Alignment of IL_48076.6 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_48076.6
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	10 3 4	12 2 5	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_48076.6_Instance_1 IL_48076.6,IL_9DFE_092,C2496_G2455	C		A		C		G	G
IL_48076.6_Sequence_1 IL_48076.69DFE_C_2496_G_2455	C		A		C	*	G	G	true	100	0	0	0.00
IL_48076.6_Instance_2 IL_48076.6,IL_5J7L_392,C2496_G2455	C		A		C		G	G
IL_48076.6_Sequence_2 IL_48076.65J7L_C_2496_G_2455	C		A		C	*	G	G	true	100	0	0	0.00
IL_48076.6_Instance_3 IL_48076.6,IL_4V9F_082,U2531_A2490	U		A		C		G	A
IL_48076.6_Sequence_3 IL_48076.64V9F_U_2531_A_2490	U		A		C	*	G	A	true	94	0	0	0.53
IL_48076.6_Instance_4 IL_48076.6,IL_7A0S_084,C2475_G2434	C		A		C		G	G
IL_48076.6_Sequence_4 IL_48076.67A0S_C_2475_G_2434	C		A		C	*	G	G	true	100	0	0	0.00
IL_48076.6_Instance_5 IL_48076.6,IL_4WF9_090,C2523_G2482	C		A		C		G	G
IL_48076.6_Sequence_5 IL_48076.64WF9_C_2523_G_2482	C		A		C	*	G	G	true	100	0	0	0.00
IL_48076.6_Instance_6 IL_48076.6,IL_8TSV_001,U6_A20	U		G		C		G	A
IL_48076.6_Sequence_6 IL_48076.68TSV_U6_A20	U		G		C	*	G	A	true	79	0	0	1.96
IL_48076.6_Instance_7 IL_48076.6,IL_3NKB_002,G55_C48	G		U		A		U	C
IL_48076.6_Sequence_7 IL_48076.63NKB_G55_C48	G		U		A	*	U	C	true	87	0	0	1.21
IL_48076.6_Instance_8 IL_48076.6,IL_7A0S_082,U2380_G2394	U		A		C		G	G
IL_48076.6_Sequence_8 IL_48076.67A0S_U_2380_G_2394	U		A		C	*	G	G	true	96	0	0	0.35
IL_48076.6_Instance_9 IL_48076.6,IL_1I6U_001,U9_G29	U		A		A		U	G
IL_48076.6_Sequence_9 IL_48076.61I6U_U9_G29	U		A		A	*	U	G	true	92	0	0	0.73
IL_48076.6_Instance_10 IL_48076.6,IL_5J7L_028,U594_G645	U		A		A		U	G
IL_48076.6_Sequence_10 IL_48076.65J7L_U594_G645	U		A		A	*	U	G	true	92	0	0	0.73
IL_48076.6_Instance_11 IL_48076.6,IL_9DFE_090,U2401_G2415	U		C		C		G	G
IL_48076.6_Sequence_11 IL_48076.69DFE_U_2401_G_2415	U		C		C	*	G	G	true	92	0	0	0.81
IL_48076.6_Instance_12 IL_48076.6,IL_8P9A_329,U2865_G2824	U		U		C		G	G
IL_48076.6_Sequence_12 IL_48076.68P9A_U_2865_G_2824	U		U		C	*	G	G	true	91	0	0	0.85
IL_48076.6_Instance_13 IL_48076.6,IL_5T5A_002,C50_G11	C		G		C		G	G
IL_48076.6_Sequence_13 IL_48076.65T5A_C50_G11	C		G		C	*	G	G	true	85	0	0	1.43
IL_48076.6_Instance_14 IL_48076.6,IL_4OQU_002,C42_G30	C		A		A		U	G
IL_48076.6_Sequence_14 IL_48076.64OQU_C42_G30	C		A		A	*	U	G	true	96	0	0	0.38
IL_48076.6_Instance_15 IL_48076.6,IL_1XJR_002,U37_G14	U		A		C		G	G
IL_48076.6_Sequence_15 IL_48076.61XJR_U37_G14	U		A		C	*	G	G	true	96	0	0	0.35
IL_48076.6_Instance_16 IL_48076.6,IL_5J7L_320,C2050_G2618	C		A		A		U	G
