Alignment of IL_66635.5 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 4 I	6 5 3	8 6	10 5 4	12 2 5	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_66635.5_Instance_1 IL_66635.5,IL_6XH2_001,A22_U40	A		U	CU	G		C	U
IL_66635.5_Sequence_1 IL_66635.56XH2_A22_U40	A		U	CU	G	*	C	U	true	39	0	0	5.76
IL_66635.5_Instance_2 IL_66635.5,IL_6DLR_004,G36_C23	G		G	A	C		G	C
IL_66635.5_Sequence_2 IL_66635.56DLR_G36_C23	G		G	A	C	*	G	C	true	88	0	0	1.13
IL_66635.5_Instance_3 IL_66635.5,IL_1XOK_001,A864_U847	A		A	U	G		C	U
IL_66635.5_Sequence_3 IL_66635.51XOK_A864_U847	A		A	U	G	*	C	U	true	86	0	0	1.32
IL_66635.5_Instance_4 IL_66635.5,IL_1XOK_002,G877_C869	G		A	U	G		C	C
IL_66635.5_Sequence_4 IL_66635.51XOK_G877_C869	G		A	U	G	*	C	C	true	91	0	0	0.87
IL_66635.5_Instance_5 IL_66635.5,IL_6CF2_002,C22_G11	C		U	G	G		C	G
IL_66635.5_Sequence_5 IL_66635.56CF2_C22_G11	C		U	G	G	*	C	G	true	69	0	0	2.98
IL_66635.5_Instance_6 IL_66635.5,IL_5LYS_007,A39_U68	A		U	U	G		C	U
IL_66635.5_Sequence_6 IL_66635.55LYS_A39_U68	A		U	U	G	*	C	U	true	89	0	0	1.05
IL_66635.5_Instance_7 IL_66635.5,IL_9DFE_072,U1898_G1842	U		G	A	A		U	G
IL_66635.5_Sequence_7 IL_66635.59DFE_U_1898_G_1842	U		G	A	A	*	U	G	true	81	0	0	1.79
IL_66635.5_Instance_8 IL_66635.5,IL_8K7W_004,G30_C15	G		U	C	G		C	C
IL_66635.5_Sequence_8 IL_66635.58K7W_G30_C15	G		U	C	G	*	C	C	true	79	0	0	2.04
IL_66635.5_Instance_9 IL_66635.5,IL_5T83_004,G33_C23	G		G	U	C		G	C
IL_66635.5_Sequence_9 IL_66635.55T83_G33_C23	G		G	U	C	*	G	C	true	97	0	0	0.28
IL_66635.5_Instance_10 IL_66635.5,IL_5LYS_006,G70_C37	G		C	U	G		C	C
IL_66635.5_Sequence_10 IL_66635.55LYS_G70_C37	G		C	U	G	*	C	C	true	75	0	0	2.34
IL_66635.5_Instance_11 IL_66635.5,IL_7MLW_005,U43_G18	U		G		C		G	G
IL_66635.5_Sequence_11 IL_66635.57MLW_U43_G18	U		G		C	*	G	G	true	96	0	0	0.38
IL_66635.5_Instance_12 IL_66635.5,IL_387D_001,G15_C2	G		G	A	A		U	C
IL_66635.5_Sequence_12 IL_66635.5387D_G15_C2	G		G	A	A	*	U	C	true	85	0	0	1.40
IL_66635.5_Instance_13 IL_66635.5,IL_8K85_004,G36_C16	G		U	U	G		C	C
IL_66635.5_Sequence_13 IL_66635.58K85_G36_C16	G		U	U	G	*	C	C	true	94	0	0	0.61
IL_66635.5_Instance_14 IL_66635.5,IL_5WT1_001,G43_C27	G		G		U		A	C
IL_66635.5_Sequence_14 IL_66635.55WT1_G43_C27	G		G		U	*	A	C	true	97	0	0	0.32
IL_66635.5_Instance_15 IL_66635.5,IL_4KZD_006,G49_C31	G		U	U	G		C	C
IL_66635.5_Sequence_15 IL_66635.54KZD_G49_C31	G		U	U	G	*	C	C	true	94	0	0	0.61
IL_66635.5_Instance_16 IL_66635.5,IL_6JQ6_004,U62_G32	U		G		C		G	G
IL_66635.5_Sequence_16 IL_66635.56JQ6_U62_G32	U		G		C	*	G	G	true	96	0	0	0.38
IL_66635.5_Instance_17 IL_66635.5,IL_7L0Z_004,G41_C24	G		U	U	G		C	C
IL_66635.5_Sequence_17 IL_66635.57L0Z_G41_C24	G		U	U	G	*	C	C	true	94	0	0	0.61
IL_66635.5_Instance_18 IL_66635.5,IL_5J7L_352,U2878_G2839	U		A		C		G	G
IL_66635.5_Sequence_18 IL_66635.55J7L_U_2878_G_2839	U		A		C	*	G	G	true	89	0	0	1.04
IL_66635.5_Instance_19 IL_66635.5,IL_1U9S_008,G217_C196	G		G		C		G	C
IL_66635.5_Sequence_19 IL_66635.51U9S_G217_C196	G		G		C	*	G	C	true	100	0	0	0.00
IL_66635.5_Instance_20 IL_66635.5,IL_8K85_009,G36_C16	G		U	U	G		C	C
IL_66635.5_Sequence_20 IL_66635.58K85_G36_C16	G		U	U	G	*	C	C	true	94	0	0	0.61
IL_66635.5_Instance_21 IL_66635.5,IL_4WF9_106,U2898_G2859	U		A		C		G	G
IL_66635.5_Sequence_21 IL_66635.54WF9_U_2898_G_2859	U		A		C	*	G	G	true	89	0	0	1.04
IL_66635.5_Instance_22 IL_66635.5,IL_9FN3_002,C29_G16	C		G		C		G	G
IL_66635.5_Sequence_22 IL_66635.59FN3_C29_G16	C		G		C	*	G	G	true	95	0	0	0.43
IL_66635.5_Instance_23 IL_66635.5,IL_7A0S_067,U1881_G1834	U		G	A	A		U	G
IL_66635.5_Sequence_23 IL_66635.57A0S_U_1881_G_1834	U		G	A	A	*	U	G	true	81	0	0	1.79
IL_66635.5_Instance_24 IL_66635.5,IL_7OAX_001,U8_G45	U		G		G		C	G
IL_66635.5_Sequence_24 IL_66635.57OAX_U8_G45	U		G		G	*	C	G	true	97	0	0	0.32
IL_66635.5_Instance_25 IL_66635.5,IL_1NTA_001,C5_G115	C		G		C		G	G
IL_66635.5_Sequence_25 IL_66635.51NTA_C5_G115	C		G		C	*	G	G	true	95	0	0	0.43
IL_66635.5_Instance_26 IL_66635.5,IL_7VTI_003,U27_G10	U	G	A		U		A	G
IL_66635.5_Sequence_26 IL_66635.57VTI_U27_G10	U		G	A	U	*	A	G	true	81	0	0	1.83
IL_66635.5_Instance_27 IL_66635.5,IL_3DD2_003,G16_C11	G	U	A		C		G	C
IL_66635.5_Sequence_27 IL_66635.53DD2_G16_C11	G		U	A	C	*	G	C	true	84	0	0	1.52

