| 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 3 I | 10 4 5 | 11 5 I | 12 6 | 13 5 I | 14 4 6 | 15 4 I | 16 4 7 | 17 4 I | 18 4 8 | 19 4 I | 20 4 9 | 21 3 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_70237.3_Instance_1 IL_70237.3_IL_1S72_102_U33_A47 | U | A | C | C | C | G | A | A | C | A | ||||||||||||||||||
| IL_70237.3_Sequence_1 IL_70237.3_IL_1S72_102_U33_A47 | U | A | C | C | C | * | G | A | A | C | A | true | 92 | 0 | 0 | 1.04 | ||||||||||||
| IL_70237.3_Instance_2 IL_70237.3_IL_3V2F_110_U34_A48 | U | U | C | C | C | G | A | A | C | A | ||||||||||||||||||
| IL_70237.3_Sequence_2 IL_70237.3_IL_3V2F_110_U34_A48 | U | U | C | C | C | * | G | A | A | C | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_70237.3_Instance_3 IL_70237.3_IL_4A1C_007_A32_U45 | A | U | C | C | C | G | A | A | C | U | ||||||||||||||||||
| IL_70237.3_Sequence_3 IL_70237.3_IL_4A1C_007_A32_U45 | A | U | C | C | C | * | G | A | A | C | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_70237.3_Instance_4 IL_70237.3_IL_1MJI_002_A34_U48 | A | C | C | C | C | G | A | A | C | U | ||||||||||||||||||
| IL_70237.3_Sequence_4 IL_70237.3_IL_1MJI_002_A34_U48 | A | C | C | C | C | * | G | A | A | C | U | true | 97 | 0 | 0 | 0.39 | ||||||||||||
| IL_70237.3_Instance_5 IL_70237.3_IL_3U5H_147_U32_A45 | U | U | C | C | C | G | A | U | C | A | ||||||||||||||||||
| IL_70237.3_Sequence_5 IL_70237.3_IL_3U5H_147_U32_A45 | U | U | C | C | C | * | G | A | U | C | A | true | 89 | 0 | 0 | 1.53 | ||||||||||||
| IL_70237.3_Instance_6 IL_70237.3_IL_2QBG_004_A34_U48 | A | C | C | C | C | G | A | A | C | U | ||||||||||||||||||
| IL_70237.3_Sequence_6 IL_70237.3_IL_2QBG_004_A34_U48 | A | C | C | C | C | * | G | A | A | C | U | true | 97 | 0 | 0 | 0.39 |
1 6 s33 1 10 cWW 2 3 s35 4 5 s35 4 10 cWS 5 6 cWW 6 9 tSW 6 10 s35 7 8 s35 8 9 s35 9 10 s35 2 1 7BR 8 6 7BRJAR3D SCFG/MRF model for IL_70237.3:
Character Definition | A,C,G,U,* // Define characters here InitialNode | 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 [1] | Right Index [10] // Initial node U33 - A47 from junction ClusterNode | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [1] | Right Index [10] | Norm Constant [0.251650942015211] // Cluster node U33:C36 and A47:A47 Interaction | Interacting Bases [1,5] | Pair Probability [[0.008836923,0.021444779,0.009444062,0.231391450,0.000000000],[0.021450321,0.009062771,0.185760612,0.009937356,0.000000000],[0.009444083,0.185759190,0.002069769,0.024746647,0.000000000],[0.231401709,0.009937264,0.024751992,0.014561070,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U33 - A47 cWW Interaction | Interacting Bases [4,5] | Pair Probability [[0.011432356,0.021811391,0.011494353,0.016673006,0.000000000],[0.228765464,0.193675299,0.188597845,0.228798602,0.000000000],[0.014037200,0.009841650,0.018209719,0.008628830,0.000000000],[0.013451764,0.014992714,0.009651048,0.009938760,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C36 - A47 cWS Interaction | Interacting Bases [2,2] | Pair Probability [[0.171875000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.328125000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.484375000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A34 Interaction | Interacting Bases [3,3] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.812500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion C35 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 [9] // New Initial node after Cluster ClusterNode | Deletion Probability [0.0000000000031250] | Num Left Bases [1] | Num Right Bases [4] | Left Index [5] | Right Index [9] | Norm Constant [0.257704817211151] // Cluster node C37:C37 and G43:C46 Interaction | Interacting Bases [1,2] | Pair Probability [[0.009652285,0.016556223,0.011218237,0.185136336,0.000000000],[0.019989741,0.008244143,0.263484907,0.013400077,0.000000000],[0.011361251,0.200559255,0.002068811,0.022890146,0.000000000],[0.186211624,0.012765515,0.026535995,0.009925452,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C37 - G43 cWW Interaction | Interacting Bases [2,5] | Pair Probability [[0.193309940,0.027745336,0.002379316,0.076728268,0.000000000],[0.055696564,0.025093188,0.025457850,0.017196014,0.000000000],[0.064841819,0.294535384,0.002379316,0.010117074,0.000000000],[0.022532745,0.014381501,0.157640183,0.009965502,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G43 - C46 tSW Interaction | Interacting Bases [3,3] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A44 Interaction | Interacting Bases [4,4] | Pair Probability [[0.796875000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.015625000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.171875000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A45 InitialNode | 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 [6] | Right Index [5] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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_70237.3:
> IL_70237.3 IL_1S72_102 U 33 A 47 UACCC*GAACA > IL_70237.3 IL_3V2F_110 U 34 A 48 UUCCC*GAACA > IL_70237.3 IL_4A1C_007 A 32 U 45 AUCCC*GAACU > IL_70237.3 IL_1MJI_002 A 34 U 48 ACCCC*GAACU > IL_70237.3 IL_3U5H_147 U 32 A 45 UUCCC*GAUCA > IL_70237.3 IL_2QBG_004 A 34 U 48 ACCCC*GAACU