IL_48076.6_Sequence_16 IL_48076.65J7L_C_2050_G_2618	C		A		A	*	U	G	true	96	0	0	0.38
IL_48076.6_Instance_17 IL_48076.6,IL_1S03_004,C34_G17	C		A		A		U	G
IL_48076.6_Sequence_17 IL_48076.61S03_C34_G17	C		A		A	*	U	G	true	96	0	0	0.38
IL_48076.6_Instance_18 IL_48076.6,IL_1S03_008,C34_G17	C		A		A		U	G
IL_48076.6_Sequence_18 IL_48076.61S03_C34_G17	C		A		A	*	U	G	true	96	0	0	0.38
IL_48076.6_Instance_19 IL_48076.6,IL_4LFB_024,G594_C645	G		G		C		G	C
IL_48076.6_Sequence_19 IL_48076.64LFB_G594_C645	G		G		C	*	G	C	true	81	0	0	1.84
IL_48076.6_Instance_20 IL_48076.6,IL_3OXE_003,C68_G36	C		U		C		G	G
IL_48076.6_Sequence_20 IL_48076.63OXE_C68_G36	C		U		C	*	G	G	true	95	0	0	0.50
IL_48076.6_Instance_21 IL_48076.6,IL_7A0S_073,C2033_G2597	C		A		G		C	G
IL_48076.6_Sequence_21 IL_48076.67A0S_C_2033_G_2597	C		A		G	*	C	G	true	85	0	0	1.40
IL_48076.6_Instance_22 IL_48076.6,IL_9DFE_008,U363E_G272E	U		A		C		G	G
IL_48076.6_Sequence_22 IL_48076.69DFE_U_363E_G_272E	U		A		C	*	G	G	true	96	0	0	0.35
IL_48076.6_Instance_23 IL_48076.6,IL_9DFE_078,C2050_G2618	C		A		G		C	G
IL_48076.6_Sequence_23 IL_48076.69DFE_C_2050_G_2618	C		A		G	*	C	G	true	85	0	0	1.40
IL_48076.6_Instance_24 IL_48076.6,IL_5VOE_005,U24_G13	U		G		G		C	G
IL_48076.6_Sequence_24 IL_48076.65VOE_U24_G13	U		G		G	*	C	G	true	83	0	0	1.62
IL_48076.6_Instance_25 IL_48076.6,IL_7EOG_001,C5_G45	C		A		C		G	G
IL_48076.6_Sequence_25 IL_48076.67EOG_C5_G45	C		A		C	*	G	G	true	100	0	0	0.00
IL_48076.6_Instance_26 IL_48076.6,IL_5Y85_005,C40_G10	C		G		C		G	G
IL_48076.6_Sequence_26 IL_48076.65Y85_C40_G10	C		G		C	*	G	G	true	85	0	0	1.43
IL_48076.6_Instance_27 IL_48076.6,IL_4WF9_078,C2077_G2645	C		A		G		C	G
IL_48076.6_Sequence_27 IL_48076.64WF9_C_2077_G_2645	C		A		G	*	C	G	true	85	0	0	1.40
IL_48076.6_Instance_28 IL_48076.6,IL_9FN3_003,G33_C13	G		C		A		U	C
IL_48076.6_Sequence_28 IL_48076.69FN3_G33_C13	G		C		A	*	U	C	true	87	0	0	1.23
IL_48076.6_Instance_29 IL_48076.6,IL_9FN3_001,G33_C13	G		C		A		U	C
IL_48076.6_Sequence_29 IL_48076.69FN3_G33_C13	G		C		A	*	U	C	true	87	0	0	1.23
IL_48076.6_Instance_30 IL_48076.6,IL_1G1X_002,C747_G658	C		C		C		G	G
IL_48076.6_Sequence_30 IL_48076.61G1X_C747_G658	C		C		C	*	G	G	true	95	0	0	0.45
IL_48076.6_Instance_31 IL_48076.6,IL_1G1X_005,C747_G658	C		C		C		G	G
IL_48076.6_Sequence_31 IL_48076.61G1X_C747_G658	C		C		C	*	G	G	true	95	0	0	0.45
IL_48076.6_Instance_32 IL_48076.6,IL_4LFB_028,C747_G658	C		C		C		G	G
IL_48076.6_Sequence_32 IL_48076.64LFB_C747_G658	C		C		C	*	G	G	true	95	0	0	0.45
IL_48076.6_Instance_33 IL_48076.6,IL_9DFE_093,U2457_G2494	U		G		A		U	G
