Alignment of IL_51454.3 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 2 2	5 3 I	6 4 3	8 5	10 4 4	12 2 5	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_51454.3_Instance_1 IL_51454.3,IL_6DLR_003,C39_G22	C		U		G		C	G
IL_51454.3_Sequence_1 IL_51454.36DLR_C39_G22	C		U		G	*	C	G	true	87	0	0	1.22
IL_51454.3_Instance_2 IL_51454.3,IL_8CRE_042,U1046_A994	U		U		U		A	A
IL_51454.3_Sequence_2 IL_51454.38CRE_U_1046_A994	U		U		U	*	A	A	true	75	0	0	2.34
IL_51454.3_Instance_3 IL_51454.3,IL_7MLW_004,C45_G17	C		U		G		C	G
IL_51454.3_Sequence_3 IL_51454.37MLW_C45_G17	C		U		G	*	C	G	true	87	0	0	1.22
IL_51454.3_Instance_4 IL_51454.3,IL_5T83_003,C36_G22	C		U		G		C	G
IL_51454.3_Sequence_4 IL_51454.35T83_C36_G22	C		U		G	*	C	G	true	87	0	0	1.22
IL_51454.3_Instance_5 IL_51454.3,IL_8P9A_267,U1050_A998	U		U		U		A	A
IL_51454.3_Sequence_5 IL_51454.38P9A_U_1050_A998	U		U		U	*	A	A	true	75	0	0	2.34
IL_51454.3_Instance_6 IL_51454.3,IL_8CRE_017,C439_G488	C		U	U	G		C	G
IL_51454.3_Sequence_6 IL_51454.38CRE_C439_G488	C		U	U	G	*	C	G	true	41	0	0	5.65
IL_51454.3_Instance_7 IL_51454.3,IL_4V9F_034,U1009_A957	U		C		C		G	A
IL_51454.3_Sequence_7 IL_51454.34V9F_U_1009_A957	U		C		C	*	G	A	true	100	0	0	0.01
IL_51454.3_Instance_8 IL_51454.3,IL_2QWY_009,U40_A24	U		A		G		C	A
IL_51454.3_Sequence_8 IL_51454.32QWY_U40_A24	U		A		G	*	C	A	true	82	0	0	1.74
IL_51454.3_Instance_9 IL_51454.3,IL_7A0S_028,U925_A876	U		C		C		G	A
IL_51454.3_Sequence_9 IL_51454.37A0S_U925_A876	U		C		C	*	G	A	true	100	0	0	0.01
IL_51454.3_Instance_10 IL_51454.3,IL_5J7L_247,U434_A44	U		C		C		G	A
IL_51454.3_Sequence_10 IL_51454.35J7L_U434_A44	U		C		C	*	G	A	true	100	0	0	0.01
IL_51454.3_Instance_11 IL_51454.3,IL_8CRE_457,C1291_G1303	C		U		G		C	G
IL_51454.3_Sequence_11 IL_51454.38CRE_C_1291_G_1303	C		U		G	*	C	G	true	87	0	0	1.22
IL_51454.3_Instance_12 IL_51454.3,IL_4WF9_032,U958_A908	U		C		C		G	A
IL_51454.3_Sequence_12 IL_51454.34WF9_U958_A908	U		C		C	*	G	A	true	100	0	0	0.01
IL_51454.3_Instance_13 IL_51454.3,IL_9DFE_027,U913_A863	U		C		C		G	A
IL_51454.3_Sequence_13 IL_51454.39DFE_U913_A863	U		C		C	*	G	A	true	100	0	0	0.01
IL_51454.3_Instance_14 IL_51454.3,IL_9C75_001,U35_G10	U		A		C		G	G
IL_51454.3_Sequence_14 IL_51454.39C75_U35_G10	U		A		C	*	G	G	true	76	0	0	2.28
IL_51454.3_Instance_15 IL_51454.3,IL_4LFB_038,C1226_G954	C		A		C		G	G
IL_51454.3_Sequence_15 IL_51454.34LFB_C_1226_G954	C		A		C	*	G	G	true	100	0	0	0.00
IL_51454.3_Instance_16 IL_51454.3,IL_5ML7_009,C2177_G2202	C		A		G		C	G
IL_51454.3_Sequence_16 IL_51454.35ML7_C_2177_G_2202	C		A		G	*	C	G	true	97	0	0	0.29
IL_51454.3_Instance_17 IL_51454.3,IL_8P9A_443,C1306_G1318	C		U		G		C	G
IL_51454.3_Sequence_17 IL_51454.38P9A_C_1306_G_1318	C		U		G	*	C	G	true	87	0	0	1.22
