| 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 5 2 | 5 6 I | 6 7 3 | 7 7 I | 8 7 4 | 9 7 I | 10 7 5 | 11 7 I | 12 7 6 | 13 8 I | 14 9 | 15 8 I | 16 7 7 | 17 4 I | 18 11 8 | 19 12 I | 20 13 9 | 21 13 I | 22 14 | 23 13 I | 24 13 10 | 25 2 I | 26 2 11 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_39238.2_Instance_1 J3_39238.2,J3_4V9F_002,C774_G887 | C | G | A | U | C | U | A | U | A | G | C | GA | G | |||||||||||||||||||
| J3_39238.2_Sequence_1 J3_39238.24V9F_C774_G887 | C | G | A | U | C | U | A | * | U | A | G | * | C | GA | G | true | 100 | 0 | 0 | 0.10 | ||||||||||||
| J3_39238.2_Instance_2 J3_39238.2,J3_4WF9_002,U728_A839 | U | G | A | U | C | U | A | U | A | G | C | GA | A | |||||||||||||||||||
| J3_39238.2_Sequence_2 J3_39238.24WF9_U728_A839 | U | G | A | U | C | U | A | * | U | A | G | * | C | GA | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| J3_39238.2_Instance_3 J3_39238.2,J3_7A0S_004,U696_A807 | U | G | A | G | C | U | A | U | A | G | C | GA | A | |||||||||||||||||||
| J3_39238.2_Sequence_3 J3_39238.27A0S_U696_A807 | U | G | A | G | C | U | A | * | U | A | G | * | C | GA | A | true | 98 | 0 | 0 | 0.34 | ||||||||||||
| J3_39238.2_Instance_4 J3_39238.2,J3_5TBW_004,U814_A926 | U | G | A | A | C | U | A | U | A | G | C | GA | A | |||||||||||||||||||
| J3_39238.2_Sequence_4 J3_39238.25TBW_U814_A926 | U | G | A | A | C | U | A | * | U | A | G | * | C | GA | A | true | 96 | 0 | 0 | 0.85 | ||||||||||||
| J3_39238.2_Instance_5 J3_39238.2,J3_5J7L_038,U683_A794 | U | G | A | U | C | U | A | U | G | G | C | AA | A | |||||||||||||||||||
| J3_39238.2_Sequence_5 J3_39238.25J7L_U683_A794 | U | G | A | U | C | U | A | * | U | G | G | * | C | AA | A | true | 95 | 0 | 0 | 0.99 | ||||||||||||
| J3_39238.2_Instance_6 J3_39238.2,J3_4Y4O_019,C683_G794 | C | G | A | G | C | U | A | U | A | G | C | GA | G | |||||||||||||||||||
| J3_39238.2_Sequence_6 J3_39238.24Y4O_C683_G794 | C | G | A | G | C | U | A | * | U | A | G | * | C | GA | G | true | 98 | 0 | 0 | 0.43 |
1 2 s35 1 11 cWW 2 8 s33 2 9 tWH 2 11 s55 3 5 tSW 3 6 s35 3 7 s33 3 8 s55 4 5 s35 5 6 s35 6 7 cWW 9 10 cWW 9 11 s35 4 3 7BRJAR3D SCFG/MRF model for J3_39238.2:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000000006156681] | Pair Probability [[0.008854514,0.016740477,0.009873999,0.189704501,0.000000000],[0.020645154,0.009422516,0.212263396,0.011508821,0.000000000],[0.009925891,0.189884907,0.001981704,0.022312113,0.000000000],[0.233465652,0.010917253,0.042775962,0.009723142,0.000000000],[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 [0.000000000,0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.535714286,0.035714286,0.392857143,0.035714286,0.000000000] | Left Index [1] | Right Index [11] // Basepair C774 - G887 cWW JunctionNode | Branches [2] | Left Index [2] | Right Index [10] // Junction node G775 - C884 ID J8234 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.222222222,0.222222222,0.333333333,0.222222222,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Initial node 4V9F|1|0|G|775 - 4V9F|1|0|U|866 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left for 4V9F|1|0|G|775 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 [7] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000015557317266020809512875033260945487973765004666] | Num Left Bases [4] | Num Right Bases [1] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Cluster node 4V9F|1|0|A|776:4V9F|1|0|A|780 and 4V9F|1|0|U|866:4V9F|1|0|U|866 Interaction | Interacting Bases [4,5] | Pair Probability [[0.008932627,0.021179957,0.009540239,0.253016483,0.000000000],[0.016857107,0.009218740,0.186838956,0.009967940,0.000000000],[0.009521668,0.189261136,0.001964127,0.051205712,0.000000000],[0.188626503,0.010612004,0.022144213,0.011112588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|A|780 - 4V9F|1|0|U|866 cWW Interaction | Interacting Bases [1,3] | Pair Probability [[0.014891944,0.013905790,0.002823376,0.338941367,0.000000000],[0.013878528,0.014035418,0.002823376,0.121062079,0.000000000],[0.013652211,0.002823376,0.002823376,0.013741685,0.000000000],[0.013159833,0.028084494,0.132673385,0.270679762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|A|776 - 4V9F|1|0|U|779 tSW Interaction | Interacting Bases [2,2] | Pair Probability [[0.015625000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.953125000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.015625000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|0|C|778 Insertion | Location [1] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.187500000,0.062500000,0.312500000,0.437500000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [6] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | 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 [8] | Right Index [10] // Initial node 4V9F|1|0|A|867 - 4V9F|1|0|C|884 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.687500000,0.062500000,0.187500000,0.062500000,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 4V9F|1|0|U|866 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 [9] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009366383,0.019506822,0.010665810,0.193723744,0.000000000],[0.016452306,0.009184679,0.195365254,0.012782718,0.000000000],[0.010547361,0.257647718,0.002010439,0.025755166,0.000000000],[0.191244451,0.013267227,0.022575563,0.009904357,0.000000000],[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 G868 - C884 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 truncationSequences of instances from J3_39238.2:
> J3_39238.2 4V9F C 774 G 887 CGAUCUA*UAG*CGAG > J3_39238.2 4WF9 U 728 A 839 UGAUCUA*UAG*CGAA > J3_39238.2 7A0S U 696 A 807 UGAGCUA*UAG*CGAA > J3_39238.2 5TBW U 814 A 926 UGAACUA*UAG*CGAA > J3_39238.2 5J7L U 683 A 794 UGAUCUA*UGG*CAAA > J3_39238.2 4Y4O C 683 G 794 CGAGCUA*UAG*CGAG