| 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 15 I | 20 15 8 | 21 16 I | 22 17 9 | 23 18 I | 24 25 10 | 25 25 I | 26 26 | 27 25 I | 28 25 11 | 29 24 I | 30 23 12 | 31 22 I | 32 21 13 | 33 20 I | 34 19 14 | 35 16 I | 36 15 15 | 37 2 I | 38 2 16 | 39 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_59845.1_Instance_1 J4_59845.1,J4_6CK5_001,A5_U106 | A | G | U | A | G | C | A | C | A | C | G | A | U | A | G | G | U | |||||||||||||||||||||||||||
| J4_59845.1_Sequence_1 J4_59845.16CK5_A5_U106 | A | G | U | * | A | G | * | C | A | C | A | C | * | G | A | U | A | G | G | U | true | 98 | 0 | 0 | 0.32 | |||||||||||||||||||
| J4_59845.1_Instance_2 J4_59845.1,J4_6DLR_001,A5_U104 | A | G | U | A | G | U | A | C | A | C | G | G | U | A | G | G | U | |||||||||||||||||||||||||||
| J4_59845.1_Sequence_2 J4_59845.16DLR_A5_U104 | A | G | U | * | A | G | * | U | A | C | A | C | * | G | G | U | A | G | G | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 16 cWW 2 7 tSW 3 4 cWW 3 5 s55 4 5 s35 5 6 cWW 7 8 s35 7 15 cSS 7 16 s55 8 9 s35 8 15 cSS 10 11 cWW 10 12 s55 11 12 s35 12 13 s35 14 15 s35 15 16 s35 7 2 7BR 10 9 7BR 14 9 2BRJAR3D SCFG/MRF model for J4_59845.1:
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 [16] // Initial node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [16] // Basepair A5 - U106 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [15] // Fixed node on left for 6CK5|1|A|G|6 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [15] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [3] | Right Index [15] // Junction node U7 - G105 ID J8142 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[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 U7 - A55 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 [15] // Initial node 6CK5|1|A|G|56 - 6CK5|1|A|G|105 from node JunctionNode | Branches [2] | Left Index [5] | Right Index [15] // Junction node G56 - G105 ID J2435 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [[0.012786759,0.158579378,0.012700856,0.142951775,0.000000000],[0.015410127,0.011167131,0.119729226,0.013844477,0.000000000],[0.012485943,0.135049418,0.002666836,0.185406071,0.000000000],[0.117661282,0.014761069,0.018929413,0.025870238,0.000000000],[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 G56 - C73 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 [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [7] | Right Index [15] // Initial node ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [7] | Right Index [15] | Norm Constant [0.233981204475456] // Cluster node 6CK5|1|A|A|74:6CK5|1|A|C|75 and 6CK5|1|A|G|105:6CK5|1|A|G|105 Interaction | Interacting Bases [1,3] | Pair Probability [[0.172124582,0.178857033,0.205679247,0.175564768,0.000000000],[0.032251992,0.035157435,0.001442792,0.032377888,0.000000000],[0.033018160,0.001411656,0.003198930,0.032634865,0.000000000],[0.030489147,0.004808714,0.025662894,0.035319897,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CK5|1|A|A|74 - 6CK5|1|A|G|105 cSS Interaction | Interacting Bases [2,3] | Pair Probability [[0.016174982,0.016328316,0.016514392,0.016866023,0.000000000],[0.015629942,0.015793414,0.412550022,0.017104362,0.000000000],[0.014905543,0.366395803,0.014851255,0.014584059,0.000000000],[0.015353183,0.015389974,0.016572118,0.014986613,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CK5|1|A|C|75 - 6CK5|1|A|G|105 cSS InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [14] // Initial node 6CK5|1|A|A|76 - 6CK5|1|A|G|104 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [9] | Right Index [14] // Fixed node on left for 6CK5|1|A|A|76 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [10] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.041666667,0.875000000,0.041666667,0.000000000] | Position [2] | Left Index [10] | Right Index [14] // Fixed node on right for 6CK5|1|A|A|103 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Left Index [10] | Right Index [13] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [10] | Right Index [13] // Fixed node on right for 6CK5|1|A|U|102 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [2] | Left Index [10] | Right Index [12] // Fixed node on right for 6CK5|1|A|A|101 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.004694951,0.008419175,0.005397424,0.097865947,0.000000000],[0.049911347,0.023908359,0.534011162,0.033946338,0.000000000],[0.005458039,0.099974695,0.001028807,0.011552643,0.000000000],[0.099134681,0.006541329,0.013179748,0.004975356,0.000000000],[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 [10] | Right Index [11] // Basepair C77 - G100 cWW HairpinNode | Num Bases [1] | Left Index [11] | Right Index [11] | 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_59845.1:
> J4_59845.1 6CK5 A 5 U 106 AGU*AG*CACAC*GAUAGGU > J4_59845.1 6DLR A 5 U 104 AGU*AG*UACAC*GGUAGGU