Alignment of IL_68140.4 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 2 2	5 2 I	6 2 3	8 4 4	10 5	12 4 5	14 2 6	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_68140.4_Instance_1 IL_68140.4,IL_1S03_003,A12_U38	A	A		A	C		G	U
IL_68140.4_Sequence_1 IL_68140.41S03_A12_U38	A	A		A	C	*	G	U	true	94	0	0	0.59
IL_68140.4_Instance_2 IL_68140.4,IL_1S03_007,A12_U38	A	A		A	C		G	U
IL_68140.4_Sequence_2 IL_68140.41S03_A12_U38	A	A		A	C	*	G	U	true	94	0	0	0.59
IL_68140.4_Instance_3 IL_68140.4,IL_5J7L_029,A640_U598	A	U		A	C		G	U
IL_68140.4_Sequence_3 IL_68140.45J7L_A640_U598	A	U		A	C	*	G	U	true	89	0	0	1.06
IL_68140.4_Instance_4 IL_68140.4,IL_4PDB_002,A24_U15	A	U		A	U		A	U
IL_68140.4_Sequence_4 IL_68140.44PDB_A24_U15	A	U		A	U	*	A	U	true	88	0	0	1.11
IL_68140.4_Instance_5 IL_68140.4,IL_4LFB_025,A640_U598	A	U		A	C		G	U
IL_68140.4_Sequence_5 IL_68140.44LFB_A640_U598	A	U		A	C	*	G	U	true	89	0	0	1.06
IL_68140.4_Instance_6 IL_68140.4,IL_1I6U_002,A24_U13	A	U		A	C		G	U
IL_68140.4_Sequence_6 IL_68140.41I6U_A24_U13	A	U		A	C	*	G	U	true	89	0	0	1.06
IL_68140.4_Instance_7 IL_68140.4,IL_8P9A_412,G802_C747	G	A		A	U		A	C
IL_68140.4_Sequence_7 IL_68140.48P9A_G802_C747	G	A		A	U	*	A	C	true	98	0	0	0.20
IL_68140.4_Instance_8 IL_68140.4,IL_8CRE_428,G786_C732	G	A		A	U		A	C
IL_68140.4_Sequence_8 IL_68140.48CRE_G786_C732	G	A		A	U	*	A	C	true	98	0	0	0.20
IL_68140.4_Instance_9 IL_68140.4,IL_9DFE_112,G51_C31	G	A		A	G		C	C
IL_68140.4_Sequence_9 IL_68140.49DFE_G51_C31	G	A		A	G	*	C	C	true	100	0	0	0.00
IL_68140.4_Instance_10 IL_68140.4,IL_4V9F_103,G50_C30	G	A		A	G		C	C
IL_68140.4_Sequence_10 IL_68140.44V9F_G50_C30	G	A		A	G	*	C	C	true	100	0	0	0.00
IL_68140.4_Instance_11 IL_68140.4,IL_4WF9_126,G49_C29	G	A		A	G		C	C
IL_68140.4_Sequence_11 IL_68140.44WF9_G49_C29	G	A		A	G	*	C	C	true	100	0	0	0.00
IL_68140.4_Instance_12 IL_68140.4,IL_5J7L_316,G1846_C1894	G	A		A	G		C	C
IL_68140.4_Sequence_12 IL_68140.45J7L_G_1846_C_1894	G	A		A	G	*	C	C	true	100	0	0	0.00
IL_68140.4_Instance_13 IL_68140.4,IL_5J7L_357,G51_C31	G	A		A	G		C	C
IL_68140.4_Sequence_13 IL_68140.45J7L_G51_C31	G	A		A	G	*	C	C	true	100	0	0	0.00
IL_68140.4_Instance_14 IL_68140.4,IL_7A0S_068,G1838_C1877	G	A		A	G		C	C
IL_68140.4_Sequence_14 IL_68140.47A0S_G_1838_C_1877	G	A		A	G	*	C	C	true	100	0	0	0.00
IL_68140.4_Instance_15 IL_68140.4,IL_4WF9_072,G1873_C1921	G	A		A	G		C	C
IL_68140.4_Sequence_15 IL_68140.44WF9_G_1873_C_1921	G	A		A	G	*	C	C	true	100	0	0	0.00
IL_68140.4_Instance_16 IL_68140.4,IL_4V9F_068,G1902_C1935	G	U		A	U		A	C
IL_68140.4_Sequence_16 IL_68140.44V9F_G_1902_C_1935	G	U		A	U	*	A	C	true	93	0	0	0.67
IL_68140.4_Instance_17 IL_68140.4,IL_1U9S_004,C164_G134	C	A		A	G		C	G
IL_68140.4_Sequence_17 IL_68140.41U9S_C164_G134	C	A		A	G	*	C	G	true	91	0	0	0.86
IL_68140.4_Instance_18 IL_68140.4,IL_1U9S_002,G111_C229	G	A	A	A	G		C	C
IL_68140.4_Sequence_18 IL_68140.41U9S_G111_C229	G	A	A	A	G	*	C	C	true	63	0	0	3.48

