Alignment of IL_51387.2 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	5 3 I	6 3 3	8 5 4	10 6	12 5 5	14 3 6	16 2 7	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_51387.2_Instance_1 IL_51387.2,IL_9DFE_020,G738_C758	G		G		U	G		C	U	C
IL_51387.2_Sequence_1 IL_51387.29DFE_G738_C758	G		G		U	G	*	C	U	C	true	100	0	0	0.00
IL_51387.2_Instance_2 IL_51387.2,IL_8P9A_259,G869_C890	G		G		U	U		A	U	C
IL_51387.2_Sequence_2 IL_51387.28P9A_G869_C890	G		G		U	U	*	A	U	C	true	100	0	0	0.01
IL_51387.2_Instance_3 IL_51387.2,IL_7A0S_019,G751_C771	G		G		U	G		C	U	C
IL_51387.2_Sequence_3 IL_51387.27A0S_G751_C771	G		G		U	G	*	C	U	C	true	100	0	0	0.00
IL_51387.2_Instance_4 IL_51387.2,IL_8CRE_034,G865_C886	G		G		U	U		A	U	C
IL_51387.2_Sequence_4 IL_51387.28CRE_G865_C886	G		G		U	U	*	A	U	C	true	100	0	0	0.01
IL_51387.2_Instance_5 IL_51387.2,IL_4V9F_028,G830_C851	G		U		U	G		C	U	C
IL_51387.2_Sequence_5 IL_51387.24V9F_G830_C851	G		U		U	G	*	C	U	C	true	96	0	0	0.38
IL_51387.2_Instance_6 IL_51387.2,IL_8CRE_403,U257_A204	U	U	U		U	C		G	U	A
IL_51387.2_Sequence_6 IL_51387.28CRE_U257_A204	U		U	U	U	C	*	G	U	A	true	81	0	0	1.82
IL_51387.2_Instance_7 IL_51387.2,IL_8P9A_386,U259_A206	U	U	U		U	C		G	U	A
IL_51387.2_Sequence_7 IL_51387.28P9A_U259_A206	U		U	U	U	C	*	G	U	A	true	81	0	0	1.82
IL_51387.2_Instance_8 IL_51387.2,IL_5D8H_003,G1197_C1212	G	A	G		U	G		C	U	C
IL_51387.2_Sequence_8 IL_51387.25D8H_G_1197_C_1212	G	A	G		U	G	*	C	U	C	true	85	0	0	1.42
IL_51387.2_Instance_9 IL_51387.2,IL_1MMS_002,G1087_C1102	G	A	G		U	G		C	U	C
IL_51387.2_Sequence_9 IL_51387.21MMS_G_1087_C_1102	G	A	G		U	G	*	C	U	C	true	85	0	0	1.42
IL_51387.2_Instance_10 IL_51387.2,IL_8P9A_332,U2858_G2830	U		U	U	U	U		G	U	G
IL_51387.2_Sequence_10 IL_51387.28P9A_U_2858_G_2830	U		U	U	U	U	*	G	U	G	true	63	0	0	3.53
IL_51387.2_Instance_11 IL_51387.2,IL_8CRE_113,U2830_G2802	U		U	U	U	U		G	U	G
IL_51387.2_Sequence_11 IL_51387.28CRE_U_2830_G_2802	U		U	U	U	U	*	G	U	G	true	63	0	0	3.53
IL_51387.2_Instance_12 IL_51387.2,IL_8CRE_059,G1258_C1273	G	A	G		U	G		C	U	C
IL_51387.2_Sequence_12 IL_51387.28CRE_G_1258_C_1273	G	A	G		U	G	*	C	U	C	true	85	0	0	1.42
IL_51387.2_Instance_13 IL_51387.2,IL_4V9F_084,G2524_C2496	G		G	C	U	U		G	U	C
IL_51387.2_Sequence_13 IL_51387.24V9F_G_2524_C_2496	G		G	C	U	U	*	G	U	C	true	66	0	0	3.23
IL_51387.2_Instance_14 IL_51387.2,IL_8P9A_284,G1262_C1277	G	A	G		U	G		C	U	C
IL_51387.2_Sequence_14 IL_51387.28P9A_G_1262_C_1277	G	A	G		U	G	*	C	U	C	true	85	0	0	1.42
IL_51387.2_Instance_15 IL_51387.2,IL_9DFE_094,G2489_C2461	G		G	U	U	U		A	U	C
IL_51387.2_Sequence_15 IL_51387.29DFE_G_2489_C_2461	G		G	U	U	U	*	A	U	C	true	90	0	0	0.95
IL_51387.2_Instance_16 IL_51387.2,IL_4WF9_092,G2516_C2488	G		G	U	U	U		A	U	C
IL_51387.2_Sequence_16 IL_51387.24WF9_G_2516_C_2488	G		G	U	U	U	*	A	U	C	true	90	0	0	0.95
IL_51387.2_Instance_17 IL_51387.2,IL_7A0S_086,G2468_C2440	G		G	U	U	U		A	U	C
IL_51387.2_Sequence_17 IL_51387.27A0S_G_2468_C_2440	G		G	U	U	U	*	A	U	C	true	90	0	0	0.95
IL_51387.2_Instance_18 IL_51387.2,IL_5J7L_337,U2489_A2461	U		G	U	U	U		A	U	A
IL_51387.2_Sequence_18 IL_51387.25J7L_U_2489_A_2461	U		G	U	U	U	*	A	U	A	true	86	0	0	1.33
IL_51387.2_Instance_19 IL_51387.2,IL_4V9F_003,C440_G41	C		A		A	C		G	C	G
IL_51387.2_Sequence_19 IL_51387.24V9F_C440_G41	C		A		A	C	*	G	C	G	true	77	0	0	2.16
IL_51387.2_Instance_20 IL_51387.2,IL_3PDR_004,C33_G151	C		U		C	C		G	U	G
IL_51387.2_Sequence_20 IL_51387.23PDR_C33_G151	C		U		C	C	*	G	U	G	true	53	0	0	4.43