IL_51454.3_Instance_18 IL_51454.3,IL_8P9A_401,A518_U533	A		C		A		U	U
IL_51454.3_Sequence_18 IL_51454.38P9A_A518_U533	A		C		A	*	U	U	true	73	0	0	2.59
IL_51454.3_Instance_19 IL_51454.3,IL_6DTD_003,G22_C16	G		A		A		U	C
IL_51454.3_Sequence_19 IL_51454.36DTD_G22_C16	G		A		A	*	U	C	true	72	0	0	2.71
IL_51454.3_Instance_20 IL_51454.3,IL_8CRE_420,A516_U531	A		C		A		U	U
IL_51454.3_Sequence_20 IL_51454.38CRE_A516_U531	A		C		A	*	U	U	true	73	0	0	2.59
IL_51454.3_Instance_21 IL_51454.3,IL_8CRE_099,U2779_A2391	U	A	C		C		G	A
IL_51454.3_Sequence_21 IL_51454.38CRE_U_2779_A_2391	U	A	C		C	*	G	A	true	80	0	0	1.88
IL_51454.3_Instance_22 IL_51454.3,IL_5J7L_042,C1226_G954	C		A		C		G	G
IL_51454.3_Sequence_22 IL_51454.35J7L_C_1226_G954	C		A		C	*	G	G	true	100	0	0	0.00
IL_51454.3_Instance_23 IL_51454.3,IL_8CRE_447,C1445_G1164	C		A		C		G	G
IL_51454.3_Sequence_23 IL_51454.38CRE_C_1445_G_1164	C		A		C	*	G	G	true	100	0	0	0.00
IL_51454.3_Instance_24 IL_51454.3,IL_7TZS_003,C23_G36	C		C		U		A	G
IL_51454.3_Sequence_24 IL_51454.37TZS_C23_G36	C		C		U	*	A	G	true	67	0	0	3.14
IL_51454.3_Instance_25 IL_51454.3,IL_4UYK_001,C122_G78	C		A		C		G	G
IL_51454.3_Sequence_25 IL_51454.34UYK_C122_G78	C		A		C	*	G	G	true	100	0	0	0.00
IL_51454.3_Instance_26 IL_51454.3,IL_8CRE_394,C50_G427	C		A		U		A	G
IL_51454.3_Sequence_26 IL_51454.38CRE_C50_G427	C		A		U	*	A	G	true	97	0	0	0.29
IL_51454.3_Instance_27 IL_51454.3,IL_1U6B_007,G128_C178	G		A		G		C	C
IL_51454.3_Sequence_27 IL_51454.31U6B_G128_C178	G		A		G	*	C	C	true	73	0	0	2.53
IL_51454.3_Instance_28 IL_51454.3,IL_5J7L_324,U2438_A2071	U	A	C		U		A	A
IL_51454.3_Sequence_28 IL_51454.35J7L_U_2438_A_2071	U	A	C		U	*	A	A	true	77	0	0	2.17
IL_51454.3_Instance_29 IL_51454.3,IL_7A0S_003,U447_A43	U		C		C		G	A
IL_51454.3_Sequence_29 IL_51454.37A0S_U447_A43	U		C		C	*	G	A	true	100	0	0	0.01
IL_51454.3_Instance_30 IL_51454.3,IL_9DFE_031,U877_A899	U		A		G		C	A
IL_51454.3_Sequence_30 IL_51454.39DFE_U877_A899	U		A		G	*	C	A	true	82	0	0	1.74
IL_51454.3_Instance_31 IL_51454.3,IL_7A0S_076,U2417_A2054	U	A	C		C		G	A
IL_51454.3_Sequence_31 IL_51454.37A0S_U_2417_A_2054	U	A	C		C	*	G	A	true	80	0	0	1.88
IL_51454.3_Instance_32 IL_51454.3,IL_4V9F_075,U2473_A2112	U	A	C		C		G	A
IL_51454.3_Sequence_32 IL_51454.34V9F_U_2473_A_2112	U	A	C		C	*	G	A	true	80	0	0	1.88
IL_51454.3_Instance_33 IL_51454.3,IL_9DFE_348,U434_A43	U		C		C		G	A
IL_51454.3_Sequence_33 IL_51454.39DFE_U434_A43	U		C		C	*	G	A	true	100	0	0	0.01
IL_51454.3_Instance_34 IL_51454.3,IL_8P9A_377,C50_G429	C		A		U		A	G
IL_51454.3_Sequence_34 IL_51454.38P9A_C50_G429	C		A		U	*	A	G	true	97	0	0	0.29
IL_51454.3_Instance_35 IL_51454.3,IL_9DFE_081,U2438_A2071	U	A	C		C		G	A
IL_51454.3_Sequence_35 IL_51454.39DFE_U_2438_A_2071	U	A	C		C	*	G	A	true	80	0	0	1.88
IL_51454.3_Instance_36 IL_51454.3,IL_4LFB_054,C1260_G1274	C		A		C		G	G
