Alignment of HL_23509.1 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:	1 1 I	2 2 1	3 2 I	4 2 2	5 3 I	6 4 3	7 5 I	8 8 4	9 8 I	10 9 5	11 9 I	12 9 6	13 9 I	14 9 7	15 9 I	16 9 8	17 8 I	18 8 9	19 7 I	20 6 10	21 3 I	22 2 11	23 1 I	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
HL_23509.1_Instance_1 HL_23509.1,HL_8P9A_163,G2534_C2545		G		A		A		U		U	C	A		U		U		U		U		C
HL_23509.1_Sequence_1 HL_23509.18P9A_G_2534_C_2545		G		A		A		U		U	C	A		U		U		U		U		C		true	100	0	0	0.00

Conserved interactions between motif group positions in HL_23509.1:

1 2 cSH 
1 3 s35 
1 11 cWW 
2 11 bif 
3 4 perp 
4 5 s35 
4 9 cWW 
5 7 perp 
6 7 perp 
7 8 perp 
8 10 s35 
10 11 s35 
3 2 7BPh

JAR3D SCFG/MRF model for HL_23509.1:

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 [11] // Initial node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [11] | Norm Constant [0.032544916349567] // Cluster node 8P9A|1|AR|G|2534:8P9A|1|AR|A|2535 and 8P9A|1|AR|C|2545:8P9A|1|AR|C|2545
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.009830065,0.020472507,0.011193821,0.203314028,0.000000000],[0.017266777,0.009639366,0.205036802,0.013415526,0.000000000],[0.011069507,0.220897605,0.002109966,0.027030175,0.000000000],[0.200711998,0.013924020,0.023693165,0.010394672,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|G|2534 - 8P9A|1|AR|C|2545 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.028776211,0.712040258,0.007021393,0.007021393,0.000000000],[0.032326394,0.082230039,0.007021393,0.007021393,0.000000000],[0.007021393,0.007021393,0.029462996,0.007021393,0.000000000],[0.007021393,0.007021393,0.044950176,0.007021393,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|A|2535 - 8P9A|1|AR|C|2545 bif 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.012230644,0.015054486,0.008372813,0.150869555,0.000000000],[0.015268224,0.127062259,0.001726179,0.162814127,0.000000000],[0.182518857,0.001726179,0.021556007,0.121577824,0.000000000],[0.014733840,0.021808946,0.001726179,0.140953883,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|G|2534 - 8P9A|1|AR|A|2535 cSH 
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Initial node 8P9A|1|AR|A|2536 - 8P9A|1|AR|U|2544 from node 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.833333333,0.055555556,0.055555556,0.055555556,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 8P9A|1|AR|A|2536
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [10] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [4] | Right Index [10] // Fixed node on right for 8P9A|1|AR|U|2543
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | 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
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.015580470,0.285764820,0.013910732,0.024295965,0.000000000],[0.017220118,0.018567546,0.020767248,0.015270770,0.000000000],[0.013620185,0.021155527,0.004294262,0.054860011,0.000000000],[0.021224145,0.016538232,0.017602771,0.439327198,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair U2537 - U2543 cWW 
HairpinNode  | Num Bases [4] | Left Index [5] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node U2538:U2542
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2538
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2540
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2541
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2542
Insertion    | Location [1] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 5, position 1

Sequences of instances from HL_23509.1:> HL_23509.1 8P9A G 2534 C 2545 GAAUUCAUUUUC