IL_48076.6_Sequence_33 IL_48076.69DFE_U_2457_G_2494	U		G		A	*	U	G	true	79	0	0	2.00
IL_48076.6_Instance_34 IL_48076.6,IL_4V9F_044,A1191_U1206	A	A	A		A		U	U
IL_48076.6_Sequence_34 IL_48076.64V9F_A_1191_U_1206	A	A	A		A	*	U	U	true	52	0	0	4.52
IL_48076.6_Instance_35 IL_48076.6,IL_7A0S_085,U2436_G2473	U		G		A		U	G
IL_48076.6_Sequence_35 IL_48076.67A0S_U_2436_G_2473	U		G		A	*	U	G	true	79	0	0	2.00
IL_48076.6_Instance_36 IL_48076.6,IL_4WF9_091,U2484_G2521	U		U		A		U	G
IL_48076.6_Sequence_36 IL_48076.64WF9_U_2484_G_2521	U		U		A	*	U	G	true	88	0	0	1.16
IL_48076.6_Instance_37 IL_48076.6,IL_4WF9_026,G783_C803	G		A		C		G	C
IL_48076.6_Sequence_37 IL_48076.64WF9_G783_C803	G		A		C	*	G	C	true	96	0	0	0.40
IL_48076.6_Instance_38 IL_48076.6,IL_5J7L_385,G1087_C1102	G	A	A		A		U	C
IL_48076.6_Sequence_38 IL_48076.65J7L_G_1087_C_1102	G	A	A		A	*	U	C	true	56	0	0	4.20
IL_48076.6_Instance_39 IL_48076.6,IL_5J7L_264,G738_C758	G		A		C		G	C
IL_48076.6_Sequence_39 IL_48076.65J7L_G738_C758	G		A		C	*	G	C	true	96	0	0	0.40
IL_48076.6_Instance_40 IL_48076.6,IL_3SUX_002,U47_A38	U		G		U		G	A
IL_48076.6_Sequence_40 IL_48076.63SUX_U47_A38	U		G		U	*	G	A	true	62	0	0	3.58
IL_48076.6_Instance_41 IL_48076.6,IL_8P9A_293,U1819_G1624	U		U	U	C		G	G
IL_48076.6_Sequence_41 IL_48076.68P9A_U_1819_G_1624	U		U	U	C	*	G	G	true	45	0	0	5.19

Conserved interactions between motif group positions in IL_48076.6:

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

JAR3D SCFG/MRF model for IL_48076.6:

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 [0.0000189657778974] | Pair Probability [[0.007254050,0.012212825,0.008573343,0.116976024,0.000000000],[0.074083044,0.010870955,0.241924012,0.010182756,0.000000000],[0.008664105,0.161567920,0.001765957,0.016023730,0.000000000],[0.142304215,0.009774436,0.169733779,0.008088849,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.950006015,0.049873682,0.000117332,0.000002970] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | 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 C2496 - G2455 cWW 
ClusterNode  | Deletion Probability [0.0000001090702450] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [4] | Norm Constant [0.269997599475133] // Cluster node 9DFE|1|1A|A|2497:9DFE|1|1A|C|2498 and 9DFE|1|1A|G|2454:9DFE|1|1A|G|2454
