Alignment of J3_98985.1 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 5 2	6 5 3	8 5 4	10 5 5	12 5 6	14 7 7	16 8	18 7 8	20 5 9	22 10 10	24 11	26 10 11	28 2 12	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
J3_98985.1_Instance_1 J3_98985.1,J3_6CZR_015,G357_C48	G	G	A	A	U	C	U		A	G	C		G	C
J3_98985.1_Sequence_1 J3_98985.16CZR_G357_C48	G	G	A	A	U	C	U	*	A	G	C	*	G	C	true	100	0	0	0.00
J3_98985.1_Instance_2 J3_98985.1,J3_5J7L_001,G361_C47	G	G	A	A	U	A	U		A	G	C		G	C
J3_98985.1_Sequence_2 J3_98985.15J7L_G361_C47	G	G	A	A	U	A	U	*	A	G	C	*	G	C	true	98	0	0	0.33

Conserved interactions between motif group positions in J3_98985.1:

1 2 s35 
1 12 cWW 
2 4 s33 
2 5 tSW 
3 4 s35 
4 5 s33 
5 12 s55 
6 9 cSW 
6 11 s53 
7 8 cWW 
7 9 s55 
8 9 s35 
9 10 s35 
10 11 cWW 
2 5 6BPh
12 6 7BPh
6 12 7BPh
9 6 6BR

JAR3D SCFG/MRF model for J3_98985.1:

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 [12] // Initial node
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.003823887,0.055746509,0.004354386,0.079088977,0.000000000],[0.006716761,0.026247934,0.079759134,0.005218628,0.000000000],[0.004306029,0.594150318,0.000820775,0.010514714,0.000000000],[0.078076789,0.037915021,0.009216620,0.004043518,0.000000000],[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 [12] // Basepair G357 - C48 cWW 
JunctionNode | Branches [2]  | Left Index [2] | Right Index [11] // Junction node G358 - G47 ID J7572
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 [2] | Right Index [9] // Initial node 6CZR|1|1a|G|358 - 6CZR|1|1a|G|390 from node 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [5] | Num Right Bases [1] | Left Index [2] | Right Index [9] | Norm Constant [1.000000000000000] // Cluster node 6CZR|1|1a|G|358:6CZR|1|1a|C|362 and 6CZR|1|1a|G|390:6CZR|1|1a|G|390
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.033552090,0.037679500,0.341389009,0.015955153,0.000000000],[0.008614636,0.008823351,0.476977808,0.006861411,0.000000000],[0.004863415,0.003218728,0.039281526,0.002512034,0.000000000],[0.006789432,0.005026129,0.005634134,0.002821645,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CZR|1|1a|C|362 - 6CZR|1|1a|G|390 cSW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.004493731,0.003915250,0.001247311,0.006070803,0.000000000],[0.004053447,0.005072777,0.001247311,0.013448873,0.000000000],[0.028632475,0.008731179,0.008731179,0.892725760,0.000000000],[0.003946259,0.005485358,0.006047659,0.006150628,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6CZR|1|1a|G|358 - 6CZR|1|1a|U|361 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6CZR|1|1a|A|359
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6CZR|1|1a|A|360
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 [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009034335,0.017544761,0.009910087,0.196321162,0.000000000],[0.022043953,0.009831675,0.196981684,0.011044900,0.000000000],[0.009929415,0.194460696,0.002044250,0.023047545,0.000000000],[0.224032836,0.010374563,0.053294552,0.010103588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Basepair U363 - A389 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [10] | Right Index [11] // Initial node
BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // Basepair C391 - G47 cWW 
HairpinNode  | Num Bases [1] | Left Index [11] | Right Index [11] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation

Sequences of instances from J3_98985.1:> J3_98985.1 6CZR G 357 C 48 GGAAUCU*AGC*GC > J3_98985.1 5J7L G 361 C 47 GGAAUAU*AGC*GC