| 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 9 I | 18 9 9 | 19 9 I | 20 9 10 | 21 9 I | 22 9 11 | 23 10 I | 24 11 | 25 10 I | 26 9 12 | 27 2 I | 28 2 13 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_32056.1_Instance_1 IL_32056.1,IL_5ML7_006,G2151_C2224 | G | U | G | C | A | G | C | A | U | A | G | C | C | |||||||||||||||||||||
| IL_32056.1_Sequence_1 IL_32056.15ML7_G_2151_C_2224 | G | U | G | C | A | G | C | A | U | A | G | * | C | C | true | 92 | 0 | 0 | 1.53 | |||||||||||||||
| IL_32056.1_Instance_2 IL_32056.1,IL_3U4M_002,G2110_C2179 | G | C | G | U | A | G | G | A | U | A | G | C | C | |||||||||||||||||||||
| IL_32056.1_Sequence_2 IL_32056.13U4M_G_2110_C_2179 | G | C | G | U | A | G | G | A | U | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| IL_32056.1_Instance_3 IL_32056.1,IL_1MZP_002,G6_C50 | G | C | G | U | A | G | G | A | U | A | G | C | C | |||||||||||||||||||||
| IL_32056.1_Sequence_3 IL_32056.11MZP_G6_C50 | G | C | G | U | A | G | G | A | U | A | G | * | C | C | true | 100 | 0 | 0 | 0.00 |
1 11 s35 1 13 cWW 2 9 s55 3 4 s35 4 5 s35 5 6 s35 5 10 tWH 6 8 s33 7 8 s35 11 12 cWW 11 13 s55 12 13 s35 9 1 6BPh 6 10 6BPh 8 6 7BRJAR3D SCFG/MRF model for IL_32056.1:
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 BasepairNode | Deletion Probability [0.0000234451146992] | 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 [0.993970181,0.005999820,0.000029999] | 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 [1] | Right Index [13] // Basepair G2151 - C2224 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 5ML7|1|B|U|2152 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 [3] | Right Index [12] // 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 [3] | Right Index [12] // Fixed node on left for 5ML7|1|B|G|2153 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 [4] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Position [1] | Left Index [4] | Right Index [12] // Fixed node on left for 5ML7|1|B|C|2154 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 [12] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000390625000000000088131570158437809669143083] | Num Left Bases [7] | Num Right Bases [1] | Left Index [5] | Right Index [12] | Norm Constant [1.000000000000000] // Cluster node 5ML7|1|B|A|2155:5ML7|1|B|G|2161 and 5ML7|1|B|C|2223:5ML7|1|B|C|2223 Interaction | Interacting Bases [7,8] | 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 5ML7|1|B|G|2161 - 5ML7|1|B|C|2223 cWW Interaction | Interacting Bases [1,6] | Pair Probability [[0.387192728,0.003580665,0.315879003,0.003580665,0.000000000],[0.030648361,0.015195078,0.003580665,0.003580665,0.000000000],[0.003580665,0.008869795,0.131616019,0.038326316,0.000000000],[0.016180024,0.003580665,0.017162126,0.017446559,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5ML7|1|B|A|2155 - 5ML7|1|B|A|2160 tWH Interaction | Interacting Bases [2,2] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5ML7|1|B|G|2156 Interaction | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5ML7|1|B|C|2157 Interaction | Interacting Bases [4,4] | Pair Probability [[0.911764706,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5ML7|1|B|A|2158 Interaction | Interacting Bases [5,5] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.021739130,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.934782609,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5ML7|1|B|U|2159 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 [12] | Right Index [11] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [12] | Right Index [12] | 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_32056.1:
> IL_32056.1 5ML7 G 2151 C 2224 GUGCAGCAUAG*CC > IL_32056.1 3U4M G 2110 C 2179 GCGUAGGAUAG*CC > IL_32056.1 1MZP G 6 C 50 GCGUAGGAUAG*CC