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.006859043,0.013695562,0.007712596,0.241305589,0.000000000],[0.018854797,0.007295180,0.299757026,0.009097647,0.000000000],[0.007755563,0.172384196,0.001517610,0.024466163,0.000000000],[0.141737052,0.009069619,0.030763239,0.007729117,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|C|2498 - 9DFE|1|1A|G|2454 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.123752841,0.145749012,0.062196495,0.032831430,0.000000000],[0.079017867,0.092714775,0.004566895,0.016458179,0.000000000],[0.034873827,0.034831999,0.071248893,0.067003407,0.000000000],[0.081164325,0.088445651,0.004566895,0.060577510,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|A|2497 - 9DFE|1|1A|C|2498 cSH 
Insertion    | Location [1] | Length Distribution [0.974362859,0.025546540,0.000089116,0.000001485] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
InitialNode  | Left Length Distribution [0.998645549,0.001293652,0.000060798] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.998645549,0.001293652,0.000060798] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [3] // New Initial node after Cluster
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_48076.6:> IL_48076.6 9DFE C 2496 G 2455 CAC*GG > IL_48076.6 5J7L C 2496 G 2455 CAC*GG > IL_48076.6 4V9F U 2531 A 2490 UAC*GA > IL_48076.6 7A0S C 2475 G 2434 CAC*GG > IL_48076.6 4WF9 C 2523 G 2482 CAC*GG > IL_48076.6 8TSV U 6 A 20 UGC*GA > IL_48076.6 3NKB G 55 C 48 GUA*UC > IL_48076.6 7A0S U 2380 G 2394 UAC*GG > IL_48076.6 1I6U U 9 G 29 UAA*UG > IL_48076.6 5J7L U 594 G 645 UAA*UG > IL_48076.6 9DFE U 2401 G 2415 UCC*GG > IL_48076.6 8P9A U 2865 G 2824 UUC*GG > IL_48076.6 5T5A C 50 G 11 CGC*GG > IL_48076.6 4OQU C 42 G 30 CAA*UG > IL_48076.6 1XJR U 37 G 14 UAC*GG > IL_48076.6 5J7L C 2050 G 2618 CAA*UG > IL_48076.6 1S03 C 34 G 17 CAA*UG > IL_48076.6 1S03 C 34 G 17 CAA*UG > IL_48076.6 4LFB G 594 C 645 GGC*GC > IL_48076.6 3OXE C 68 G 36 CUC*GG > IL_48076.6 7A0S C 2033 G 2597 CAG*CG > IL_48076.6 9DFE U 363E G 272E UAC*GG > IL_48076.6 9DFE C 2050 G 2618 CAG*CG > IL_48076.6 5VOE U 24 G 13 UGG*CG > IL_48076.6 7EOG C 5 G 45 CAC*GG > IL_48076.6 5Y85 C 40 G 10 CGC*GG > IL_48076.6 4WF9 C 2077 G 2645 CAG*CG > IL_48076.6 9FN3 G 33 C 13 GCA*UC > IL_48076.6 9FN3 G 33 C 13 GCA*UC > IL_48076.6 1G1X C 747 G 658 CCC*GG > IL_48076.6 1G1X C 747 G 658 CCC*GG > IL_48076.6 4LFB C 747 G 658 CCC*GG > IL_48076.6 9DFE U 2457 G 2494 UGA*UG > IL_48076.6 4V9F A 1191 U 1206 AAAA*UU > IL_48076.6 7A0S U 2436 G 2473 UGA*UG > IL_48076.6 4WF9 U 2484 G 2521 UUA*UG > IL_48076.6 4WF9 G 783 C 803 GAC*GC > IL_48076.6 5J7L G 1087 C 1102 GAAA*UC > IL_48076.6 5J7L G 738 C 758 GAC*GC > IL_48076.6 3SUX U 47 A 38 UGU*GA > IL_48076.6 8P9A U 1819 G 1624 UUUC*GG