Alignment of IL_50694.7 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 3 3	8 3 4	10 5	12 3 5	14 2 6	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_50694.7_Instance_1 IL_50694.7,IL_4LFB_027,U751_A655	U	G	A	C		G	A
IL_50694.7_Sequence_1 IL_50694.74LFB_U751_A655	U	G	A	C	*	G	A	true	98	0	0	0.15
IL_50694.7_Instance_2 IL_50694.7,IL_5J7L_031,U751_A655	U	G	A	C		G	A
IL_50694.7_Sequence_2 IL_50694.75J7L_U751_A655	U	G	A	C	*	G	A	true	98	0	0	0.15
IL_50694.7_Instance_3 IL_50694.7,IL_1G1X_001,U751_A655	U	G	A	C		G	A
IL_50694.7_Sequence_3 IL_50694.71G1X_U751_A655	U	G	A	C	*	G	A	true	98	0	0	0.15
IL_50694.7_Instance_4 IL_50694.7,IL_1KUQ_001,U50_A19	U	G	A	C		G	A
IL_50694.7_Sequence_4 IL_50694.71KUQ_U50_A19	U	G	A	C	*	G	A	true	98	0	0	0.15
IL_50694.7_Instance_5 IL_50694.7,IL_1G1X_004,U751_A655	U	G	A	C		G	A
IL_50694.7_Sequence_5 IL_50694.71G1X_U751_A655	U	G	A	C	*	G	A	true	98	0	0	0.15
IL_50694.7_Instance_6 IL_50694.7,IL_9DFE_065,G1666_C1994	G	G	A	A		U	C
IL_50694.7_Sequence_6 IL_50694.79DFE_G_1666_C_1994	G	G	A	A	*	U	C	true	94	0	0	0.59
IL_50694.7_Instance_7 IL_50694.7,IL_6N5P_003,C94_G45	C	G	A	C		G	G
IL_50694.7_Sequence_7 IL_50694.76N5P_C94_G45	C	G	A	C	*	G	G	true	100	0	0	0.00
IL_50694.7_Instance_8 IL_50694.7,IL_5J7L_306,G1666_C1994	G	G	A	A		U	C
IL_50694.7_Sequence_8 IL_50694.75J7L_G_1666_C_1994	G	G	A	A	*	U	C	true	94	0	0	0.59
IL_50694.7_Instance_9 IL_50694.7,IL_8P9A_417,C962_G866	C	A	U	U		A	G
IL_50694.7_Sequence_9 IL_50694.78P9A_C962_G866	C	A	U	U	*	A	G	true	79	0	0	1.97
IL_50694.7_Instance_10 IL_50694.7,IL_4QLM_004,C91_G40	C	G	U	C		G	G
IL_50694.7_Sequence_10 IL_50694.74QLM_C91_G40	C	G	U	C	*	G	G	true	99	0	0	0.07
IL_50694.7_Instance_11 IL_50694.7,IL_4W90_004,C96_G59	C	G	U	C		G	G
IL_50694.7_Sequence_11 IL_50694.74W90_C96_G59	C	G	U	C	*	G	G	true	99	0	0	0.07
IL_50694.7_Instance_12 IL_50694.7,IL_9DFE_049,G1310_C1604	G	G	U	U		A	C
IL_50694.7_Sequence_12 IL_50694.79DFE_G_1310_C_1604	G	G	U	U	*	A	C	true	91	0	0	0.81
IL_50694.7_Instance_13 IL_50694.7,IL_4WF9_064,G1710_C2021	G	G	A	A		U	C
IL_50694.7_Sequence_13 IL_50694.74WF9_G_1710_C_2021	G	G	A	A	*	U	C	true	94	0	0	0.59
IL_50694.7_Instance_14 IL_50694.7,IL_4V9F_061,G1744_C2035	G	G	A	A		U	C
IL_50694.7_Sequence_14 IL_50694.74V9F_G_1744_C_2035	G	G	A	A	*	U	C	true	94	0	0	0.59
IL_50694.7_Instance_15 IL_50694.7,IL_4QK9_003,C93_G44	C	G	U	C		G	G
IL_50694.7_Sequence_15 IL_50694.74QK9_C93_G44	C	G	U	C	*	G	G	true	99	0	0	0.07
IL_50694.7_Instance_16 IL_50694.7,IL_8P9A_304,G1898_C2337	G	G	A	A		U	C
IL_50694.7_Sequence_16 IL_50694.78P9A_G_1898_C_2337	G	G	A	A	*	U	C	true	94	0	0	0.59
IL_50694.7_Instance_17 IL_50694.7,IL_7A0S_061,G1683_C1977	G	G	A	A		U	C
IL_50694.7_Sequence_17 IL_50694.77A0S_G_1683_C_1977	G	G	A	A	*	U	C	true	94	0	0	0.59
IL_50694.7_Instance_18 IL_50694.7,IL_4WF9_049,G1347_C1648	G	U	U	U		A	C
IL_50694.7_Sequence_18 IL_50694.74WF9_G_1347_C_1648	G	U	U	U	*	A	C	true	87	0	0	1.24
IL_50694.7_Instance_19 IL_50694.7,IL_4V9F_008,C245_G266	C	G	A	A		U	G
IL_50694.7_Sequence_19 IL_50694.74V9F_C245_G266	C	G	A	A	*	U	G	true	93	0	0	0.69
IL_50694.7_Instance_20 IL_50694.7,IL_8CRE_081,G1894_C2315	G	G	A	A		U	C
IL_50694.7_Sequence_20 IL_50694.78CRE_G_1894_C_2315	G	G	A	A	*	U	C	true	94	0	0	0.59
IL_50694.7_Instance_21 IL_50694.7,IL_5J7L_290,G1310_C1604	G	G	U	U		A	C
IL_50694.7_Sequence_21 IL_50694.75J7L_G_1310_C_1604	G	G	U	U	*	A	C	true	91	0	0	0.81
IL_50694.7_Instance_22 IL_50694.7,IL_4V9F_050,G1416_C1679	G	G	U	U		A	C
IL_50694.7_Sequence_22 IL_50694.74V9F_G_1416_C_1679	G	G	U	U	*	A	C	true	91	0	0	0.81
IL_50694.7_Instance_23 IL_50694.7,IL_7A0S_046,G1323_C1620	G	G	U	U		A	C
IL_50694.7_Sequence_23 IL_50694.77A0S_G_1323_C_1620	G	G	U	U	*	A	C	true	91	0	0	0.81
IL_50694.7_Instance_24 IL_50694.7,IL_1NTA_003,C15_G111	C	U	U	C		G	G
IL_50694.7_Sequence_24 IL_50694.71NTA_C15_G111	C	U	U	C	*	G	G	true	70	0	0	2.83
IL_50694.7_Instance_25 IL_50694.7,IL_7A0S_023,U857_G945	U	G	U	U		A	G
IL_50694.7_Sequence_25 IL_50694.77A0S_U857_G945	U	G	U	U	*	A	G	true	72	0	0	2.63
IL_50694.7_Instance_26 IL_50694.7,IL_3D0U_004,C35_G52	C	A	U	C		G	G
IL_50694.7_Sequence_26 IL_50694.73D0U_C35_G52	C	A	U	C	*	G	G	true	77	0	0	2.22
IL_50694.7_Instance_27 IL_50694.7,IL_3DIL_004,C38_G55	C	A	U	C		G	G
IL_50694.7_Sequence_27 IL_50694.73DIL_C38_G55	C	A	U	C	*	G	G	true	77	0	0	2.22

