Alignment of IL_00225.13 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_00225.13_Instance_1 IL_00225.13,IL_6TFF_002,C37_G23	C	G	A		U	G
IL_00225.13_Sequence_1 IL_00225.136TFF_C37_G23	C	G	A	*	U	G	true	97	0	0	0.27
IL_00225.13_Instance_2 IL_00225.13,IL_7D7W_002,C37_G23	C	G	C		G	G
IL_00225.13_Sequence_2 IL_00225.137D7W_C37_G23	C	G	C	*	G	G	true	99	0	0	0.05
IL_00225.13_Instance_3 IL_00225.13,IL_7D7V_002,U44_G22	U	G	A		U	G
IL_00225.13_Sequence_3 IL_00225.137D7V_U44_G22	U	G	A	*	U	G	true	98	0	0	0.22
IL_00225.13_Instance_4 IL_00225.13,IL_4WF9_125,C2229_G2248	C	G	C		G	G
IL_00225.13_Sequence_4 IL_00225.134WF9_C_2229_G_2248	C	G	C	*	G	G	true	99	0	0	0.05
IL_00225.13_Instance_5 IL_00225.13,IL_8CRE_444,G1134_U1615	G	G	A		U	U
IL_00225.13_Sequence_5 IL_00225.138CRE_G_1134_U_1615	G	G	A	*	U	U	true	95	0	0	0.48
IL_00225.13_Instance_6 IL_00225.13,IL_8P9A_430,G1149_U1628	G	G	A		U	U
IL_00225.13_Sequence_6 IL_00225.138P9A_G_1149_U_1628	G	G	A	*	U	U	true	95	0	0	0.48
IL_00225.13_Instance_7 IL_00225.13,IL_3NDB_004,C239_G138	C	G	C		G	G
IL_00225.13_Sequence_7 IL_00225.133NDB_C239_G138	C	G	C	*	G	G	true	99	0	0	0.05
IL_00225.13_Instance_8 IL_00225.13,IL_8TSV_002,U6_A20	U	G	C		G	A
IL_00225.13_Sequence_8 IL_00225.138TSV_U6_A20	U	G	C	*	G	A	true	99	0	0	0.09
IL_00225.13_Instance_9 IL_00225.13,IL_4LFB_036,G925_U1391	G	G	G		U	U
IL_00225.13_Sequence_9 IL_00225.134LFB_G925_U_1391	G	G	G	*	U	U	true	78	0	0	2.09
IL_00225.13_Instance_10 IL_00225.13,IL_8P9A_265,A983_U1100	A	G	U		A	U
IL_00225.13_Sequence_10 IL_00225.138P9A_A983_U_1100	A	G	U	*	A	U	true	92	0	0	0.78
IL_00225.13_Instance_11 IL_00225.13,IL_5J7L_040,G925_U1391	G	G	G		U	U
IL_00225.13_Sequence_11 IL_00225.135J7L_G925_U_1391	G	G	G	*	U	U	true	78	0	0	2.09
IL_00225.13_Instance_12 IL_00225.13,IL_8CRE_040,A979_U1096	A	G	U		A	U
IL_00225.13_Sequence_12 IL_00225.138CRE_A979_U_1096	A	G	U	*	A	U	true	92	0	0	0.78
IL_00225.13_Instance_13 IL_00225.13,IL_8ZA0_002,C5_G11	C	G	C		G	G
IL_00225.13_Sequence_13 IL_00225.138ZA0_C5_G11	C	G	C	*	G	G	true	99	0	0	0.05
IL_00225.13_Instance_14 IL_00225.13,IL_2IZN_001,C5_G15	C	G	C		G	G
IL_00225.13_Sequence_14 IL_00225.132IZN_C5_G15	C	G	C	*	G	G	true	99	0	0	0.05
IL_00225.13_Instance_15 IL_00225.13,IL_8CRE_048,U1070_A1080	U	G	C		G	A
IL_00225.13_Sequence_15 IL_00225.138CRE_U_1070_A_1080	U	G	C	*	G	A	true	99	0	0	0.09
IL_00225.13_Instance_16 IL_00225.13,IL_3IGI_004,U82_A100	U	G	U		A	A
IL_00225.13_Sequence_16 IL_00225.133IGI_U82_A100	U	G	U	*	A	A	true	94	0	0	0.56
IL_00225.13_Instance_17 IL_00225.13,IL_8VFS_001,U5_G23	U	G	C		G	G
IL_00225.13_Sequence_17 IL_00225.138VFS_U5_G23	U	G	C	*	G	G	true	100	0	0	0.00
