Alignment of HL_57176.2 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	3 2 I	4 3 2	6 3 3	8 3 4	9 2 I	10 2 5	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
HL_57176.2_Instance_1 HL_57176.2,HL_4V9F_035,G1430_C1436	G	C	U	G	A	U	C
HL_57176.2_Sequence_1 HL_57176.24V9F_G_1430_C_1436	G	C	U	G	A	U	C	true	79	0	0	2.01
HL_57176.2_Instance_2 HL_57176.2,HL_4WF9_033,G1361_C1367	G	C	U	C	G	U	C
HL_57176.2_Sequence_2 HL_57176.24WF9_G_1361_C_1367	G	C	U	C	G	U	C	true	100	0	0	0.00
HL_57176.2_Instance_3 HL_57176.2,HL_7A0S_033,G1337_C1343	G	G	U	C	G	U	C
HL_57176.2_Sequence_3 HL_57176.27A0S_G_1337_C_1343	G	G	U	C	G	U	C	true	100	0	0	0.00
HL_57176.2_Instance_4 HL_57176.2,HL_9DFE_032,G1324_C1330	G	G	U	C	G	U	C
HL_57176.2_Sequence_4 HL_57176.29DFE_G_1324_C_1330	G	G	U	C	G	U	C	true	100	0	0	0.00
HL_57176.2_Instance_5 HL_57176.2,HL_5J7L_170,G1492_C1498	G	C	A	A	A	U	C
HL_57176.2_Sequence_5 HL_57176.25J7L_G_1492_C_1498	G	C	A	A	A	U	C	true	98	0	0	0.24
HL_57176.2_Instance_6 HL_57176.2,HL_5J7L_166,G1324_C1330	G	U	U	A	A	U	C
HL_57176.2_Sequence_6 HL_57176.25J7L_G_1324_C_1330	G	U	U	A	A	U	C	true	84	0	0	1.50
HL_57176.2_Instance_7 HL_57176.2,HL_8P9A_144,A1506_U1512	A	G	C	A	G	U	U
HL_57176.2_Sequence_7 HL_57176.28P9A_A_1506_U_1512	A	G	C	A	G	U	U	true	93	0	0	0.64
HL_57176.2_Instance_8 HL_57176.2,HL_9DFE_036,G1492_C1498	G	C	A	A	A	U	C
HL_57176.2_Sequence_8 HL_57176.29DFE_G_1492_C_1498	G	C	A	A	A	U	C	true	98	0	0	0.24
HL_57176.2_Instance_9 HL_57176.2,HL_8CRE_031,A1502_U1508	A	G	C	A	G	U	U
HL_57176.2_Sequence_9 HL_57176.28CRE_A_1502_U_1508	A	G	C	A	G	U	U	true	93	0	0	0.64
HL_57176.2_Instance_10 HL_57176.2,HL_5VJ9_003,G6_C11	G		A	C	G	A	C
HL_57176.2_Sequence_10 HL_57176.25VJ9_G6_C11	G		A	C	G	A	C	true	96	0	0	0.37
HL_57176.2_Instance_11 HL_57176.2,HL_7A0S_073,U1647_G1652	U		C	A	A	U	G
HL_57176.2_Sequence_11 HL_57176.27A0S_U_1647_G_1652	U		C	A	A	U	G	true	77	0	0	2.21
HL_57176.2_Instance_12 HL_57176.2,HL_5NDI_002,G8_C13	G		A	C	G	A	C
HL_57176.2_Sequence_12 HL_57176.25NDI_G8_C13	G		A	C	G	A	C	true	96	0	0	0.37
HL_57176.2_Instance_13 HL_57176.2,HL_5NDH_002,G6_C11	G		A	C	G	A	C
HL_57176.2_Sequence_13 HL_57176.25NDH_G6_C11	G		A	C	G	A	C	true	96	0	0	0.37
HL_57176.2_Instance_14 HL_57176.2,HL_9DFE_039,C1631_G1635	C		A	A	G	A	G
HL_57176.2_Sequence_14 HL_57176.29DFE_C_1631_G_1635	C		A	A	G	A	G	true	94	0	0	0.60

Conserved interactions between motif group positions in HL_57176.2:

JAR3D SCFG/MRF model for HL_57176.2:

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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000000040855542] | Pair Probability [[0.008735539,0.017755694,0.009964210,0.187384201,0.000000000],[0.033797140,0.009731709,0.179406419,0.011719932,0.000000000],[0.009910918,0.261735677,0.001941004,0.026344728,0.000000000],[0.170450490,0.012008493,0.049547647,0.009566200,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.357278698,0.640261683,0.002345513,0.000114106] | Left Letter Distribution [0.045454545,0.409090909,0.409090909,0.136363636,0.000000000] | Right Length Distribution [0.003545471,0.992731785,0.003545471,0.000177274] | Right Letter Distribution [0.281250000,0.031250000,0.031250000,0.656250000,0.000000000] | Left Index [1] | Right Index [5] // Basepair G1430 - C1436 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U1432:A1434
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.406250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.218750000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.031250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.343750000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1432
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.468750000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.406250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.093750000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1433
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.343750000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.593750000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1434

Sequences of instances from HL_57176.2:> HL_57176.2 4V9F G 1430 C 1436 GCUGAUC > HL_57176.2 4WF9 G 1361 C 1367 GCUCGUC > HL_57176.2 7A0S G 1337 C 1343 GGUCGUC > HL_57176.2 9DFE G 1324 C 1330 GGUCGUC > HL_57176.2 5J7L G 1492 C 1498 GCAAAUC > HL_57176.2 5J7L G 1324 C 1330 GUUAAUC > HL_57176.2 8P9A A 1506 U 1512 AGCAGUU > HL_57176.2 9DFE G 1492 C 1498 GCAAAUC > HL_57176.2 8CRE A 1502 U 1508 AGCAGUU > HL_57176.2 5VJ9 G 6 C 11 GACGAC > HL_57176.2 7A0S U 1647 G 1652 UCAAUG > HL_57176.2 5NDI G 8 C 13 GACGAC > HL_57176.2 5NDH G 6 C 11 GACGAC > HL_57176.2 9DFE C 1631 G 1635 CAAGAG