Conserved interactions between motif group positions in IL_51387.2:

1 2 s35 
1 7 cWW 
2 3 cSH 
3 4 s35 
3 6 cWW 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35

JAR3D SCFG/MRF model for IL_51387.2:

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 [0.0000049795766094] | Pair Probability [[0.008296274,0.016079379,0.009532980,0.156326100,0.000000000],[0.039696207,0.009728470,0.175317062,0.011282741,0.000000000],[0.009504468,0.268976635,0.001873621,0.020968068,0.000000000],[0.185312914,0.011317480,0.066801669,0.008985932,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.698392924,0.300735019,0.000834683,0.000037374] | Left Letter Distribution [0.562500000,0.062500000,0.062500000,0.312500000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G738 - C758 cWW 
ClusterNode  | Deletion Probability [0.0000000193172804] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [6] | Norm Constant [0.343191264578553] // Cluster node 9DFE|1|1A|G|739:9DFE|1|1A|U|740 and 9DFE|1|1A|U|757:9DFE|1|1A|U|757
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.012969457,0.250787748,0.011579538,0.020224389,0.000000000],[0.014334329,0.015455952,0.017287022,0.025623745,0.000000000],[0.011337681,0.017610232,0.003574619,0.045666438,0.000000000],[0.017667351,0.013766715,0.014652856,0.507461926,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|740 - 9DFE|1|1A|U|757 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.076991900,0.069414143,0.003947522,0.063819619,0.000000000],[0.056053966,0.075662938,0.000836233,0.060049250,0.000000000],[0.053968695,0.000836233,0.071714411,0.189305808,0.000000000],[0.069505340,0.077477395,0.000836233,0.129580317,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|739 - 9DFE|1|1A|U|740 cSH 
Insertion    | Location [1] | Length Distribution [0.648604883,0.350398605,0.000952915,0.000043597] | Letter Distribution [0.055555556,0.166666667,0.055555556,0.722222222,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
InitialNode  | 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 [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008254631,0.015194963,0.009508769,0.148501521,0.000000000],[0.052728315,0.010561558,0.184890064,0.011157201,0.000000000],[0.009537860,0.209332735,0.001919637,0.019699699,0.000000000],[0.206476664,0.010877682,0.092274218,0.009084483,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // Basepair G741 - C756 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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 IL_51387.2:> IL_51387.2 9DFE G 738 C 758 GGUG*CUC > IL_51387.2 8P9A G 869 C 890 GGUU*AUC > IL_51387.2 7A0S G 751 C 771 GGUG*CUC > IL_51387.2 8CRE G 865 C 886 GGUU*AUC > IL_51387.2 4V9F G 830 C 851 GUUG*CUC > IL_51387.2 8CRE U 257 A 204 UUUUC*GUA > IL_51387.2 8P9A U 259 A 206 UUUUC*GUA > IL_51387.2 5D8H G 1197 C 1212 GAGUG*CUC > IL_51387.2 1MMS G 1087 C 1102 GAGUG*CUC > IL_51387.2 8P9A U 2858 G 2830 UUUUU*GUG > IL_51387.2 8CRE U 2830 G 2802 UUUUU*GUG > IL_51387.2 8CRE G 1258 C 1273 GAGUG*CUC > IL_51387.2 4V9F G 2524 C 2496 GGCUU*GUC > IL_51387.2 8P9A G 1262 C 1277 GAGUG*CUC > IL_51387.2 9DFE G 2489 C 2461 GGUUU*AUC > IL_51387.2 4WF9 G 2516 C 2488 GGUUU*AUC > IL_51387.2 7A0S G 2468 C 2440 GGUUU*AUC > IL_51387.2 5J7L U 2489 A 2461 UGUUU*AUA > IL_51387.2 4V9F C 440 G 41 CAAC*GCG > IL_51387.2 3PDR C 33 G 151 CUCC*GUG