| 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 5 I | 8 6 4 | 9 7 I | 10 8 5 | 11 9 I | 12 10 6 | 13 11 I | 14 12 7 | 15 13 I | 16 14 8 | 17 15 I | 18 16 9 | 19 17 I | 20 18 10 | 21 19 I | 22 20 11 | 23 21 I | 24 22 12 | 25 23 I | 26 24 13 | 27 25 I | 28 26 14 | 29 27 I | 30 32 15 | 31 32 I | 32 33 | 33 32 I | 34 32 16 | 35 31 I | 36 30 17 | 37 29 I | 38 28 18 | 39 3 I | 40 2 19 | 41 2 I | 42 2 20 | 43 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_34739.3_Instance_1 IL_34739.3,IL_4N0T_002,G39_C92 | G | A | A | A | C | A | A | U | A | C | A | G | A | G | A | UG | A | UC | A | U | U | U | A | C | ||||||||||||||||||||||||
| IL_34739.3_Sequence_1 IL_34739.34N0T_G39_C92 | G | A | A | A | C | A | A | U | A | C | A | G | A | G | A | UG | A | UC | A | * | U | U | U | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||
| IL_34739.3_Instance_2 IL_34739.3,IL_6ASO_001,G39_C92 | G | A | A | A | C | A | A | U | A | C | A | G | A | G | A | UG | A | UC | A | U | U | U | A | C | ||||||||||||||||||||||||
| IL_34739.3_Sequence_2 IL_34739.36ASO_G39_C92 | G | A | A | A | C | A | A | U | A | C | A | G | A | G | A | UG | A | UC | A | * | U | U | U | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||
| IL_34739.3_Instance_3 IL_34739.3,IL_5VSU_001,G39_C92 | G | A | A | A | C | A | A | U | A | C | A | G | A | G | A | UG | A | UC | A | U | U | U | A | C | ||||||||||||||||||||||||
| IL_34739.3_Sequence_3 IL_34739.35VSU_G39_C92 | G | A | A | A | C | A | A | U | A | C | A | G | A | G | A | UG | A | UC | A | * | U | U | U | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s33 1 20 cWW 2 3 s53 2 19 tWW 2 20 tWW 4 5 s35 7 8 s35 8 9 s35 10 12 s53 11 13 s55 14 15 s55 14 16 s53 14 17 s35 15 16 cWW 17 18 s35 19 20 s35 9 8 7BPhJAR3D SCFG/MRF model for IL_34739.3:
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 [20] // Initial node ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [1] | Right Index [20] | Norm Constant [0.102960781865258] // Cluster node 4N0T|1|B|G|39:4N0T|1|B|A|40 and 4N0T|1|B|A|91:4N0T|1|B|C|92 Interaction | Interacting Bases [2,3] | Pair Probability [[0.414443196,0.029718936,0.003853170,0.018419488,0.000000000],[0.028948610,0.014046437,0.011475468,0.014056646,0.000000000],[0.003853170,0.011491976,0.356313449,0.021716090,0.000000000],[0.018397520,0.014053216,0.021246137,0.017966491,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4N0T|1|B|A|40 - 4N0T|1|B|A|91 tWW Interaction | Interacting Bases [1,4] | 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 4N0T|1|B|G|39 - 4N0T|1|B|C|92 cWW Interaction | Interacting Bases [2,4] | Pair Probability [[0.027592739,0.433108352,0.003577501,0.042260225,0.000000000],[0.016009541,0.015725019,0.010497055,0.015889125,0.000000000],[0.003577501,0.013947311,0.020907921,0.328397734,0.000000000],[0.016793903,0.015291395,0.016168069,0.020256609,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4N0T|1|B|A|40 - 4N0T|1|B|C|92 tWW 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 [18] // Initial node 4N0T|1|B|A|41 - 4N0T|1|B|U|90 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|41 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|42 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 [5] | Right Index [18] // 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 [5] | Right Index [18] // Fixed node on left for 4N0T|1|B|C|43 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 [6] | Right Index [18] // 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 [6] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|44 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 [7] | Right Index [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [1] | Left Index [7] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|45 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 [8] | Right Index [18] // 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 [8] | Right Index [18] // Fixed node on left for 4N0T|1|B|U|46 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 [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.021739130,0.934782609,0.021739130,0.021739130,0.000000000] | Position [1] | Left Index [9] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|47 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [10] | Right Index [18] // Fixed node on left for 4N0T|1|B|C|48 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 [11] | Right Index [18] // 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 [11] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|49 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 [12] | Right Index [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [12] | Right Index [18] // Fixed node on left for 4N0T|1|B|G|50 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 [13] | Right Index [18] // 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 [13] | Right Index [18] // Fixed node on left for 4N0T|1|B|A|51 InitialNode | Left Length Distribution [0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.062500000,0.062500000,0.437500000,0.437500000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [14] | Right Index [18] // 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 [14] | Right Index [18] // Fixed node on left for 4N0T|1|B|G|52 InitialNode | Left Length Distribution [0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.062500000,0.437500000,0.062500000,0.437500000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [15] | Right Index [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [2] | Left Index [15] | Right Index [18] // Fixed node on right for 4N0T|1|B|A|56 InitialNode | Left Length Distribution [1.000000000] | 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 [15] | Right Index [17] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Position [2] | Left Index [15] | Right Index [17] // Fixed node on right for 4N0T|1|B|G|55 InitialNode | Left Length Distribution [1.000000000] | 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 [15] | Right Index [16] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009192800,0.021796849,0.009818110,0.231259682,0.000000000],[0.017348091,0.009487247,0.192280868,0.010258268,0.000000000],[0.009798999,0.194773596,0.002021335,0.052697140,0.000000000],[0.194120479,0.010921091,0.022789191,0.011436255,0.000000000],[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 [15] | Right Index [16] // Basepair A59 - U88 cWW HairpinNode | Num Bases [1] | Left Index [16] | Right Index [16] | 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_34739.3:
> IL_34739.3 4N0T G 39 C 92 GAAACAAUACAGAGAUGAUCA*UUUAC > IL_34739.3 6ASO G 39 C 92 GAAACAAUACAGAGAUGAUCA*UUUAC > IL_34739.3 5VSU G 39 C 92 GAAACAAUACAGAGAUGAUCA*UUUAC