Conserved interactions between motif group positions in IL_66635.5:

JAR3D SCFG/MRF model for IL_66635.5:

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 [0.0000165268883850] | Pair Probability [[0.008119714,0.014657209,0.009546989,0.146298096,0.000000000],[0.081979454,0.012064144,0.148187680,0.011107664,0.000000000],[0.009583035,0.227663485,0.001963330,0.020684472,0.000000000],[0.132828683,0.010994712,0.155183622,0.009137711,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.924139394,0.075631316,0.000222445,0.000006844] | Left Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | 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 [5] // Basepair A22 - U40 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.224137931,0.051724138,0.431034483,0.293103448,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left for 6XH2|1|D|U|23
InitialNode  | Left Length Distribution [0.407197585,0.554691320,0.037988013,0.000119663,0.000003419] | Left Letter Distribution [0.236842105,0.131578947,0.078947368,0.552631579,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.007677145,0.015331128,0.008692069,0.184511666,0.000000000],[0.015009270,0.007736109,0.242420128,0.010425499,0.000000000],[0.008684182,0.258593498,0.001671172,0.022654190,0.000000000],[0.176244577,0.010475269,0.021562187,0.008311913,0.000000000],[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 G26 - C39 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_66635.5:> IL_66635.5 6XH2 A 22 U 40 AUCUG*CU > IL_66635.5 6DLR G 36 C 23 GGAC*GC > IL_66635.5 1XOK A 864 U 847 AAUG*CU > IL_66635.5 1XOK G 877 C 869 GAUG*CC > IL_66635.5 6CF2 C 22 G 11 CUGG*CG > IL_66635.5 5LYS A 39 U 68 AUUG*CU > IL_66635.5 9DFE U 1898 G 1842 UGAA*UG > IL_66635.5 8K7W G 30 C 15 GUCG*CC > IL_66635.5 5T83 G 33 C 23 GGUC*GC > IL_66635.5 5LYS G 70 C 37 GCUG*CC > IL_66635.5 7MLW U 43 G 18 UGC*GG > IL_66635.5 387D G 15 C 2 GGAA*UC > IL_66635.5 8K85 G 36 C 16 GUUG*CC > IL_66635.5 5WT1 G 43 C 27 GGU*AC > IL_66635.5 4KZD G 49 C 31 GUUG*CC > IL_66635.5 6JQ6 U 62 G 32 UGC*GG > IL_66635.5 7L0Z G 41 C 24 GUUG*CC > IL_66635.5 5J7L U 2878 G 2839 UAC*GG > IL_66635.5 1U9S G 217 C 196 GGC*GC > IL_66635.5 8K85 G 36 C 16 GUUG*CC > IL_66635.5 4WF9 U 2898 G 2859 UAC*GG > IL_66635.5 9FN3 C 29 G 16 CGC*GG > IL_66635.5 7A0S U 1881 G 1834 UGAA*UG > IL_66635.5 7OAX U 8 G 45 UGG*CG > IL_66635.5 1NTA C 5 G 115 CGC*GG > IL_66635.5 7VTI U 27 G 10 UGAU*AG > IL_66635.5 3DD2 G 16 C 11 GUAC*GC