IL_00225.13_Instance_18 IL_00225.13,IL_5J7L_019,U387_G376	U	G	A		U	G
IL_00225.13_Sequence_18 IL_00225.135J7L_U387_G376	U	G	A	*	U	G	true	98	0	0	0.22
IL_00225.13_Instance_19 IL_00225.13,IL_4WF9_023,G773_U748	G	G	A		U	U
IL_00225.13_Sequence_19 IL_00225.134WF9_G773_U748	G	G	A	*	U	U	true	95	0	0	0.48
IL_00225.13_Instance_20 IL_00225.13,IL_4V9F_026,A819_U794	A	G	U		A	U
IL_00225.13_Sequence_20 IL_00225.134V9F_A819_U794	A	G	U	*	A	U	true	92	0	0	0.78
IL_00225.13_Instance_21 IL_00225.13,IL_4LFB_016,U387_G376	U	G	A		U	G
IL_00225.13_Sequence_21 IL_00225.134LFB_U387_G376	U	G	A	*	U	G	true	98	0	0	0.22
IL_00225.13_Instance_22 IL_00225.13,IL_8CRE_032,G855_U830	G	G	C		G	U
IL_00225.13_Sequence_22 IL_00225.138CRE_G855_U830	G	G	C	*	G	U	true	97	0	0	0.25
IL_00225.13_Instance_23 IL_00225.13,IL_7A0S_017,G741_U716	G	G	A		U	U
IL_00225.13_Sequence_23 IL_00225.137A0S_G741_U716	G	G	A	*	U	U	true	95	0	0	0.48
IL_00225.13_Instance_24 IL_00225.13,IL_9DFE_018,G728_U703	G	G	C		G	U
IL_00225.13_Sequence_24 IL_00225.139DFE_G728_U703	G	G	C	*	G	U	true	97	0	0	0.25
IL_00225.13_Instance_25 IL_00225.13,IL_5J7L_262,G728_U703	G	G	A		U	U
IL_00225.13_Sequence_25 IL_00225.135J7L_G728_U703	G	G	A	*	U	U	true	95	0	0	0.48
IL_00225.13_Instance_26 IL_00225.13,IL_8P9A_257,G859_U834	G	G	C		G	U
IL_00225.13_Sequence_26 IL_00225.138P9A_G859_U834	G	G	C	*	G	U	true	97	0	0	0.25
IL_00225.13_Instance_27 IL_00225.13,IL_4C7O_004,U27_A16	U	G	U		A	A
IL_00225.13_Sequence_27 IL_00225.134C7O_U27_A16	U	G	U	*	A	A	true	94	0	0	0.56
IL_00225.13_Instance_28 IL_00225.13,IL_4LVW_002,G67_C18	G	G	U		G	C
IL_00225.13_Sequence_28 IL_00225.134LVW_G67_C18	G	G	U	*	G	C	true	76	0	0	2.25
IL_00225.13_Instance_29 IL_00225.13,IL_4V9F_041,U1136_G1226	U	G	G		C	G
IL_00225.13_Sequence_29 IL_00225.134V9F_U_1136_G_1226	U	G	G	*	C	G	true	95	0	0	0.51
IL_00225.13_Instance_30 IL_00225.13,IL_3SUX_001,G76_C21	G	G	U		G	C
IL_00225.13_Sequence_30 IL_00225.133SUX_G76_C21	G	G	U	*	G	C	true	76	0	0	2.25
IL_00225.13_Instance_31 IL_00225.13,IL_8TSV_003,U6_A20	U	G	C		G	A
IL_00225.13_Sequence_31 IL_00225.138TSV_U6_A20	U	G	C	*	G	A	true	99	0	0	0.09
IL_00225.13_Instance_32 IL_00225.13,IL_8P9A_398,G458_C448	G	G	A		U	C
IL_00225.13_Sequence_32 IL_00225.138P9A_G458_C448	G	G	A	*	U	C	true	94	0	0	0.59
IL_00225.13_Instance_33 IL_00225.13,IL_8CRE_415,G456_C446	G	G	A		U	C
IL_00225.13_Sequence_33 IL_00225.138CRE_G456_C446	G	G	A	*	U	C	true	94	0	0	0.59
IL_00225.13_Instance_34 IL_00225.13,IL_4V9F_010,U374_G275	U	G	C		G	G
IL_00225.13_Sequence_34 IL_00225.134V9F_U374_G275	U	G	C	*	G	G	true	100	0	0	0.00
IL_00225.13_Instance_35 IL_00225.13,IL_5J7L_001,U30_A553	U	G	A		U	A
