| 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 6 3 | 7 6 I | 8 6 4 | 9 7 I | 10 10 5 | 11 10 I | 12 11 | 13 10 I | 14 10 6 | 15 9 I | 16 13 7 | 17 14 I | 18 15 8 | 19 16 I | 20 19 9 | 21 19 I | 22 20 | 23 19 I | 24 19 10 | 25 18 I | 26 22 11 | 27 23 I | 28 24 12 | 29 24 I | 30 25 | 31 24 I | 32 24 13 | 33 7 I | 34 6 14 | 35 5 I | 36 4 15 | 37 3 I | 38 3 16 | 39 2 I | 40 2 17 | 41 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_71729.2_Instance_1 J4_71729.2,J4_4Y4O_015,C297_G341 | C | G | A | A | G | C | G | C | C | G | A | G | C | G | U | A | G | |||||||||||||||||||||||||||||
| J4_71729.2_Sequence_1 J4_71729.24Y4O_C297_G341 | C | G | A | A | G | * | C | G | C | C | * | G | A | G | * | C | G | U | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||||
| J4_71729.2_Instance_2 J4_71729.2,J4_4WF9_002,C340_G384 | C | G | A | A | U | A | A | U | C | G | A | A | U | G | U | A | G | |||||||||||||||||||||||||||||
| J4_71729.2_Sequence_2 J4_71729.24WF9_C340_G384 | C | G | A | A | U | * | A | A | U | C | * | G | A | A | * | U | G | U | A | G | true | 95 | 0 | 0 | 0.96 | |||||||||||||||||||||
| J4_71729.2_Instance_3 J4_71729.2,J4_5J7L_019,G297_C341 | G | G | A | A | G | C | G | C | G | C | A | G | C | G | U | A | C | |||||||||||||||||||||||||||||
| J4_71729.2_Sequence_3 J4_71729.25J7L_G297_C341 | G | G | A | A | G | * | C | G | C | G | * | C | A | G | * | C | G | U | A | C | true | 99 | 0 | 0 | 0.20 | |||||||||||||||||||||
| J4_71729.2_Instance_4 J4_71729.2,J4_7A0S_002,C308_G352 | C | G | A | A | G | C | A | C | C | G | A | A | U | G | U | A | G | |||||||||||||||||||||||||||||
| J4_71729.2_Sequence_4 J4_71729.27A0S_C308_G352 | C | G | A | A | G | * | C | A | C | C | * | G | A | A | * | U | G | U | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 17 cWW 2 15 s33 2 16 tSH 2 17 s55 3 4 s35 3 14 cHH 4 8 cSS 4 14 wat 5 6 cWW 5 7 s55 6 7 s35 7 8 s35 8 9 s35 9 10 cWW 11 12 s35 11 14 tHS 12 13 cWW 12 14 s55 13 14 s35 14 15 s35 15 16 s35 16 17 s35 14 10 6BPh 2 15 6BPh 16 2 6BR 11 14 6BRJAR3D SCFG/MRF model for J4_71729.2:
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 [17] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009401513,0.017549866,0.010782207,0.195587161,0.000000000],[0.019107025,0.009484786,0.232344244,0.013401212,0.000000000],[0.010842591,0.210218542,0.002049451,0.023823814,0.000000000],[0.196851077,0.013154215,0.025444740,0.009957556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [17] // Basepair C297 - G341 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.041475144,0.043907030,0.000497881,0.002346517,0.000000000],[0.041783275,0.043805359,0.000497881,0.000497881,0.000000000],[0.417995930,0.003485170,0.017037890,0.295808071,0.000000000],[0.046297338,0.043568868,0.000497881,0.000497881,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [16] // Basepair G298 - A340 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Position [2] | Left Index [3] | Right Index [15] // Fixed node on right for 4Y4O|1|2A|U|339 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [14] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [14] | Norm Constant [0.964318176859914] // Cluster node 4Y4O|1|2A|A|299:4Y4O|1|2A|A|300 and 4Y4O|1|2A|G|338:4Y4O|1|2A|G|338 Interaction | Interacting Bases [1,3] | Pair Probability [[0.001304669,0.001304669,0.951729817,0.001304669,0.000000000],[0.001304669,0.001304669,0.009132683,0.001304669,0.000000000],[0.006520776,0.001304669,0.009132683,0.001304669,0.000000000],[0.001304669,0.001304669,0.009132683,0.001304669,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4Y4O|1|2A|A|299 - 4Y4O|1|2A|G|338 cHH Interaction | Interacting Bases [2,3] | Pair Probability [[0.001269469,0.001269469,0.958107509,0.001269469,0.000000000],[0.001269469,0.001269469,0.008886286,0.001269469,0.000000000],[0.001269469,0.001269469,0.008886286,0.001269469,0.000000000],[0.001269469,0.001269469,0.008886286,0.001269469,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4Y4O|1|2A|A|300 - 4Y4O|1|2A|G|338 wat InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [13] // Initial node 4Y4O|1|2A|G|301 - 4Y4O|1|2A|C|337 from node JunctionNode | Branches [2] | Left Index [5] | Right Index [13] // Junction node G301 - C337 ID J1621 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009375029,0.019213306,0.010583069,0.196223339,0.000000000],[0.017981530,0.009431632,0.197640103,0.012479529,0.000000000],[0.010497262,0.230209052,0.002038061,0.025338924,0.000000000],[0.205930492,0.012685537,0.030324695,0.010048441,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair G301 - C316 cWW HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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 truncation InitialNode | Left Length Distribution [1.000000000] | 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 [13] // Initial node 4Y4O|1|2A|G|317 - 4Y4O|1|2A|C|337 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.416666667,0.083333333,0.000000000] | Position [1] | Left Index [7] | Right Index [13] // Fixed node on left for 4Y4O|1|2A|G|317 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [8] | Right Index [13] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.583333333,0.083333333,0.250000000,0.000000000] | Position [1] | Left Index [8] | Right Index [13] // Fixed node on left for 4Y4O|1|2A|C|318 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [9] | Right Index [13] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [9] | Right Index [13] // Junction node C319 - C337 ID J7942 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009401513,0.017549866,0.010782207,0.195587161,0.000000000],[0.019107025,0.009484786,0.232344244,0.013401212,0.000000000],[0.010842591,0.210218542,0.002049451,0.023823814,0.000000000],[0.196851077,0.013154215,0.025444740,0.009957556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Basepair C319 - G323 cWW HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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 truncation InitialNode | Left Length Distribution [1.000000000] | 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 [13] // Initial node 4Y4O|1|2A|A|324 - 4Y4O|1|2A|C|337 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.931818182,0.022727273,0.022727273,0.022727273,0.000000000] | Position [1] | Left Index [11] | Right Index [13] // Fixed node on left for 4Y4O|1|2A|A|324 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [12] | Right Index [13] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009325457,0.020734609,0.010297314,0.218050308,0.000000000],[0.016974989,0.009378665,0.194777146,0.011594085,0.000000000],[0.010227486,0.218136243,0.002025500,0.039220448,0.000000000],[0.193588082,0.012169223,0.022789886,0.010710558,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [12] | Right Index [13] // Basepair G325 - C337 cWW HairpinNode | Num Bases [1] | Left Index [13] | Right Index [13] | 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 J4_71729.2:
> J4_71729.2 4Y4O C 297 G 341 CGAAG*CGCC*GAG*CGUAG > J4_71729.2 4WF9 C 340 G 384 CGAAU*AAUC*GAA*UGUAG > J4_71729.2 5J7L G 297 C 341 GGAAG*CGCG*CAG*CGUAC > J4_71729.2 7A0S C 308 G 352 CGAAG*CACC*GAA*UGUAG