| 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 3 I | 6 8 3 | 7 8 I | 8 11 4 | 9 11 I | 10 12 5 | 11 12 I | 12 12 6 | 13 12 I | 14 12 7 | 15 11 I | 16 11 8 | 17 10 I | 18 9 9 | 19 8 I | 20 8 10 | 21 7 I | 22 6 11 | 23 5 I | 24 4 12 | 25 3 I | 26 3 13 | 27 2 I | 28 2 14 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_81205.2_Instance_1 HL_81205.2_HL_4LFB_008_C320_G333 | C | A | C | U | G | A | G | A | C | A | C | G | G | G | ||||||||||||||||||||
| HL_81205.2_Sequence_1 HL_81205.2_HL_4LFB_008_C320_G333 | C | A | C | U | G | A | G | A | C | A | C | G | G | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| HL_81205.2_Instance_2 HL_81205.2_HL_5J7L_008_A320_U333 | A | A | C | U | G | A | G | A | C | A | C | G | G | U | ||||||||||||||||||||
| HL_81205.2_Sequence_2 HL_81205.2_HL_5J7L_008_A320_U333 | A | A | C | U | G | A | G | A | C | A | C | G | G | U | true | 97 | 0 | 0 | 0.53 | |||||||||||||||
| HL_81205.2_Instance_3 HL_81205.2_HL_6CZR_079_C316_G329 | C | A | C | U | G | A | G | A | C | A | C | G | G | G | ||||||||||||||||||||
| HL_81205.2_Sequence_3 HL_81205.2_HL_6CZR_079_C316_G329 | C | A | C | U | G | A | G | A | C | A | C | G | G | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 14 cWW 2 3 s35 2 9 s35 2 13 cWW 2 14 s55 3 4 s35 3 10 tWH 4 5 s35 4 8 tWH 5 8 s55 6 7 s35 8 10 s35 10 13 s35 13 14 s35 5 8 6BPh 1 10 7BPh 2 10 7BPhJAR3D SCFG/MRF model for HL_81205.2:
Character Definition | A,C,G,U,* // Define characters here InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Initial node C320 - G333 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.011047284,0.024765524,0.012000462,0.249792715,0.000000000],[0.039103953,0.018888315,0.424233191,0.026390557,0.000000000],[0.004179666,0.078595762,0.000811066,0.013105297,0.000000000],[0.078066430,0.004899587,0.009976494,0.004143697,0.000000000],[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 [1] | Right Index [14] // Basepair C320 - G333 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.057673175,0.028250710,0.725663104,0.033832476,0.000000000],[0.003941052,0.002684127,0.005220341,0.011730572,0.000000000],[0.095600616,0.005278967,0.000995053,0.004391209,0.000000000],[0.004823803,0.012394310,0.004297135,0.003223350,0.000000000],[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 [2] | Right Index [13] // Basepair A321 - G332 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [12] // Fixed node on right 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 [3] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [3] | Right Index [11] // Fixed node on right 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 [3] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.030419083,0.003553878,0.101665438,0.003553878,0.000000000],[0.384514062,0.025892298,0.003553878,0.003553878,0.000000000],[0.003553878,0.012407604,0.031958440,0.032758932,0.000000000],[0.035738931,0.003553878,0.015978312,0.307343630,0.000000000],[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 [3] | Right Index [10] // Basepair C322 - A329 tWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // Fixed node on right 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 [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.018593320,0.004114731,0.019312206,0.004114731,0.000000000],[0.041379046,0.331568716,0.004114731,0.004114731,0.000000000],[0.004114731,0.009863283,0.031292185,0.018300908,0.000000000],[0.440599350,0.004114731,0.023873178,0.040529420,0.000000000],[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 [4] | Right Index [8] // Basepair U323 - A327 tWH HairpinNode | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [0.999999999999999] // Hairpin node G324:G326 Interaction | Interacting Bases [1,1] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G324 Interaction | Interacting Bases [2,2] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A325 Interaction | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G326Sequences of instances from HL_81205.2:
> HL_81205.2 HL_4LFB_008 C 320 G 333 CACUGAGACACGGG > HL_81205.2 HL_5J7L_008 A 320 U 333 AACUGAGACACGGU > HL_81205.2 HL_6CZR_079 C 316 G 329 CACUGAGACACGGG