Alignment of HL_45785.1 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.

Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group:	2 2 1	4 3 2	6 5 3	8 9 4	10 9 5	12 9 6	14 9 7	15 9 I	16 9 8	18 7 9	20 2 10	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
HL_45785.1_Instance_1 HL_45785.1,HL_8FZA_001,G5_C15	G	U	U	C	C	C	U	C	A	C	C
HL_45785.1_Sequence_1 HL_45785.18FZA_G5_C15	G	U	U	C	C	C	U	C	A	C	C	true	100	0	0	0.00
HL_45785.1_Instance_2 HL_45785.1,HL_8FZA_002,G5_C15	G	U	U	C	C	C	U	C	A	C	C
HL_45785.1_Sequence_2 HL_45785.18FZA_G5_C15	G	U	U	C	C	C	U	C	A	C	C	true	100	0	0	0.00

Conserved interactions between motif group positions in HL_45785.1:

1 10 cWW 
2 3 s35 
3 4 s33 
4 6 cSH 
5 6 s35 
6 7 s35 
7 8 tSW 
8 9 s35 
9 10 s35 
9 8 7BPh
5 4 7BR
8 7 7BR

JAR3D SCFG/MRF model for HL_45785.1:

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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 [10] // Basepair G5 - C15 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 8FZA|1|A|U|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 [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 8FZA|1|A|U|7
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 [4] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.031250000,0.906250000,0.031250000,0.031250000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // Fixed node on right for 8FZA|1|A|A|13
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 [4] | Right Index [8] // New Initial node after Fixed node
HairpinNode  | Num Bases [5] | Left Index [4] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node C8:A13
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.080836218,0.081466713,0.004498789,0.079696409,0.000000000],[0.081651522,0.113731496,0.000941237,0.065486665,0.000000000],[0.069283465,0.000941237,0.082635802,0.085367026,0.000000000],[0.082787923,0.082778754,0.000941237,0.086955509,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction C8 - C10 cSH 
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.193779308,0.020503326,0.002181697,0.010168952,0.000000000],[0.194107252,0.010445755,0.002181697,0.008687179,0.000000000],[0.188803695,0.002181697,0.002181697,0.006902480,0.000000000],[0.326904136,0.009979626,0.010820733,0.010170768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U11 - A13 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.875000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C9
Insertion    | Location [4] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000]// Insertion in Hairpin after nucleotide 7, position 4

Sequences of instances from HL_45785.1:> HL_45785.1 8FZA G 5 C 15 GUUCCCUCACC > HL_45785.1 8FZA G 5 C 15 GUUCCCUCACC