Alignment of IL_61258.15 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 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_61258.15_Instance_1 IL_61258.15,IL_9DFE_034,C994_G1160	C	C	A		U	G
IL_61258.15_Sequence_1 IL_61258.159DFE_C994_G_1160	C	C	A	*	U	G	true	91	0	0	0.87
IL_61258.15_Instance_2 IL_61258.15,IL_5J7L_276,C994_G1160	C	C	A		U	G
IL_61258.15_Sequence_2 IL_61258.155J7L_C994_G_1160	C	C	A	*	U	G	true	91	0	0	0.87
IL_61258.15_Instance_3 IL_61258.15,IL_7A0S_032,U1005_A1171	U	C	A		U	A
IL_61258.15_Sequence_3 IL_61258.157A0S_U_1005_A_1171	U	C	A	*	U	A	true	93	0	0	0.65
IL_61258.15_Instance_4 IL_61258.15,IL_4WF9_035,C1038_G1204	C	C	A		U	G
IL_61258.15_Sequence_4 IL_61258.154WF9_C_1038_G_1204	C	C	A	*	U	G	true	91	0	0	0.87
IL_61258.15_Instance_5 IL_61258.15,IL_7KGA_004,A44_U11	A	C	U		A	U
IL_61258.15_Sequence_5 IL_61258.157KGA_A44_U11	A	C	U	*	A	U	true	91	0	0	0.82
IL_61258.15_Instance_6 IL_61258.15,IL_1DQF_001,U15_A4	U	C	G		C	A
IL_61258.15_Sequence_6 IL_61258.151DQF_U15_A4	U	C	G	*	C	A	true	97	0	0	0.28
IL_61258.15_Instance_7 IL_61258.15,IL_1S03_006,G9_C40	G	C	G		C	C
IL_61258.15_Sequence_7 IL_61258.151S03_G9_C40	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_8 IL_61258.15,IL_3HHN_003,G46_C113	G	C	U		A	C
IL_61258.15_Sequence_8 IL_61258.153HHN_G46_C113	G	C	U	*	A	C	true	98	0	0	0.23
IL_61258.15_Instance_9 IL_61258.15,IL_6XKO_001,G78_C57	G	C	G		C	C
IL_61258.15_Sequence_9 IL_61258.156XKO_G78_C57	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_10 IL_61258.15,IL_7PMM_001,U33_A14	U	C	G		C	A
IL_61258.15_Sequence_10 IL_61258.157PMM_U33_A14	U	C	G	*	C	A	true	97	0	0	0.28
IL_61258.15_Instance_11 IL_61258.15,IL_9DE7_001,U4_A56	U	C	U		A	A
IL_61258.15_Sequence_11 IL_61258.159DE7_U4_A56	U	C	U	*	A	A	true	95	0	0	0.52
IL_61258.15_Instance_12 IL_61258.15,IL_8F5G_002,G8_C20	G	C	U		A	C
IL_61258.15_Sequence_12 IL_61258.158F5G_G8_C20	G	C	U	*	A	C	true	98	0	0	0.23
IL_61258.15_Instance_13 IL_61258.15,IL_1S03_002,G9_C40	G	C	G		C	C
IL_61258.15_Sequence_13 IL_61258.151S03_G9_C40	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_14 IL_61258.15,IL_3IVK_001,G46_C113	G	C	U		A	C
IL_61258.15_Sequence_14 IL_61258.153IVK_G46_C113	G	C	U	*	A	C	true	98	0	0	0.23
IL_61258.15_Instance_15 IL_61258.15,IL_1DQH_001,U15_A4	U	C	G		C	A
IL_61258.15_Sequence_15 IL_61258.151DQH_U15_A4	U	C	G	*	C	A	true	97	0	0	0.28
IL_61258.15_Instance_16 IL_61258.15,IL_5F5H_001,G18_C5	G	C	U		A	C
IL_61258.15_Sequence_16 IL_61258.155F5H_G18_C5	G	C	U	*	A	C	true	98	0	0	0.23
IL_61258.15_Instance_17 IL_61258.15,IL_8CRE_074,G1774_C1666	G	C	G		C	C
IL_61258.15_Sequence_17 IL_61258.158CRE_G_1774_C_1666	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_18 IL_61258.15,IL_5F5H_002,G18_C5	G	C	U		A	C
IL_61258.15_Sequence_18 IL_61258.155F5H_G18_C5	G	C	U	*	A	C	true	98	0	0	0.23
IL_61258.15_Instance_19 IL_61258.15,IL_6ZDP_001,A1346_U1291	A	C	U		A	U
IL_61258.15_Sequence_19 IL_61258.156ZDP_A_1346_U_1291	A	C	U	*	A	U	true	91	0	0	0.82
IL_61258.15_Instance_20 IL_61258.15,IL_7A0S_055,G1488_C1535	G	C	U		A	C
