Alignment of IL_82444.1 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 3 2	5 3 I	6 4 3	8 5	10 4 4	11 3 I	12 3 5	13 2 I	14 2 6
IL_82444.1_Instance_1 IL_82444.1_IL_3CZW_002_U10_A9	U	G		A		U		G		A
IL_82444.1_Sequence_1 IL_82444.1_IL_3CZW_002_U10_A9	U	G		A	*	U		G		A
IL_82444.1_Instance_2 IL_82444.1_IL_3CZW_001_U10_A9	U	G		A		U		G		A
IL_82444.1_Sequence_2 IL_82444.1_IL_3CZW_001_U10_A9	U	G		A	*	U		G		A
IL_82444.1_Instance_3 IL_82444.1_IL_2R22_001_U6_A21	U	G		A		U		G		A
IL_82444.1_Sequence_3 IL_82444.1_IL_2R22_001_U6_A21	U	G		A	*	U		G		A
IL_82444.1_Instance_4 IL_82444.1_IL_4BPP_012_C144_G158	C	G		A		U		G		G
IL_82444.1_Sequence_4 IL_82444.1_IL_4BPP_012_C144_G158	C	G		A	*	U		G		G
IL_82444.1_Instance_5 IL_82444.1_IL_3SJ2_003_C13_G9	C	G		G		C		G		G
IL_82444.1_Sequence_5 IL_82444.1_IL_3SJ2_003_C13_G9	C	G		G	*	C		G		G
IL_82444.1_Instance_6 IL_82444.1_IL_3SJ2_001_C13_G9	C	G		G		C		G		G
IL_82444.1_Sequence_6 IL_82444.1_IL_3SJ2_001_C13_G9	C	G		G	*	C		G		G
IL_82444.1_Instance_7 IL_82444.1_IL_3SJ2_002_C10_G12	C	G		G		C		G		G
IL_82444.1_Sequence_7 IL_82444.1_IL_3SJ2_002_C10_G12	C	G		G	*	C		G		G
IL_82444.1_Instance_8 IL_82444.1_IL_4E5C_001_C9_G11	C	G		G		C		G		G
IL_82444.1_Sequence_8 IL_82444.1_IL_4E5C_001_C9_G11	C	G		G	*	C		G		G
IL_82444.1_Instance_9 IL_82444.1_IL_3R1D_002_C5_G7	C	G		G		C		G		G
IL_82444.1_Sequence_9 IL_82444.1_IL_3R1D_002_C5_G7	C	G		G	*	C		G		G
IL_82444.1_Instance_10 IL_82444.1_IL_2AW7_011_G144_C178	G	G		G		C		G		C
IL_82444.1_Sequence_10 IL_82444.1_IL_2AW7_011_G144_C178	G	G		G	*	C		G		C
IL_82444.1_Instance_11 IL_82444.1_IL_3U5F_070_C1323_G1292	C	G		A		U		G		G
IL_82444.1_Sequence_11 IL_82444.1_IL_3U5F_070_C_1323_G_1292	C	G		A	*	U		G		G
IL_82444.1_Instance_12 IL_82444.1_IL_3U5F_044_C848_G824	C	C		A		U		G		G
IL_82444.1_Sequence_12 IL_82444.1_IL_3U5F_044_C848_G824	C	C		A	*	U		G		G
IL_82444.1_Instance_13 IL_82444.1_IL_3W3S_003_A47N_U47C	A	G		C		G		G		U
IL_82444.1_Sequence_13 IL_82444.1_IL_3W3S_003_A47N_U47C	A	G		C	*	G		G		U
IL_82444.1_Instance_14 IL_82444.1_IL_420D_001_A26_U7	A	A		U		A		G		U
IL_82444.1_Sequence_14 IL_82444.1_IL_420D_001_A26_U7	A	A		U	*	A		G		U
IL_82444.1_Instance_15 IL_82444.1_IL_4BPP_020_U397_A382	U	A		C		G		G		A
IL_82444.1_Sequence_15 IL_82444.1_IL_4BPP_020_U397_A382	U	A		C	*	G		G		A
IL_82444.1_Instance_16 IL_82444.1_IL_420D_002_A10_U23	A	A		U		A		G		U
IL_82444.1_Sequence_16 IL_82444.1_IL_420D_002_A10_U23	A	A		U	*	A		G		U
IL_82444.1_Instance_17 IL_82444.1_IL_3U5F_022_U406_A391	U	A		C		G		G		A
IL_82444.1_Sequence_17 IL_82444.1_IL_3U5F_022_U406_A391	U	A		C	*	G		G		A
