Alignment of HL_01962.2 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 4 3	7 4 I	8 5 4	10 4 5	12 3 6	13 2 I	14 2 7	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
HL_01962.2_Instance_1 HL_01962.2,HL_5J7L_178,U1777_A1787	U	U	U	AUU	A	A	A	A	A
HL_01962.2_Sequence_1 HL_01962.25J7L_U_1777_A_1787	U	U	U	AUU	A	A	A	A	A	true	100	0	0	0.00
HL_01962.2_Instance_2 HL_01962.2,HL_9DFE_043,U1777_A1787	U	U	U	ACC	A	A	A	A	A
HL_01962.2_Sequence_2 HL_01962.29DFE_U_1777_A_1787	U	U	U	ACC	A	A	A	A	A	true	93	0	0	1.24
HL_01962.2_Instance_3 HL_01962.2,HL_4V9F_047,U1833_A1843	U	C	U	AGU	A	A	C	A	A
HL_01962.2_Sequence_3 HL_01962.24V9F_U_1833_A_1843	U	C	U	AGU	A	A	C	A	A	true	90	0	0	1.64
HL_01962.2_Instance_4 HL_01962.2,HL_4WF9_043,U1804_A1814	U	U	U	AUC	A	A	A	A	A
HL_01962.2_Sequence_4 HL_01962.24WF9_U_1804_A_1814	U	U	U	AUC	A	A	A	A	A	true	96	0	0	0.62
HL_01962.2_Instance_5 HL_01962.2,HL_8CRE_044,U2113_A2123	U	C	U	AAU	U	A	A	A	A
HL_01962.2_Sequence_5 HL_01962.28CRE_U_2113_A_2123	U	C	U	AAU	U	A	A	A	A	true	94	0	0	1.02
HL_01962.2_Instance_6 HL_01962.2,HL_8P9A_157,U2135_A2145	U	C	U	AAU	U	A	A	A	A
HL_01962.2_Sequence_6 HL_01962.28P9A_U_2135_A_2145	U	C	U	AAU	U	A	A	A	A	true	94	0	0	1.02

Conserved interactions between motif group positions in HL_01962.2:

1 2 s35 
1 7 cWW 
2 5 s35 
2 6 tWH 
2 7 s55 
3 4 s53 
3 5 tWH 
3 6 s35 
6 7 s35 
5 3 6BPh
4 3 7BR

JAR3D SCFG/MRF model for HL_01962.2:

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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.008693416,0.016882694,0.009536121,0.188912817,0.000000000],[0.021212105,0.009460668,0.189548413,0.010628111,0.000000000],[0.009554720,0.187122556,0.001967108,0.022177826,0.000000000],[0.253314615,0.009983070,0.051283436,0.009722321,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Left Index [1] | Right Index [7] // Basepair U1777 - A1787 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.021774901,0.003830933,0.045403346,0.003830933,0.000000000],[0.159041103,0.246982386,0.003830933,0.003830933,0.000000000],[0.003830933,0.009802312,0.029731307,0.022707913,0.000000000],[0.294642610,0.003830933,0.019745733,0.127182789,0.000000000],[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 [2] | Right Index [6] // Basepair U1778 - A1785 tWH 
BasepairNode | Deletion Probability [0.0000000000030783] | Pair Probability [[0.031477798,0.000995155,0.004670692,0.000995155,0.000000000],[0.070053184,0.080190499,0.000995155,0.000995155,0.000000000],[0.006966087,0.002385453,0.007568072,0.004426108,0.000000000],[0.771710443,0.000995155,0.005773772,0.009802114,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.000000000,0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.425000000,0.175000000,0.075000000,0.325000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // Basepair U1779 - A1784 tWH 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A1783:A1783
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.640625000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.015625000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.015625000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.328125000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1783

Sequences of instances from HL_01962.2:> HL_01962.2 5J7L U 1777 A 1787 UUUAUUAAAAA > HL_01962.2 9DFE U 1777 A 1787 UUUACCAAAAA > HL_01962.2 4V9F U 1833 A 1843 UCUAGUAACAA > HL_01962.2 4WF9 U 1804 A 1814 UUUAUCAAAAA > HL_01962.2 8CRE U 2113 A 2123 UCUAAUUAAAA > HL_01962.2 8P9A U 2135 A 2145 UCUAAUUAAAA