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8K85|1|A|G|8 - 8K85|1|A|G|12 cWH Interaction | Interacting Bases [4,4] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.312500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8K85|1|B|U|45 Insertion | Location [2] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node Insertion | Location [5] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.062500000,0.062500000,0.062500000,0.812500000,0.000000000]// Insertion after nucleotide 6, position 5 in cluster node Insertion | Location [10] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.312500000,0.062500000,0.062500000,0.562500000,0.000000000]// Insertion after nucleotide 17, position 10 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 [10] | Right Index [15] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.249153714,0.021920143,0.024885446,0.124177707,0.000000000],[0.016670575,0.009303910,0.125178380,0.017438416,0.000000000],[0.020436395,0.157035067,0.031362300,0.026124160,0.000000000],[0.122430467,0.018976185,0.020925698,0.013981436,0.000000000],[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 [10] | Right Index [15] // Basepair G51 - C6 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.022071540,0.013806419,0.334911111,0.016898899,0.000000000],[0.014138398,0.009771948,0.018493445,0.043420140,0.000000000],[0.405193794,0.018288065,0.003485900,0.015053859,0.000000000],[0.016931858,0.041094913,0.015383423,0.011056290,0.000000000],[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 [11] | Right Index [14] // Basepair G52 - A5 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009176708,0.016456041,0.010549755,0.191287868,0.000000000],[0.019511251,0.009346211,0.257693361,0.013270239,0.000000000],[0.010668232,0.195409608,0.002010896,0.022580688,0.000000000],[0.193767724,0.012785620,0.025761014,0.009724784,0.000000000],[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 [12] | Right Index [13] // Basepair C53 - G4 cWW HairpinNode | Num Bases [1] | Left Index [13] | Right Index [13] | 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_64858.3:
> IL_64858.3 8K85 A 40 U 14 AGUAGUGUGUGGGC*GACGGUCGGGU > IL_64858.3 8K85 A 40 U 14 AGUAGUGUGUGGGC*GACGGUCGGGU > IL_64858.3 8K7W A 34 U 13 AGUAGAGUGUGGGC*GACGGUCGGGU > IL_64858.3 4TS2 A 64 U 32 AGUAGAGUGUGAGC*GAAGGACGGGU > IL_64858.3 7L0Z A 45 U 22 AGUAGAGUGUGGGC*GAGGGUCGGGU > IL_64858.3 4KZD A 53 U 29 AGUAGAGUGUGAGC*GAAGGACGGGU