IL_82444.1_Instance_18 IL_82444.1_IL_406D_002_U8_G27	U	G		G		U		G		G
IL_82444.1_Sequence_18 IL_82444.1_IL_406D_002_U8_G27	U	G		G	*	U		G		G
IL_82444.1_Instance_19 IL_82444.1_IL_2XXA_011_A19_U81	A	G		C		G		G	G	U
IL_82444.1_Sequence_19 IL_82444.1_IL_2XXA_011_A19_U81	A	G		C	*	G		G	G	U
IL_82444.1_Instance_20 IL_82444.1_IL_4IOA_029_U917_A885	U	A		U		A		C		A
IL_82444.1_Sequence_20 IL_82444.1_IL_4IOA_029_U917_A885	U	A		U	*	A		C		A
IL_82444.1_Instance_21 IL_82444.1_IL_3U5F_023_A420_U413	A	A		G		C		A		U
IL_82444.1_Sequence_21 IL_82444.1_IL_3U5F_023_A420_U413	A	A		G	*	C		A		U
IL_82444.1_Instance_22 IL_82444.1_IL_3NJ7_001_C3_G8	C	A		G		C		A		G
IL_82444.1_Sequence_22 IL_82444.1_IL_3NJ7_001_C3_G8	C	A		G	*	C		A		G
IL_82444.1_Instance_23 IL_82444.1_IL_3U5H_151_U64_A96	U	A		A		U		C	G	A
IL_82444.1_Sequence_23 IL_82444.1_IL_3U5H_151_U64_A96	U	A		A	*	U	C	G		A
IL_82444.1_Instance_24 IL_82444.1_IL_3U5H_072_G1623_C1822	G	G		A		U		U	UU	C
IL_82444.1_Sequence_24 IL_82444.1_IL_3U5H_072_G_1623_C_1822	G	G		A	*	U		U	UU	C
IL_82444.1_Instance_25 IL_82444.1_IL_4KYY_002_U8_G10	U	U		G		U		U		G
IL_82444.1_Sequence_25 IL_82444.1_IL_4KYY_002_U8_G10	U	U		G	*	U		U		G
IL_82444.1_Instance_26 IL_82444.1_IL_2QEK_002_C15_G10	C	A		C		G	A	A		G
IL_82444.1_Sequence_26 IL_82444.1_IL_2QEK_002_C15_G10	C	A		C	*	G	A	A		G
IL_82444.1_Instance_27 IL_82444.1_IL_2QBG_065_C1990_G1674	C	U	G	U		A		C	UAG	G
IL_82444.1_Sequence_27 IL_82444.1_IL_2QBG_065_C_1990_G_1674	C	U	G	U	*	A		C	UAG	G
IL_82444.1_Instance_28 IL_82444.1_IL_3V2F_064_C1990_G1674	C	U	G	U		A		C	UCU	G
IL_82444.1_Sequence_28 IL_82444.1_IL_3V2F_064_C_1990_G_1674	C	U	G	U	*	A		C	UCU	G
IL_82444.1_Instance_29 IL_82444.1_IL_1S72_062_C2031_G1752	C	U	G	U		A		U	UCG	G
IL_82444.1_Sequence_29 IL_82444.1_IL_1S72_062_C_2031_G_1752	C	U	G	U	*	A		U	UCG	G

Conserved interactions between motif group positions in IL_82444.1:

1 2 s35 
1 6 cWW 
2 3 s35 
2 5 cWH 
2 6 s55 
3 4 cWW 
3 5 s53 
4 5 s33 
5 6 s55 
5 5 2BPh

JAR3D SCFG/MRF model for IL_82444.1:

Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [6] // Initial node U10 - A9 from junction 
BasepairNode | Deletion Probability [0.0000022743263860] | Pair Probability [[0.007822282,0.015211771,0.008835548,0.188466571,0.000000000],[0.033000285,0.007458781,0.254016983,0.009993188,0.000000000],[0.008900242,0.166374685,0.001775563,0.019081185,0.000000000],[0.205125114,0.009698657,0.054346970,0.009892175,0.000000000],[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 [0.791507109,0.070240175,0.034773039,0.103289839,0.000180940,0.000008899] | Right Letter Distribution [0.100000000,0.166666667,0.300000000,0.433333333,0.000000000] | Left Index [1] | Right Index [6] // Basepair U10 - A9 cWW 