IL_51454.3_Sequence_36 IL_51454.34LFB_C_1260_G_1274	C		A		C	*	G	G	true	100	0	0	0.00
IL_51454.3_Instance_37 IL_51454.3,IL_4R4V_001,U777_G608	U		U		A		U	G
IL_51454.3_Sequence_37 IL_51454.34R4V_U777_G608	U		U		A	*	U	G	true	68	0	0	3.06
IL_51454.3_Instance_38 IL_51454.3,IL_4WF9_081,U2465_A2098	U	A	C		C		G	A
IL_51454.3_Sequence_38 IL_51454.34WF9_U_2465_A_2098	U	A	C		C	*	G	A	true	80	0	0	1.88
IL_51454.3_Instance_39 IL_51454.3,IL_8P9A_322,U2807_A2413	U	A	C		C		G	A
IL_51454.3_Sequence_39 IL_51454.38P9A_U_2807_A_2413	U	A	C		C	*	G	A	true	80	0	0	1.88
IL_51454.3_Instance_40 IL_51454.3,IL_3IWN_001,G89_C3	G		A		U		A	C
IL_51454.3_Sequence_40 IL_51454.33IWN_G89_C3	G		A		U	*	A	C	true	73	0	0	2.53
IL_51454.3_Instance_41 IL_51454.3,IL_4LFB_004,C54_G357	C		A		U		A	G
IL_51454.3_Sequence_41 IL_51454.34LFB_C54_G357	C		A		U	*	A	G	true	97	0	0	0.29
IL_51454.3_Instance_42 IL_51454.3,IL_3K0J_002,C18_G36	C		C		U		A	G
IL_51454.3_Sequence_42 IL_51454.33K0J_C18_G36	C		C		U	*	A	G	true	67	0	0	3.14
IL_51454.3_Instance_43 IL_51454.3,IL_5J7L_004,C54_G357	C		A		U		A	G
IL_51454.3_Sequence_43 IL_51454.35J7L_C54_G357	C		A		U	*	A	G	true	97	0	0	0.29
IL_51454.3_Instance_44 IL_51454.3,IL_8CRE_419,U531_A516	U		A		A		U	A
IL_51454.3_Sequence_44 IL_51454.38CRE_U531_A516	U		A		A	*	U	A	true	80	0	0	1.92
IL_51454.3_Instance_45 IL_51454.3,IL_8P9A_433,C1459_G1179	C		A		C		G	G
IL_51454.3_Sequence_45 IL_51454.38P9A_C_1459_G_1179	C		A		C	*	G	G	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_51454.3:

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

JAR3D SCFG/MRF model for IL_51454.3:

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
ClusterNode  | Deletion Probability [0.0000000544785060] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [5] | Norm Constant [0.026384285500560] // Cluster node 6DLR|1|A|C|39:6DLR|1|A|U|40 and 6DLR|1|A|G|22:6DLR|1|A|G|22
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.006614080,0.012366324,0.007475838,0.148133616,0.000000000],[0.023377803,0.007425917,0.268524319,0.008824574,0.000000000],[0.007521544,0.155869528,0.001493007,0.017192719,0.000000000],[0.269702946,0.008478071,0.049729738,0.007269978,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DLR|1|A|C|39 - 6DLR|1|A|G|22 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.078658574,0.076390655,0.187722203,0.097106617,0.000000000],[0.184525663,0.072113430,0.019597915,0.094015495,0.000000000],[0.001297261,0.001297261,0.023570233,0.001297261,0.000000000],[0.038434952,0.001297261,0.121377959,0.001297261,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DLR|1|A|U|40 - 6DLR|1|A|G|22 tHS 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.042390954,0.063911666,0.005045895,0.069886495,0.000000000],[0.146727447,0.080996712,0.000821349,0.089193701,0.000000000],[0.066182965,0.000821349,0.047061250,0.066326255,0.000000000],[0.081194623,0.146797857,0.000821349,0.091820134,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DLR|1|A|C|39 - 6DLR|1|A|U|40 cSH 
