| 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 3 I | 6 4 3 | 7 4 I | 8 4 4 | 9 4 I | 10 4 5 | 11 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 5 I | 16 6 8 | 17 7 I | 18 8 9 | 19 9 I | 20 10 10 | 21 10 I | 22 11 | 23 10 I | 24 10 11 | 25 5 I | 26 4 12 | 27 3 I | 28 2 13 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_96303.1_Instance_1 IL_96303.1,IL_8HBA_004,G6_C32 | G | U | U | GCG | U | C | C | G | A | A | A | G | C | A | C | |||||||||||||||||||
| IL_96303.1_Sequence_1 IL_96303.18HBA_G6_C32 | G | U | U | GCG | U | C | C | G | A | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_96303.1_Instance_2 IL_96303.1,IL_8I3Z_002,G6_C32 | G | U | U | GCG | U | C | C | G | A | A | A | G | C | A | C | |||||||||||||||||||
| IL_96303.1_Sequence_2 IL_96303.18I3Z_G6_C32 | G | U | U | GCG | U | C | C | G | A | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_96303.1_Instance_3 IL_96303.1,IL_8GXB_002,G6_C40 | G | U | U | ACG | U | C | C | G | A | A | A | G | C | A | C | |||||||||||||||||||
| IL_96303.1_Sequence_3 IL_96303.18GXB_G6_C40 | G | U | U | ACG | U | C | C | G | A | A | A | G | * | C | A | C | true | 94 | 0 | 0 | 1.30 |
1 2 cSH 1 7 s33 1 13 cWW 2 3 s35 3 7 tHW 4 5 s35 5 6 s35 6 7 s35 6 8 perp 7 12 tSW 8 9 s35 9 10 s35 10 11 cWW 12 13 s35 2 1 7BRJAR3D SCFG/MRF model for IL_96303.1:
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 [13] // Initial node ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [13] | Norm Constant [0.251053096726546] // Cluster node 8HBA|1|B|G|6:8HBA|1|B|U|7 and 8HBA|1|B|C|32:8HBA|1|B|C|32 Interaction | Interacting Bases [1,3] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8HBA|1|B|G|6 - 8HBA|1|B|C|32 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.078527006,0.080015416,0.004399495,0.078197963,0.000000000],[0.058625540,0.088349717,0.000974123,0.078361895,0.000000000],[0.068609208,0.000974123,0.083691539,0.126538511,0.000000000],[0.079745425,0.079266702,0.000974123,0.092749213,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8HBA|1|B|G|6 - 8HBA|1|B|U|7 cSH InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // Initial node 8HBA|1|B|U|8 - 8HBA|1|B|A|31 from node ClusterNode | Deletion Probability [0.000000000000000000001936518681344305608638723392518587066677] | Num Left Bases [5] | Num Right Bases [1] | Left Index [3] | Right Index [12] | Norm Constant [0.273844023924617] // Cluster node 8HBA|1|B|U|8:8HBA|1|B|G|15 and 8HBA|1|B|A|31:8HBA|1|B|A|31 Interaction | Interacting Bases [5,6] | Pair Probability [[0.163352215,0.162569599,0.002030346,0.009817578,0.000000000],[0.189995469,0.008952434,0.002030346,0.008117296,0.000000000],[0.232160826,0.002030346,0.002030346,0.006658188,0.000000000],[0.175705789,0.008823801,0.015975555,0.009749864,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8HBA|1|B|G|15 - 8HBA|1|B|A|31 tSW Interaction | Interacting Bases [1,5] | Pair Probability [[0.043222547,0.037222380,0.004038099,0.017960075,0.000000000],[0.004038099,0.019018019,0.007058475,0.004038099,0.000000000],[0.323955368,0.004038099,0.040666371,0.015639489,0.000000000],[0.004038099,0.004038099,0.432936133,0.038092549,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8HBA|1|B|U|8 - 8HBA|1|B|G|15 tHW Interaction | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8HBA|1|B|U|12 Interaction | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8HBA|1|B|C|13 Interaction | Interacting Bases [4,4] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8HBA|1|B|C|14 Insertion | Location [1] | Length Distribution [0.000000000,0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.136363636,0.318181818,0.500000000,0.045454545,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node InitialNode | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [11] // Initial node 8HBA|1|B|A|17 - 8HBA|1|B|C|30 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [8] | Right Index [11] // Fixed node on left for 8HBA|1|B|C|13 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [9] | Right Index [11] // Fixed node on left for 8HBA|1|B|C|14 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [10] | Right Index [11] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[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 [10] | Right Index [11] // Basepair G19 - C30 cWW HairpinNode | Num Bases [1] | Left Index [11] | Right Index [11] | 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_96303.1:
> IL_96303.1 8HBA G 6 C 32 GUUGCGUCCGAAAG*CAC > IL_96303.1 8I3Z G 6 C 32 GUUGCGUCCGAAAG*CAC > IL_96303.1 8GXB G 6 C 40 GUUACGUCCGAAAG*CAC