BasepairNode | Deletion Probability [0.0000118002824533] | Pair Probability [[0.035467769,0.023839862,0.144309590,0.003917147,0.000000000],[0.000584048,0.012153125,0.230639564,0.005843907,0.000000000],[0.012326241,0.000584048,0.448316792,0.012211955,0.000000000],[0.002449461,0.023839862,0.013330949,0.030185680,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.894950292,0.104785667,0.000255141,0.000008900] | Left Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Right Length Distribution [0.963774631,0.036079981,0.000142421,0.000002967] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [2] | Right Index [5] // Basepair G11 - G8 cWH 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008000198,0.032420260,0.008759319,0.213649271,0.000000000],[0.015762103,0.007220259,0.189250168,0.009572296,0.000000000],[0.008727472,0.213435371,0.001771176,0.053523146,0.000000000],[0.197250027,0.009720924,0.019476146,0.011461864,0.000000000],[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 [3] | Right Index [4] // Basepair A12 - U7 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_82444.1:> IL_82444.1 IL_3CZW_002 U 10 A 9 UGA*UGA > IL_82444.1 IL_3CZW_001 U 10 A 9 UGA*UGA > IL_82444.1 IL_2R22_001 U 6 A 21 UGA*UGA > IL_82444.1 IL_4BPP_012 C 144 G 158 CGA*UGG > IL_82444.1 IL_3SJ2_003 C 13 G 9 CGG*CGG > IL_82444.1 IL_3SJ2_001 C 13 G 9 CGG*CGG > IL_82444.1 IL_3SJ2_002 C 10 G 12 CGG*CGG > IL_82444.1 IL_4E5C_001 C 9 G 11 CGG*CGG > IL_82444.1 IL_3R1D_002 C 5 G 7 CGG*CGG > IL_82444.1 IL_2AW7_011 G 144 C 178 GGG*CGC > IL_82444.1 IL_3U5F_070 C 1323 G 1292 CGA*UGG > IL_82444.1 IL_3U5F_044 C 848 G 824 CCA*UGG > IL_82444.1 IL_3W3S_003 A 47N U 47C AGC*GGU > IL_82444.1 IL_420D_001 A 26 U 7 AAU*AGU > IL_82444.1 IL_4BPP_020 U 397 A 382 UAC*GGA > IL_82444.1 IL_420D_002 A 10 U 23 AAU*AGU > IL_82444.1 IL_3U5F_022 U 406 A 391 UAC*GGA > IL_82444.1 IL_406D_002 U 8 G 27 UGG*UGG > IL_82444.1 IL_2XXA_011 A 19 U 81 AGC*GGGU > IL_82444.1 IL_4IOA_029 U 917 A 885 UAU*ACA > IL_82444.1 IL_3U5F_023 A 420 U 413 AAG*CAU > IL_82444.1 IL_3NJ7_001 C 3 G 8 CAG*CAG > IL_82444.1 IL_3U5H_151 U 64 A 96 UAA*UCGA > IL_82444.1 IL_3U5H_072 G 1623 C 1822 GGA*UUUUC > IL_82444.1 IL_4KYY_002 U 8 G 10 UUG*UUG > IL_82444.1 IL_2QEK_002 C 15 G 10 CAC*GAAG > IL_82444.1 IL_2QBG_065 C 1990 G 1674 CUGU*ACUAGG > IL_82444.1 IL_3V2F_064 C 1990 G 1674 CUGU*ACUCUG > IL_82444.1 IL_1S72_062 C 2031 G 1752 CUGU*AUUCGG