IL_00225.13_Sequence_35 IL_00225.135J7L_U30_A553	U	G	A	*	U	A	true	97	0	0	0.31
IL_00225.13_Instance_36 IL_00225.13,IL_8I3Z_004,C10_G54	C	G	U		A	G
IL_00225.13_Sequence_36 IL_00225.138I3Z_C10_G54	C	G	U	*	A	G	true	95	0	0	0.52
IL_00225.13_Instance_37 IL_00225.13,IL_4LFB_001,U30_A553	U	G	A		U	A
IL_00225.13_Sequence_37 IL_00225.134LFB_U30_A553	U	G	A	*	U	A	true	97	0	0	0.31
IL_00225.13_Instance_38 IL_00225.13,IL_5U30_002,A7_U4	A	G	G		C	U
IL_00225.13_Sequence_38 IL_00225.135U30_A7_U4	A	G	G	*	C	U	true	91	0	0	0.83
IL_00225.13_Instance_39 IL_00225.13,IL_5J7L_271,U913_A863	U	G	C		G	A
IL_00225.13_Sequence_39 IL_00225.135J7L_U913_A863	U	G	C	*	G	A	true	99	0	0	0.09
IL_00225.13_Instance_40 IL_00225.13,IL_3DIL_005,U109_G85	U	G	C		G	G
IL_00225.13_Sequence_40 IL_00225.133DIL_U109_G85	U	G	C	*	G	G	true	100	0	0	0.00
IL_00225.13_Instance_41 IL_00225.13,IL_3D0U_005,U106_G82	U	G	G		C	G
IL_00225.13_Sequence_41 IL_00225.133D0U_U106_G82	U	G	G	*	C	G	true	95	0	0	0.51
IL_00225.13_Instance_42 IL_00225.13,IL_6JQ5_004,U62_G32	U	G	C		G	G
IL_00225.13_Sequence_42 IL_00225.136JQ5_U62_G32	U	G	C	*	G	G	true	100	0	0	0.00
IL_00225.13_Instance_43 IL_00225.13,IL_1U9S_006,U158_G141	U	G	C		G	G
IL_00225.13_Sequence_43 IL_00225.131U9S_U158_G141	U	G	C	*	G	G	true	100	0	0	0.00
IL_00225.13_Instance_44 IL_00225.13,IL_7A0S_099,U2853_G2814	U	G	C		G	G
IL_00225.13_Sequence_44 IL_00225.137A0S_U_2853_G_2814	U	G	C	*	G	G	true	100	0	0	0.00
IL_00225.13_Instance_45 IL_00225.13,IL_5DEA_002,C5_G31	C	G	G		C	G
IL_00225.13_Sequence_45 IL_00225.135DEA_C5_G31	C	G	G	*	C	G	true	94	0	0	0.57
IL_00225.13_Instance_46 IL_00225.13,IL_9FN3_004,C29_G16	C	G	C		G	G
IL_00225.13_Sequence_46 IL_00225.139FN3_C29_G16	C	G	C	*	G	G	true	99	0	0	0.05
IL_00225.13_Instance_47 IL_00225.13,IL_6JQ5_001,U62_G32	U	G	C		G	G
IL_00225.13_Sequence_47 IL_00225.136JQ5_U62_G32	U	G	C	*	G	G	true	100	0	0	0.00
IL_00225.13_Instance_48 IL_00225.13,IL_5DE8_001,C5_G31	C	G	G		C	G
IL_00225.13_Sequence_48 IL_00225.135DE8_C5_G31	C	G	G	*	C	G	true	94	0	0	0.57
IL_00225.13_Instance_49 IL_00225.13,IL_5J7L_395,U93_G76	U	G	C		G	G
IL_00225.13_Sequence_49 IL_00225.135J7L_U93_G76	U	G	C	*	G	G	true	100	0	0	0.00

Conserved interactions between motif group positions in IL_00225.13:

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

JAR3D SCFG/MRF model for IL_00225.13:

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 [[0.007660200,0.050729841,0.008406084,0.117803264,0.000000000],[0.064094753,0.010387694,0.153303467,0.009406887,0.000000000],[0.008431404,0.112166255,0.001804973,0.125428946,0.000000000],[0.147496430,0.009266822,0.161599412,0.012013570,0.000000000],[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 C37 - G23 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.009803922,0.009803922,0.970588235,0.009803922,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left for 6TFF|1|A|G|23
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 [[0.006677886,0.020587701,0.007421105,0.216565478,0.000000000],[0.021009312,0.007218729,0.270409288,0.008631594,0.000000000],[0.007446907,0.161950318,0.001484145,0.043248882,0.000000000],[0.169396965,0.008583674,0.041202938,0.008165078,0.000000000],[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 A39 - U22 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_00225.13:> IL_00225.13 6TFF C 37 G 23 CGA*UG > IL_00225.13 7D7W C 37 G 23 CGC*GG > IL_00225.13 7D7V U 44 G 22 UGA*UG > IL_00225.13 4WF9 C 2229 G 2248 CGC*GG > IL_00225.13 8CRE G 1134 U 1615 GGA*UU > IL_00225.13 8P9A G 1149 U 1628 GGA*UU > IL_00225.13 3NDB C 239 G 138 CGC*GG > IL_00225.13 8TSV U 6 A 20 UGC*GA > IL_00225.13 4LFB G 925 U 1391 GGG*UU > IL_00225.13 8P9A A 983 U 1100 AGU*AU > IL_00225.13 5J7L G 925 U 1391 GGG*UU > IL_00225.13 8CRE A 979 U 1096 AGU*AU > IL_00225.13 8ZA0 C 5 G 11 CGC*GG > IL_00225.13 2IZN C 5 G 15 CGC*GG > IL_00225.13 8CRE U 1070 A 1080 UGC*GA > IL_00225.13 3IGI U 82 A 100 UGU*AA > IL_00225.13 8VFS U 5 G 23 UGC*GG > IL_00225.13 5J7L U 387 G 376 UGA*UG > IL_00225.13 4WF9 G 773 U 748 GGA*UU > IL_00225.13 4V9F A 819 U 794 AGU*AU > IL_00225.13 4LFB U 387 G 376 UGA*UG > IL_00225.13 8CRE G 855 U 830 GGC*GU > IL_00225.13 7A0S G 741 U 716 GGA*UU > IL_00225.13 9DFE G 728 U 703 GGC*GU > IL_00225.13 5J7L G 728 U 703 GGA*UU > IL_00225.13 8P9A G 859 U 834 GGC*GU > IL_00225.13 4C7O U 27 A 16 UGU*AA > IL_00225.13 4LVW G 67 C 18 GGU*GC > IL_00225.13 4V9F U 1136 G 1226 UGG*CG > IL_00225.13 3SUX G 76 C 21 GGU*GC > IL_00225.13 8TSV U 6 A 20 UGC*GA > IL_00225.13 8P9A G 458 C 448 GGA*UC > IL_00225.13 8CRE G 456 C 446 GGA*UC > IL_00225.13 4V9F U 374 G 275 UGC*GG > IL_00225.13 5J7L U 30 A 553 UGA*UA > IL_00225.13 8I3Z C 10 G 54 CGU*AG > IL_00225.13 4LFB U 30 A 553 UGA*UA > IL_00225.13 5U30 A 7 U 4 AGG*CU > IL_00225.13 5J7L U 913 A 863 UGC*GA > IL_00225.13 3DIL U 109 G 85 UGC*GG > IL_00225.13 3D0U U 106 G 82 UGG*CG > IL_00225.13 6JQ5 U 62 G 32 UGC*GG > IL_00225.13 1U9S U 158 G 141 UGC*GG > IL_00225.13 7A0S U 2853 G 2814 UGC*GG > IL_00225.13 5DEA C 5 G 31 CGG*CG > IL_00225.13 9FN3 C 29 G 16 CGC*GG > IL_00225.13 6JQ5 U 62 G 32 UGC*GG > IL_00225.13 5DE8 C 5 G 31 CGG*CG > IL_00225.13 5J7L U 93 G 76 UGC*GG