Conserved interactions between motif group positions in IL_50694.7:

1 2 s35 
1 4 s35 
1 6 cWW 
2 5 tSH 
3 5 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
4 2 7BR

JAR3D SCFG/MRF model for IL_50694.7:

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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.007705814,0.014839876,0.008790270,0.155389627,0.000000000],[0.023809383,0.008301058,0.229841017,0.010553458,0.000000000],[0.008791465,0.253458850,0.001707631,0.019700595,0.000000000],[0.197190366,0.010458354,0.041176743,0.008285493,0.000000000],[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 [1] | Right Index [6] // Basepair U751 - A655 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [5] | Norm Constant [0.269834917482945] // Cluster node 4LFB|1|A|G|752:4LFB|1|A|C|754 and 4LFB|1|A|G|654:4LFB|1|A|G|654
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.049969097,0.033434352,0.026086782,0.137906964,0.000000000],[0.032069949,0.023767963,0.002385199,0.002385199,0.000000000],[0.144696098,0.002385199,0.224189228,0.158804201,0.000000000],[0.094603355,0.050695225,0.014235990,0.002385199,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|G|752 - 4LFB|1|A|G|654 tSH 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.007536218,0.016378002,0.008226958,0.226355717,0.000000000],[0.022037854,0.010650771,0.320218524,0.014309867,0.000000000],[0.004712413,0.090038483,0.000933994,0.015002766,0.000000000],[0.214217315,0.008820279,0.032391549,0.008169291,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|C|754 - 4LFB|1|A|G|654 cWW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.017241379,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.017241379,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.465517241,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4LFB|1|A|A|753
InitialNode  | Left Length Distribution [0.998007243,0.001900449,0.000092308] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.998007243,0.001900449,0.000092308] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [4] // New Initial node after Cluster
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_50694.7:> IL_50694.7 4LFB U 751 A 655 UGAC*GA > IL_50694.7 5J7L U 751 A 655 UGAC*GA > IL_50694.7 1G1X U 751 A 655 UGAC*GA > IL_50694.7 1KUQ U 50 A 19 UGAC*GA > IL_50694.7 1G1X U 751 A 655 UGAC*GA > IL_50694.7 9DFE G 1666 C 1994 GGAA*UC > IL_50694.7 6N5P C 94 G 45 CGAC*GG > IL_50694.7 5J7L G 1666 C 1994 GGAA*UC > IL_50694.7 8P9A C 962 G 866 CAUU*AG > IL_50694.7 4QLM C 91 G 40 CGUC*GG > IL_50694.7 4W90 C 96 G 59 CGUC*GG > IL_50694.7 9DFE G 1310 C 1604 GGUU*AC > IL_50694.7 4WF9 G 1710 C 2021 GGAA*UC > IL_50694.7 4V9F G 1744 C 2035 GGAA*UC > IL_50694.7 4QK9 C 93 G 44 CGUC*GG > IL_50694.7 8P9A G 1898 C 2337 GGAA*UC > IL_50694.7 7A0S G 1683 C 1977 GGAA*UC > IL_50694.7 4WF9 G 1347 C 1648 GUUU*AC > IL_50694.7 4V9F C 245 G 266 CGAA*UG > IL_50694.7 8CRE G 1894 C 2315 GGAA*UC > IL_50694.7 5J7L G 1310 C 1604 GGUU*AC > IL_50694.7 4V9F G 1416 C 1679 GGUU*AC > IL_50694.7 7A0S G 1323 C 1620 GGUU*AC > IL_50694.7 1NTA C 15 G 111 CUUC*GG > IL_50694.7 7A0S U 857 G 945 UGUU*AG > IL_50694.7 3D0U C 35 G 52 CAUC*GG > IL_50694.7 3DIL C 38 G 55 CAUC*GG