| 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 11 4 | 9 12 I | 10 13 5 | 11 14 I | 12 15 6 | 13 15 I | 14 16 | 15 15 I | 16 15 7 | 17 10 I | 18 18 8 | 19 19 I | 20 20 9 | 21 21 I | 22 24 10 | 23 24 I | 24 25 | 25 24 I | 26 24 11 | 27 23 I | 28 27 12 | 29 27 I | 30 28 13 | 31 28 I | 32 29 | 33 28 I | 34 28 14 | 35 27 I | 36 27 15 | 37 8 I | 38 7 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_16596.1_Instance_1 J4_16596.1,J4_4FRG_001,G18_C73 | G | G | A | A | A | G | C | A | G | A | U | A | C | G | A | A | UG | C | ||||||||||||||||||||||||||||
| J4_16596.1_Sequence_1 J4_16596.14FRG_G18_C73 | G | G | A | A | A | G | * | C | A | G | A | * | U | A | C | * | G | A | A | UG | C | true | 97 | 0 | 0 | 0.51 | ||||||||||||||||||||
| J4_16596.1_Instance_2 J4_16596.1,J4_4FRN_002,G18_C71 | G | G | A | A | A | G | C | A | C | A | U | A | C | G | A | A | UG | C | ||||||||||||||||||||||||||||
| J4_16596.1_Sequence_2 J4_16596.14FRN_G18_C71 | G | G | A | A | A | G | * | C | A | C | A | * | U | A | C | * | G | A | A | UG | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||||
| J4_16596.1_Instance_3 J4_16596.1,J4_4GXY_001,G40_C161 | G | G | G | A | A | G | C | A | C | G | C | A | C | G | G | A | AAC | C | ||||||||||||||||||||||||||||
| J4_16596.1_Sequence_3 J4_16596.14GXY_G40_C161 | G | G | G | A | A | G | * | C | A | C | G | * | C | A | C | * | G | G | A | AAC | C | true | 80 | 0 | 0 | 3.99 |
1 2 s35 1 17 cWW 2 3 s35 2 17 s55 3 16 s33 4 5 s35 4 10 cSS 6 7 cWW 6 8 s55 7 8 s35 8 9 s35 10 11 cWW 12 13 s35 12 15 cWW 13 14 cWW 14 15 s35 15 16 s35JAR3D SCFG/MRF model for J4_16596.1:
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 [17] // Initial node BasepairNode | Deletion Probability [0.0000000001026167] | 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 [0.000000000,0.010744024,0.650013430,0.333064733,0.005909213,0.000268601] | Right Letter Distribution [0.277777778,0.166666667,0.277777778,0.277777778,0.000000000] | Left Index [1] | Right Index [17] // Basepair G18 - C73 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [16] // Fixed node on left for 4FRG|1|B|G|19 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 [16] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [16] // Fixed node on left for 4FRG|1|B|A|20 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 [16] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [4] | Right Index [16] // Fixed node on right for 4FRG|1|B|A|70 InitialNode | Left Length Distribution [1.000000000] | 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 [4] | Right Index [15] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [4] | Right Index [15] // Junction node A21 - A69 ID J7922 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.400000000,0.200000000,0.200000000,0.200000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Initial node 4FRG|1|B|A|21 - 4FRG|1|B|C|40 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 4FRG|1|B|A|21 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 [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [5] | Right Index [7] // Fixed node on left for 4FRG|1|B|A|22 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 [6] | Right Index [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | 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 [6] | Right Index [7] // Basepair G23 - C40 cWW 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 [15] // Initial node 4FRG|1|B|A|41 - 4FRG|1|B|A|69 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [8] | Right Index [15] // Fixed node on left for 4FRG|1|B|A|41 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 [9] | Right Index [15] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.500000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [9] | Right Index [15] // Fixed node on left for 4FRG|1|B|G|42 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 [10] | Right Index [15] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [10] | Right Index [15] // Junction node A43 - A69 ID J9594 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009341597,0.021222893,0.010204228,0.220628516,0.000000000],[0.017209227,0.009475562,0.195205747,0.011223855,0.000000000],[0.010150854,0.208524333,0.002037222,0.043966533,0.000000000],[0.195018545,0.011831944,0.022937162,0.011021781,0.000000000],[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 A43 - U54 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 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 [12] | Right Index [15] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.422498529,0.023090700,0.161012651,0.023652155,0.000000000],[0.016936901,0.010028190,0.024175500,0.031352212,0.000000000],[0.138982580,0.024620546,0.005119921,0.024439457,0.000000000],[0.023135612,0.034336000,0.018504623,0.018114423,0.000000000],[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 [12] | Right Index [15] // Basepair A55 - A69 cWW BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 [13] | Right Index [14] // Basepair C56 - G68 cWW HairpinNode | Num Bases [1] | Left Index [14] | Right Index [14] | 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_16596.1:
> J4_16596.1 4FRG G 18 C 73 GGAAAG*CAGA*UAC*GAAUGC > J4_16596.1 4FRN G 18 C 71 GGAAAG*CACA*UAC*GAAUGC > J4_16596.1 4GXY G 40 C 161 GGGAAG*CACG*CAC*GGAAACC