| 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 7 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 6 | 13 10 I | 14 10 7 | 15 9 I | 16 9 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_50860.2_Instance_1 HL_50860.2,HL_5J7L_219,G2304_U2312 | G | U | C | G | G | A | C | A | U | |||||||||||||||
| HL_50860.2_Sequence_1 HL_50860.25J7L_G_2304_U_2312 | G | U | C | G | G | A | C | A | U | true | 90 | 0 | 0 | 1.69 | ||||||||||
| HL_50860.2_Instance_2 HL_50860.2,HL_4V9F_057,G2338_C2346 | G | A | C | A | G | A | G | A | C | |||||||||||||||
| HL_50860.2_Sequence_2 HL_50860.24V9F_G_2338_C_2346 | G | A | C | A | G | A | G | A | C | true | 87 | 0 | 0 | 2.11 | ||||||||||
| HL_50860.2_Instance_3 HL_50860.2,HL_9DFE_198,G2304_U2312 | G | A | C | G | G | A | A | A | U | |||||||||||||||
| HL_50860.2_Sequence_3 HL_50860.29DFE_G_2304_U_2312 | G | A | C | G | G | A | A | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_50860.2_Instance_4 HL_50860.2,HL_8CRE_055,A2645_U2653 | A | A | C | A | G | A | A | A | U | |||||||||||||||
| HL_50860.2_Sequence_4 HL_50860.28CRE_A_2645_U_2653 | A | A | C | A | G | A | A | A | U | true | 98 | 0 | 0 | 0.27 | ||||||||||
| HL_50860.2_Instance_5 HL_50860.2,HL_8P9A_167,A2673_U2681 | A | A | C | A | G | A | A | A | U | |||||||||||||||
| HL_50860.2_Sequence_5 HL_50860.28P9A_A_2673_U_2681 | A | A | C | A | G | A | A | A | U | true | 98 | 0 | 0 | 0.27 | ||||||||||
| HL_50860.2_Instance_6 HL_50860.2,HL_7A0S_076,G2283_U2291 | G | U | U | G | G | A | A | A | U | |||||||||||||||
| HL_50860.2_Sequence_6 HL_50860.27A0S_G_2283_U_2291 | G | U | U | G | G | A | A | A | U | true | 88 | 0 | 0 | 1.89 |
1 9 cWW 2 3 s35 3 4 s33 4 5 s53 4 8 s53 5 8 cWH 6 7 s35 9 8 7BPhJAR3D SCFG/MRF model for HL_50860.2:
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 [9] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003694475,0.048696381,0.003663849,0.274819535,0.000000000],[0.004868624,0.006944288,0.040340841,0.022040362,0.000000000],[0.003615427,0.130066963,0.000779293,0.358275600,0.000000000],[0.040309322,0.009355405,0.006004610,0.046525023,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G2304 - U2312 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.562500000,0.062500000,0.062500000,0.312500000,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left for 5J7L|1|DA|U|2305 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 [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.687500000,0.062500000,0.187500000,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left for 5J7L|1|DA|C|2306 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 [4] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.437500000,0.062500000,0.437500000,0.062500000,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left for 5J7L|1|DA|G|2307 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 [5] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.002602019,0.002602019,0.225209864,0.215620603,0.000000000],[0.002602019,0.017846262,0.002602019,0.009851755,0.000000000],[0.361729254,0.002602019,0.108191600,0.002602019,0.000000000],[0.009586336,0.002602019,0.008888779,0.024861417,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair G2308 - A2311 cWH HairpinNode | Num Bases [2] | Left Index [6] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A2309:C2310 Interaction | Interacting Bases [1,1] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2309 Interaction | Interacting Bases [2,2] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2310Sequences of instances from HL_50860.2:
> HL_50860.2 5J7L G 2304 U 2312 GUCGGACAU > HL_50860.2 4V9F G 2338 C 2346 GACAGAGAC > HL_50860.2 9DFE G 2304 U 2312 GACGGAAAU > HL_50860.2 8CRE A 2645 U 2653 AACAGAAAU > HL_50860.2 8P9A A 2673 U 2681 AACAGAAAU > HL_50860.2 7A0S G 2283 U 2291 GUUGGAAAU