| 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 5 I | 12 6 6 | 13 6 I | 14 7 | 15 6 I | 16 6 7 | 17 5 I | 18 5 8 | 19 4 I | 20 3 9 | 21 2 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_77263.2_Instance_1 IL_77263.2_IL_3SIU_001_C33_G50 | C | A | A | U | G | A | G | U | G | A | G | |||||||||||||||||
| IL_77263.2_Sequence_1 IL_77263.2_IL_3SIU_001_C33_G50 | C | A | A | U | G | A | G | * | U | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_77263.2_Instance_2 IL_77263.2_IL_2OZB_002_C28_G45 | C | A | A | U | G | A | G | C | G | A | G | |||||||||||||||||
| IL_77263.2_Sequence_2 IL_77263.2_IL_2OZB_002_C28_G45 | C | A | A | U | G | A | G | * | C | G | A | G | true | 98 | 0 | 0 | 0.31 | |||||||||||
| IL_77263.2_Instance_3 IL_77263.2_IL_3SIV_003_C33_G50 | C | A | A | U | G | A | G | U | G | A | G | |||||||||||||||||
| IL_77263.2_Sequence_3 IL_77263.2_IL_3SIV_003_C33_G50 | C | A | A | U | G | A | G | * | U | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_77263.2_Instance_4 IL_77263.2_IL_3SIV_001_C33_G50 | C | A | A | U | G | A | G | U | G | A | G | |||||||||||||||||
| IL_77263.2_Sequence_4 IL_77263.2_IL_3SIV_001_C33_G50 | C | A | A | U | G | A | G | * | U | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_77263.2_Instance_5 IL_77263.2_IL_1E7K_002_C28_G45 | C | A | A | U | G | A | G | C | G | A | G | |||||||||||||||||
| IL_77263.2_Sequence_5 IL_77263.2_IL_1E7K_002_C28_G45 | C | A | A | U | G | A | G | * | C | G | A | G | true | 98 | 0 | 0 | 0.31 | |||||||||||
| IL_77263.2_Instance_6 IL_77263.2_IL_4LCK_001_C6_G97 | C | G | A | U | G | A | G | C | G | A | G | |||||||||||||||||
| IL_77263.2_Sequence_6 IL_77263.2_IL_4LCK_001_C6_G97 | C | G | A | U | G | A | G | * | C | G | A | G | true | 90 | 0 | 0 | 1.54 |
1 2 s35 1 10 cWW 2 9 tSS 2 10 s55 3 4 s35 3 9 s33 4 8 s33 4 9 tSH 5 6 s35 5 8 tHS 5 9 s55 6 7 cWW 6 8 s55 7 8 s35 9 10 perp 8 4 6BR 9 4 6BR 10 5 2BR 4 8 6BR 5 8 6BR 3 9 6BRJAR3D SCFG/MRF model for IL_77263.2:
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 C33 - G50 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004717578,0.008091894,0.027414702,0.090485831,0.000000000],[0.009770034,0.004029345,0.562172037,0.006549320,0.000000000],[0.005552839,0.098023820,0.005055683,0.011187614,0.000000000],[0.091011380,0.006239176,0.064847658,0.004851089,0.000000000],[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 [10] // Basepair C33 - G50 cWW ClusterNode | Deletion Probability [0.0000000000031115] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [9] | Norm Constant [0.416274113910334] // Cluster node A34:G37 and A49:A49 Interaction | Interacting Bases [1,4] | Pair Probability [[0.528849073,0.083541625,0.076461802,0.077107477,0.000000000],[0.005827225,0.001165445,0.001165445,0.001165445,0.000000000],[0.153166296,0.026129033,0.026624910,0.009472662,0.000000000],[0.005827225,0.001165445,0.001165445,0.001165445,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A34 - A49 tSS Interaction | Interacting Bases [3,4] | Pair Probability [[0.071085104,0.082858788,0.000856485,0.004078472,0.000000000],[0.071717548,0.075170449,0.000856485,0.000856485,0.000000000],[0.311861171,0.002552574,0.012366685,0.212322902,0.000000000],[0.077266991,0.074436891,0.000856485,0.000856485,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G37 - A49 tSH Interaction | Interacting Bases [2,2] | Pair Probability [[0.953125000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.015625000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.015625000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A35 Insertion | Location [2] | 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 3, position 2 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 [5] | Right Index [8] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.052788444,0.053258103,0.374620487,0.057379170,0.000000000],[0.061531689,0.055822259,0.003180167,0.055277512,0.000000000],[0.000636033,0.000636033,0.015407242,0.000636033,0.000000000],[0.003028710,0.000636033,0.264526051,0.000636033,0.000000000],[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 [5] | Right Index [8] // Basepair A38 - G48 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.012844072,0.159282715,0.013171233,0.114580161,0.000000000],[0.015240908,0.009601556,0.118644620,0.013806282,0.000000000],[0.012933937,0.153035139,0.002695858,0.207733360,0.000000000],[0.110794989,0.014924503,0.018737671,0.021972996,0.000000000],[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 [6] | Right Index [7] // Basepair G39 - U47 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | 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_77263.2:
> IL_77263.2 IL_3SIU_001 C 33 G 50 CAAUGAG*UGAG > IL_77263.2 IL_2OZB_002 C 28 G 45 CAAUGAG*CGAG > IL_77263.2 IL_3SIV_003 C 33 G 50 CAAUGAG*UGAG > IL_77263.2 IL_3SIV_001 C 33 G 50 CAAUGAG*UGAG > IL_77263.2 IL_1E7K_002 C 28 G 45 CAAUGAG*CGAG > IL_77263.2 IL_4LCK_001 C 6 G 97 CGAUGAG*CGAG