IL_61258.15_Sequence_20 IL_61258.157A0S_G_1488_C_1535	G	C	U	*	A	C	true	98	0	0	0.23
IL_61258.15_Instance_21 IL_61258.15,IL_5KPY_001,U25_A44	U	C	G		C	A
IL_61258.15_Sequence_21 IL_61258.155KPY_U25_A44	U	C	G	*	C	A	true	97	0	0	0.28
IL_61258.15_Instance_22 IL_61258.15,IL_7KGA_001,A44_U11	A	C	U		A	U
IL_61258.15_Sequence_22 IL_61258.157KGA_A44_U11	A	C	U	*	A	U	true	91	0	0	0.82
IL_61258.15_Instance_23 IL_61258.15,IL_6CK5_003,U39_A22	U	C	G		C	A
IL_61258.15_Sequence_23 IL_61258.156CK5_U39_A22	U	C	G	*	C	A	true	97	0	0	0.28
IL_61258.15_Instance_24 IL_61258.15,IL_8P9A_297,G1778_C1670	G	C	G		C	C
IL_61258.15_Sequence_24 IL_61258.158P9A_G_1778_C_1670	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_25 IL_61258.15,IL_8P9A_373,U24_A601	U	C	A		U	A
IL_61258.15_Sequence_25 IL_61258.158P9A_U24_A601	U	C	A	*	U	A	true	93	0	0	0.65
IL_61258.15_Instance_26 IL_61258.15,IL_3W3S_001,G11_C24	G	C	C		G	C
IL_61258.15_Sequence_26 IL_61258.153W3S_G11_C24	G	C	C	*	G	C	true	95	0	0	0.48
IL_61258.15_Instance_27 IL_61258.15,IL_5J7L_311,G1731_C1728	G	C	G		C	C
IL_61258.15_Sequence_27 IL_61258.155J7L_G_1731_C_1728	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_28 IL_61258.15,IL_3DIL_001,G12_C79	G	C	G		C	C
IL_61258.15_Sequence_28 IL_61258.153DIL_G12_C79	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_29 IL_61258.15,IL_3SNP_003,G7_C25	G	C	U		A	C
IL_61258.15_Sequence_29 IL_61258.153SNP_G7_C25	G	C	U	*	A	C	true	98	0	0	0.23
IL_61258.15_Instance_30 IL_61258.15,IL_3SN2_001,U7_A25	U	C	G		C	A
IL_61258.15_Sequence_30 IL_61258.153SN2_U7_A25	U	C	G	*	C	A	true	97	0	0	0.28
IL_61258.15_Instance_31 IL_61258.15,IL_8CRE_390,U24_A599	U	C	A		U	A
IL_61258.15_Sequence_31 IL_61258.158CRE_U24_A599	U	C	A	*	U	A	true	93	0	0	0.65
IL_61258.15_Instance_32 IL_61258.15,IL_3D0U_001,G9_C76	G	C	G		C	C
IL_61258.15_Sequence_32 IL_61258.153D0U_G9_C76	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_33 IL_61258.15,IL_8P9A_231,G150_C8	G	C	G		C	C
IL_61258.15_Sequence_33 IL_61258.158P9A_G150_C8	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_34 IL_61258.15,IL_8CRE_002,G150_C7	G	C	G		C	C
IL_61258.15_Sequence_34 IL_61258.158CRE_G150_C7	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_35 IL_61258.15,IL_7A0S_010,G558_C553	G	C	G		C	C
IL_61258.15_Sequence_35 IL_61258.157A0S_G558_C553	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_36 IL_61258.15,IL_8CRE_151,U90_A68	U	C	A		U	A
IL_61258.15_Sequence_36 IL_61258.158CRE_U90_A68	U	C	A	*	U	A	true	93	0	0	0.65
IL_61258.15_Instance_37 IL_61258.15,IL_4C7O_003,C31_G13	C	C	G		C	G
IL_61258.15_Sequence_37 IL_61258.154C7O_C31_G13	C	C	G	*	C	G	true	95	0	0	0.50
IL_61258.15_Instance_38 IL_61258.15,IL_1KUQ_002,C46_G22	C	C	C		G	G
IL_61258.15_Sequence_38 IL_61258.151KUQ_C46_G22	C	C	C	*	G	G	true	90	0	0	0.98
IL_61258.15_Instance_39 IL_61258.15,IL_3SN2_002,G18_C14	G	C	C		G	C
IL_61258.15_Sequence_39 IL_61258.153SN2_G18_C14	G	C	C	*	G	C	true	95	0	0	0.48
IL_61258.15_Instance_40 IL_61258.15,IL_7A0S_025,G938_C864	G	C	G		C	C