Insertion    | Location [1] | Length Distribution [0.843487427,0.156284483,0.000219459,0.000008630] | Letter Distribution [0.833333333,0.055555556,0.055555556,0.055555556,0.000000000]// Insertion after nucleotide 1, position 1 in cluster node
InitialNode  | Left Length Distribution [0.976638942,0.023280906,0.000078918,0.000001233] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.006628422,0.012892329,0.007479019,0.175917433,0.000000000],[0.013829938,0.006800654,0.280794140,0.008941245,0.000000000],[0.007500515,0.210645333,0.001456266,0.018827313,0.000000000],[0.210023899,0.008796672,0.022252410,0.007214412,0.000000000],[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 G41 - C21 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_51454.3:> IL_51454.3 6DLR C 39 G 22 CUG*CG > IL_51454.3 8CRE U 1046 A 994 UUU*AA > IL_51454.3 7MLW C 45 G 17 CUG*CG > IL_51454.3 5T83 C 36 G 22 CUG*CG > IL_51454.3 8P9A U 1050 A 998 UUU*AA > IL_51454.3 8CRE C 439 G 488 CUUG*CG > IL_51454.3 4V9F U 1009 A 957 UCC*GA > IL_51454.3 2QWY U 40 A 24 UAG*CA > IL_51454.3 7A0S U 925 A 876 UCC*GA > IL_51454.3 5J7L U 434 A 44 UCC*GA > IL_51454.3 8CRE C 1291 G 1303 CUG*CG > IL_51454.3 4WF9 U 958 A 908 UCC*GA > IL_51454.3 9DFE U 913 A 863 UCC*GA > IL_51454.3 9C75 U 35 G 10 UAC*GG > IL_51454.3 4LFB C 1226 G 954 CAC*GG > IL_51454.3 5ML7 C 2177 G 2202 CAG*CG > IL_51454.3 8P9A C 1306 G 1318 CUG*CG > IL_51454.3 8P9A A 518 U 533 ACA*UU > IL_51454.3 6DTD G 22 C 16 GAA*UC > IL_51454.3 8CRE A 516 U 531 ACA*UU > IL_51454.3 8CRE U 2779 A 2391 UACC*GA > IL_51454.3 5J7L C 1226 G 954 CAC*GG > IL_51454.3 8CRE C 1445 G 1164 CAC*GG > IL_51454.3 7TZS C 23 G 36 CCU*AG > IL_51454.3 4UYK C 122 G 78 CAC*GG > IL_51454.3 8CRE C 50 G 427 CAU*AG > IL_51454.3 1U6B G 128 C 178 GAG*CC > IL_51454.3 5J7L U 2438 A 2071 UACU*AA > IL_51454.3 7A0S U 447 A 43 UCC*GA > IL_51454.3 9DFE U 877 A 899 UAG*CA > IL_51454.3 7A0S U 2417 A 2054 UACC*GA > IL_51454.3 4V9F U 2473 A 2112 UACC*GA > IL_51454.3 9DFE U 434 A 43 UCC*GA > IL_51454.3 8P9A C 50 G 429 CAU*AG > IL_51454.3 9DFE U 2438 A 2071 UACC*GA > IL_51454.3 4LFB C 1260 G 1274 CAC*GG > IL_51454.3 4R4V U 777 G 608 UUA*UG > IL_51454.3 4WF9 U 2465 A 2098 UACC*GA > IL_51454.3 8P9A U 2807 A 2413 UACC*GA > IL_51454.3 3IWN G 89 C 3 GAU*AC > IL_51454.3 4LFB C 54 G 357 CAU*AG > IL_51454.3 3K0J C 18 G 36 CCU*AG > IL_51454.3 5J7L C 54 G 357 CAU*AG > IL_51454.3 8CRE U 531 A 516 UAA*UA > IL_51454.3 8P9A C 1459 G 1179 CAC*GG