| 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 7 3 | 7 7 I | 8 8 | 9 7 I | 10 7 4 | 11 6 I | 12 12 5 | 13 12 I | 14 13 | 15 12 I | 16 12 6 | 17 11 I | 18 15 7 | 19 16 I | 20 17 8 | 21 18 I | 22 19 9 | 23 19 I | 24 20 | 25 19 I | 26 19 10 | 27 2 I | 28 2 11 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_72305.3_Instance_1 J4_72305.3,J4_4QEI_001,C7_G66 | C | U | G | G | U | G | C | G | A | C | C | G | G | |||||||||||||||||||||
| J4_72305.3_Sequence_1 J4_72305.34QEI_C7_G66 | C | U | G | G | * | U | G | * | C | G | A | C | C | * | G | G | true | 99 | 0 | 0 | 0.07 | |||||||||||||
| J4_72305.3_Instance_2 J4_72305.3,J4_5E6M_001,C7_G66 | C | U | G | G | U | G | C | G | A | C | C | G | G | |||||||||||||||||||||
| J4_72305.3_Sequence_2 J4_72305.35E6M_C7_G66 | C | U | G | G | * | U | G | * | C | G | A | C | C | * | G | G | true | 99 | 0 | 0 | 0.07 | |||||||||||||
| J4_72305.3_Instance_3 J4_72305.3,J4_2D6F_002,G907_C966 | G | U | G | G | U | G | C | G | A | C | A | U | C | |||||||||||||||||||||
| J4_72305.3_Sequence_3 J4_72305.32D6F_G907_C966 | G | U | G | G | * | U | G | * | C | G | A | C | A | * | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| J4_72305.3_Instance_4 J4_72305.3,J4_3AL0_001,G7_C66 | G | U | C | G | C | G | U | G | G | U | G | C | C | |||||||||||||||||||||
| J4_72305.3_Sequence_4 J4_72305.33AL0_G7_C66 | G | U | C | G | * | C | G | * | U | G | G | U | G | * | C | C | true | 88 | 0 | 0 | 1.62 | |||||||||||||
| J4_72305.3_Instance_5 J4_72305.3,J4_6CU1_001,G52_C37 | G | U | A | G | C | G | U | U | G | UU | G | U | C | |||||||||||||||||||||
| J4_72305.3_Sequence_5 J4_72305.36CU1_G52_C37 | G | U | A | G | * | C | G | * | U | U | G | UU | G | * | U | C | true | 60 | 0 | 0 | 5.38 | |||||||||||||
| J4_72305.3_Instance_6 J4_72305.3,J4_5WT1_001,G7_C66 | G | U | A | G | C | A | U | G | U | C | G | C | C | |||||||||||||||||||||
| J4_72305.3_Sequence_6 J4_72305.35WT1_G7_C66 | G | U | A | G | * | C | A | * | U | G | U | C | G | * | C | C | true | 81 | 0 | 0 | 2.58 |
1 9 s35 1 11 cWW 2 7 s33 2 8 s55 3 4 cWW 3 5 s55 3 7 cHS 4 5 s35 5 6 cWW 5 7 s55 6 7 s35 9 10 cWW 9 11 s55 10 11 s35JAR3D SCFG/MRF model for J4_72305.3:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.009303158,0.018489895,0.010627125,0.192911785,0.000000000],[0.017471954,0.009238523,0.216141290,0.012945225,0.000000000],[0.010587651,0.236901681,0.002010592,0.024697007,0.000000000],[0.192085542,0.013106691,0.023637380,0.009844500,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.062500000,0.062500000,0.062500000,0.812500000,0.000000000] | 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 [11] // Basepair C7 - G66 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.312500000,0.187500000,0.437500000,0.062500000,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left for 4QEI|1|C|U|8 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 [10] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [3] | Right Index [10] // Junction node G10 - G65 ID J3112 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.012304240,0.152595251,0.012221578,0.137557369,0.000000000],[0.014828613,0.010745729,0.115211142,0.013322044,0.000000000],[0.012014775,0.148821138,0.002566200,0.197277540,0.000000000],[0.113221234,0.014204047,0.018215096,0.024894003,0.000000000],[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 [3] | Right Index [4] // Basepair G10 - U25 cWW HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | 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 [5] | Right Index [10] // Initial node 4QEI|1|C|G|26 - 4QEI|1|C|G|65 from node JunctionNode | Branches [2] | Left Index [5] | Right Index [10] // Junction node G26 - G65 ID J5285 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.011252662,0.108511297,0.011515394,0.166161617,0.000000000],[0.015437311,0.010231056,0.140508130,0.012673139,0.000000000],[0.011354688,0.173698901,0.002373228,0.144345173,0.000000000],[0.138792648,0.013449237,0.019596693,0.020098826,0.000000000],[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 G26 - C44 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 [10] // Initial node 4QEI|1|C|G|45 - 4QEI|1|C|G|65 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.687500000,0.187500000,0.000000000] | Position [1] | Left Index [7] | Right Index [10] // Fixed node on left for 4QEI|1|C|C|44 InitialNode | Left Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.437500000,0.187500000,0.312500000,0.062500000,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 4QEI|1|C|G|45 InitialNode | Left Length Distribution [0.169561056,0.659100232,0.169629427,0.001640913,0.000068371] | 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 [9] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.010210151,0.063131561,0.010958119,0.184071784,0.000000000],[0.016998190,0.009764550,0.188002203,0.012655871,0.000000000],[0.010905840,0.189228391,0.002188127,0.086112889,0.000000000],[0.165641478,0.012976428,0.022111999,0.015042420,0.000000000],[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 C49 - G65 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 J4_72305.3:
> J4_72305.3 4QEI C 7 G 66 CUGG*UG*CGACC*GG > J4_72305.3 5E6M C 7 G 66 CUGG*UG*CGACC*GG > J4_72305.3 2D6F G 907 C 966 GUGG*UG*CGACA*UC > J4_72305.3 3AL0 G 7 C 66 GUCG*CG*UGGUG*CC > J4_72305.3 6CU1 G 52 C 37 GUAG*CG*UUGUUG*UC > J4_72305.3 5WT1 G 7 C 66 GUAG*CA*UGUCG*CC