IL_61258.15_Sequence_40 IL_61258.157A0S_G938_C864	G	C	G	*	C	C	true	100	0	0	0.00
IL_61258.15_Instance_41 IL_61258.15,IL_9DFE_107,U2878_G2839	U	C	C		G	G
IL_61258.15_Sequence_41 IL_61258.159DFE_U_2878_G_2839	U	C	C	*	G	G	true	73	0	0	2.59

Conserved interactions between motif group positions in IL_61258.15:

1 3 s35 
1 5 cWW 
3 4 cWW 
3 5 s55 
4 5 s35

JAR3D SCFG/MRF model for IL_61258.15:

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 [0.0000244705618206] | Pair Probability [[0.006891097,0.013836828,0.007774207,0.162972707,0.000000000],[0.018667456,0.007301896,0.178378982,0.009113513,0.000000000],[0.007747704,0.293071724,0.001521619,0.019536079,0.000000000],[0.220990621,0.009137066,0.035541877,0.007516624,0.000000000],[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 [5] // Basepair C994 - G1160 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.011627907,0.965116279,0.011627907,0.011627907,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left for 9DFE|1|1A|C|995
InitialNode  | 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 [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 [[0.006836075,0.014126423,0.007637435,0.194477815,0.000000000],[0.013604740,0.006976679,0.173391379,0.008849605,0.000000000],[0.007606227,0.281157731,0.001496744,0.021674295,0.000000000],[0.222738202,0.008935420,0.022940209,0.007551021,0.000000000],[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 A996 - U1159 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_61258.15:> IL_61258.15 9DFE C 994 G 1160 CCA*UG > IL_61258.15 5J7L C 994 G 1160 CCA*UG > IL_61258.15 7A0S U 1005 A 1171 UCA*UA > IL_61258.15 4WF9 C 1038 G 1204 CCA*UG > IL_61258.15 7KGA A 44 U 11 ACU*AU > IL_61258.15 1DQF U 15 A 4 UCG*CA > IL_61258.15 1S03 G 9 C 40 GCG*CC > IL_61258.15 3HHN G 46 C 113 GCU*AC > IL_61258.15 6XKO G 78 C 57 GCG*CC > IL_61258.15 7PMM U 33 A 14 UCG*CA > IL_61258.15 9DE7 U 4 A 56 UCU*AA > IL_61258.15 8F5G G 8 C 20 GCU*AC > IL_61258.15 1S03 G 9 C 40 GCG*CC > IL_61258.15 3IVK G 46 C 113 GCU*AC > IL_61258.15 1DQH U 15 A 4 UCG*CA > IL_61258.15 5F5H G 18 C 5 GCU*AC > IL_61258.15 8CRE G 1774 C 1666 GCG*CC > IL_61258.15 5F5H G 18 C 5 GCU*AC > IL_61258.15 6ZDP A 1346 U 1291 ACU*AU > IL_61258.15 7A0S G 1488 C 1535 GCU*AC > IL_61258.15 5KPY U 25 A 44 UCG*CA > IL_61258.15 7KGA A 44 U 11 ACU*AU > IL_61258.15 6CK5 U 39 A 22 UCG*CA > IL_61258.15 8P9A G 1778 C 1670 GCG*CC > IL_61258.15 8P9A U 24 A 601 UCA*UA > IL_61258.15 3W3S G 11 C 24 GCC*GC > IL_61258.15 5J7L G 1731 C 1728 GCG*CC > IL_61258.15 3DIL G 12 C 79 GCG*CC > IL_61258.15 3SNP G 7 C 25 GCU*AC > IL_61258.15 3SN2 U 7 A 25 UCG*CA > IL_61258.15 8CRE U 24 A 599 UCA*UA > IL_61258.15 3D0U G 9 C 76 GCG*CC > IL_61258.15 8P9A G 150 C 8 GCG*CC > IL_61258.15 8CRE G 150 C 7 GCG*CC > IL_61258.15 7A0S G 558 C 553 GCG*CC > IL_61258.15 8CRE U 90 A 68 UCA*UA > IL_61258.15 4C7O C 31 G 13 CCG*CG > IL_61258.15 1KUQ C 46 G 22 CCC*GG > IL_61258.15 3SN2 G 18 C 14 GCC*GC > IL_61258.15 7A0S G 938 C 864 GCG*CC > IL_61258.15 9DFE U 2878 G 2839 UCC*GG