| 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 6 I | 18 7 9 | 19 7 I | 20 8 | 21 7 I | 22 7 10 | 23 6 I | 24 5 11 | 25 5 I | 26 5 12 | 27 4 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_82426.6_Instance_1 IL_82426.6,IL_8K85_003,A40_U14 | A | G | U | A | G | U | G | U | G | U | G | C | G | G | G | U | ||||||||||||||||||||
| IL_82426.6_Sequence_1 IL_82426.68K85_A40_U14 | A | G | U | A | G | U | G | U | G | U | G | * | C | G | G | G | U | true | 97 | 0 | 0 | 0.59 | ||||||||||||||
| IL_82426.6_Instance_2 IL_82426.6,IL_4TS2_006,A64_U32 | A | G | U | A | G | A | G | U | G | U | G | C | G | G | G | U | ||||||||||||||||||||
| IL_82426.6_Sequence_2 IL_82426.64TS2_A64_U32 | A | G | U | A | G | A | G | U | G | U | G | * | C | G | G | G | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_82426.6_Instance_3 IL_82426.6,IL_8K85_010,A40_U14 | A | G | U | A | G | U | G | U | G | U | G | C | G | G | G | U | ||||||||||||||||||||
| IL_82426.6_Sequence_3 IL_82426.68K85_A40_U14 | A | G | U | A | G | U | G | U | G | U | G | * | C | G | G | G | U | true | 97 | 0 | 0 | 0.59 | ||||||||||||||
| IL_82426.6_Instance_4 IL_82426.6,IL_7L0Z_003,A45_U22 | A | G | U | A | G | A | G | U | G | U | G | C | G | G | G | U | ||||||||||||||||||||
| IL_82426.6_Sequence_4 IL_82426.67L0Z_A45_U22 | A | G | U | A | G | A | G | U | G | U | G | * | C | G | G | G | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_82426.6_Instance_5 IL_82426.6,IL_8K7W_003,A34_U13 | A | G | U | A | G | A | G | U | G | U | G | C | G | G | G | U | ||||||||||||||||||||
| IL_82426.6_Sequence_5 IL_82426.68K7W_A34_U13 | A | G | U | A | G | A | G | U | G | U | G | * | C | G | G | G | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_82426.6_Instance_6 IL_82426.6,IL_4KZD_005,A53_U29 | A | G | U | A | G | A | G | U | G | U | G | C | G | G | G | U | ||||||||||||||||||||
| IL_82426.6_Sequence_6 IL_82426.64KZD_A53_U29 | A | G | U | A | G | A | G | U | G | U | G | * | C | G | G | G | U | true | 100 | 0 | 0 | 0.00 |
1 14 cWW 2 4 s53 2 6 cHW 3 4 s55 3 8 tSW 4 6 s35 4 7 cHW 4 8 s55 6 7 s53 6 12 cHW 6 13 s35 7 9 s55 7 11 cHW 7 12 s35 9 10 cWW 9 11 s55 10 11 s35 11 12 s35 12 13 s35 13 14 s35 8 4 7BPh 6 5 2BR 7 6 2BRJAR3D SCFG/MRF model for IL_82426.6:
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 [[0.008932627,0.021179957,0.009540239,0.253016483,0.000000000],[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 [14] // 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 [13] // Fixed node on right for 8K85|1|B|U|47 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 [12] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000000000048406024103125380564744386755250783] | Num Left Bases [7] | Num Right Bases [2] | Left Index [2] | Right Index [12] | Norm Constant [0.674377293971866] // Cluster node 8K85|1|B|G|41:8K85|1|B|U|49 and 8K85|1|A|G|11:8K85|1|A|G|12 Interaction | Interacting Bases [6,8] | 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 [5,9] | 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 [[0.001219366,0.001219366,0.253505381,0.004214401,0.000000000],[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|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 [[0.002332550,0.002013893,0.000416865,0.279756455,0.000000000],[0.002034867,0.002502804,0.000416865,0.234759185,0.000000000],[0.002001813,0.000416865,0.000416865,0.014389233,0.000000000],[0.001943364,0.004870140,0.017555964,0.434172274,0.000000000],[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 [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 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 [9] | Right Index [10] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | 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]] | 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 G50 - C10 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_82426.6:
> IL_82426.6 8K85 A 40 U 14 AGUAGUGUGUG*CGGGU > IL_82426.6 4TS2 A 64 U 32 AGUAGAGUGUG*CGGGU > IL_82426.6 8K85 A 40 U 14 AGUAGUGUGUG*CGGGU > IL_82426.6 7L0Z A 45 U 22 AGUAGAGUGUG*CGGGU > IL_82426.6 8K7W A 34 U 13 AGUAGAGUGUG*CGGGU > IL_82426.6 4KZD A 53 U 29 AGUAGAGUGUG*CGGGU