| 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 4 I | 6 5 3 | 7 6 I | 8 7 4 | 9 8 I | 10 9 5 | 11 9 I | 12 9 6 | 13 9 I | 14 9 7 | 15 9 I | 16 9 8 | 17 10 I | 18 11 | 19 10 I | 20 9 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_24546.4_Instance_1 IL_24546.4_IL_3V2F_037_C1004_G1151 | C | C | C | C | C | A | A | G | C | G | ||||||||||||||||||
| IL_24546.4_Sequence_1 IL_24546.4_IL_3V2F_037_C_1004_G_1151 | C | C | C | C | C | A | A | G | * | C | G | true | 98 | 0 | 0 | 0.26 | ||||||||||||
| IL_24546.4_Instance_2 IL_24546.4_IL_4IOA_033_U1015_A1162 | U | C | C | C | U | A | A | A | U | A | ||||||||||||||||||
| IL_24546.4_Sequence_2 IL_24546.4_IL_4IOA_033_U_1015_A_1162 | U | C | C | C | U | A | A | A | * | U | A | true | 91 | 0 | 0 | 1.18 | ||||||||||||
| IL_24546.4_Instance_3 IL_24546.4_IL_2QBG_037_U1004_A1151 | U | C | C | C | A | A | A | G | C | A | ||||||||||||||||||
| IL_24546.4_Sequence_3 IL_24546.4_IL_2QBG_037_U_1004_A_1151 | U | C | C | C | A | A | A | G | * | C | A | true | 95 | 0 | 0 | 0.65 | ||||||||||||
| IL_24546.4_Instance_4 IL_24546.4_IL_1S72_039_U1101_A1255 | U | C | C | C | C | A | A | G | C | A | ||||||||||||||||||
| IL_24546.4_Sequence_4 IL_24546.4_IL_1S72_039_U_1101_A_1255 | U | C | C | C | C | A | A | G | * | C | A | true | 98 | 0 | 0 | 0.24 | ||||||||||||
| IL_24546.4_Instance_5 IL_24546.4_IL_4A1B_055_C1200_G1353 | C | G | C | C | C | A | A | A | U | G | ||||||||||||||||||
| IL_24546.4_Sequence_5 IL_24546.4_IL_4A1B_055_C_1200_G_1353 | C | G | C | C | C | A | A | A | * | U | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_24546.4_Instance_6 IL_24546.4_IL_2AW7_027_C504_G541 | C | G | G | C | U | A | A | C | G | G | ||||||||||||||||||
| IL_24546.4_Sequence_6 IL_24546.4_IL_2AW7_027_C504_G541 | C | G | G | C | U | A | A | C | * | G | G | true | 91 | 0 | 0 | 1.21 | ||||||||||||
| IL_24546.4_Instance_7 IL_24546.4_IL_4BPP_029_A543_U582 | A | G | G | G | C | A | A | G | C | U | ||||||||||||||||||
| IL_24546.4_Sequence_7 IL_24546.4_IL_4BPP_029_A543_U582 | A | G | G | G | C | A | A | G | * | C | U | true | 89 | 0 | 0 | 1.56 | ||||||||||||
| IL_24546.4_Instance_8 IL_24546.4_IL_1FJG_020_C504_G541 | C | G | G | C | C | A | A | C | G | G | ||||||||||||||||||
| IL_24546.4_Sequence_8 IL_24546.4_IL_1FJG_020_C504_G541 | C | G | G | C | C | A | A | C | * | G | G | true | 97 | 0 | 0 | 0.39 | ||||||||||||
| IL_24546.4_Instance_9 IL_24546.4_IL_3U5F_030_A550_U588 | A | G | G | G | C | A | A | G | C | U | ||||||||||||||||||
| IL_24546.4_Sequence_9 IL_24546.4_IL_3U5F_030_A550_U588 | A | G | G | G | C | A | A | G | * | C | U | true | 89 | 0 | 0 | 1.56 | ||||||||||||
| IL_24546.4_Instance_10 IL_24546.4_IL_3U5H_054_U1173_A1326 | U | G | C | C | G | G | A | A | U | A | ||||||||||||||||||
| IL_24546.4_Sequence_10 IL_24546.4_IL_3U5H_054_U_1173_A_1326 | U | G | C | C | G | G | A | A | * | U | A | true | 89 | 0 | 0 | 1.54 |
1 8 s35 1 10 cWW 2 3 s35 3 4 s35 4 5 s33 5 6 cSH 6 7 s35 8 9 cWW 8 10 s55 9 10 s35JAR3D SCFG/MRF model for IL_24546.4:
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 C1004 - G1151 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008817364,0.018381954,0.009785358,0.206269672,0.000000000],[0.020516944,0.008438985,0.223661289,0.010919998,0.000000000],[0.009843600,0.184652701,0.001994662,0.022747658,0.000000000],[0.226368298,0.010661853,0.024935691,0.012003973,0.000000000],[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 C1004 - G1151 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.375000000,0.541666667,0.041666667,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.541666667,0.375000000,0.041666667,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.708333333,0.208333333,0.041666667,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [9] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [5] | Right Index [9] | Norm Constant [0.999999999999999] // Cluster node C1008:G1011 and C1150:C1150 Interaction | Interacting Bases [4,5] | Pair Probability [[0.009160501,0.019617847,0.010363923,0.212411613,0.000000000],[0.017414703,0.008074462,0.208142248,0.011590854,0.000000000],[0.010317943,0.237552545,0.001992866,0.024923795,0.000000000],[0.182586497,0.011794457,0.022702265,0.011353480,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1011 - C1150 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.108026987,0.108970689,0.008009132,0.006289163,0.000000000],[0.162368586,0.088700096,0.001351892,0.090898797,0.000000000],[0.006358471,0.028715989,0.034561486,0.088161796,0.000000000],[0.071026857,0.108115302,0.001351892,0.087092865,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1008 - A1009 cSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1010 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 [9] | Right Index [8] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | 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_24546.4:
> IL_24546.4 IL_3V2F_037 C 1004 G 1151 CCCCCAAG*CG > IL_24546.4 IL_4IOA_033 U 1015 A 1162 UCCCUAAA*UA > IL_24546.4 IL_2QBG_037 U 1004 A 1151 UCCCAAAG*CA > IL_24546.4 IL_1S72_039 U 1101 A 1255 UCCCCAAG*CA > IL_24546.4 IL_4A1B_055 C 1200 G 1353 CGCCCAAA*UG > IL_24546.4 IL_2AW7_027 C 504 G 541 CGGCUAAC*GG > IL_24546.4 IL_4BPP_029 A 543 U 582 AGGGCAAG*CU > IL_24546.4 IL_1FJG_020 C 504 G 541 CGGCCAAC*GG > IL_24546.4 IL_3U5F_030 A 550 U 588 AGGGCAAG*CU > IL_24546.4 IL_3U5H_054 U 1173 A 1326 UGCCGGAA*UA