Conserved interactions between motif group positions in IL_68140.4:

1 2 s35 
1 6 cWW 
2 3 cSH 
3 4 s35 
3 6 cWS 
4 5 cWW 
5 6 s35

JAR3D SCFG/MRF model for IL_68140.4:

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 [6] // Initial node
ClusterNode  | Deletion Probability [0.0000000004582002] | Num Left Bases [3] | Num Right Bases [1] | Left Index [1] | Right Index [6] | Norm Constant [0.107464950003689] // Cluster node 1S03|1|A|A|12:1S03|1|A|A|14 and 1S03|1|A|U|38:1S03|1|A|U|38
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.008274522,0.017871821,0.009238324,0.225554088,0.000000000],[0.015053061,0.008268904,0.181704783,0.010664268,0.000000000],[0.009173652,0.270009765,0.001792143,0.030598357,0.000000000],[0.171137883,0.011098916,0.020309554,0.009249959,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1S03|1|A|A|12 - 1S03|1|A|U|38 cWW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.160143100,0.276728388,0.173510214,0.213180316,0.000000000],[0.015419283,0.013204997,0.001726291,0.013062945,0.000000000],[0.017567998,0.001726291,0.081091882,0.007977613,0.000000000],[0.006341574,0.006722267,0.005362359,0.006234482,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1S03|1|A|A|14 - 1S03|1|A|U|38 cWS 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.232381653,0.089297886,0.004500958,0.011701737,0.000000000],[0.090898062,0.084980468,0.000982283,0.007328610,0.000000000],[0.007392794,0.000982283,0.081960984,0.079558228,0.000000000],[0.144299930,0.083068623,0.000982283,0.079683217,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1S03|1|A|A|13 - 1S03|1|A|A|14 cSH 
Insertion    | Location [2] | Length Distribution [0.941706795,0.058000892,0.000284620,0.000007692] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008232200,0.016237982,0.009326680,0.172454829,0.000000000],[0.016492653,0.008346045,0.218137694,0.011174322,0.000000000],[0.009306754,0.252685019,0.001797452,0.021629751,0.000000000],[0.207415017,0.011142248,0.026805368,0.008815987,0.000000000],[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 [4] | Right Index [5] // Basepair C15 - G37 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_68140.4:> IL_68140.4 1S03 A 12 U 38 AAAC*GU > IL_68140.4 1S03 A 12 U 38 AAAC*GU > IL_68140.4 5J7L A 640 U 598 AUAC*GU > IL_68140.4 4PDB A 24 U 15 AUAU*AU > IL_68140.4 4LFB A 640 U 598 AUAC*GU > IL_68140.4 1I6U A 24 U 13 AUAC*GU > IL_68140.4 8P9A G 802 C 747 GAAU*AC > IL_68140.4 8CRE G 786 C 732 GAAU*AC > IL_68140.4 9DFE G 51 C 31 GAAG*CC > IL_68140.4 4V9F G 50 C 30 GAAG*CC > IL_68140.4 4WF9 G 49 C 29 GAAG*CC > IL_68140.4 5J7L G 1846 C 1894 GAAG*CC > IL_68140.4 5J7L G 51 C 31 GAAG*CC > IL_68140.4 7A0S G 1838 C 1877 GAAG*CC > IL_68140.4 4WF9 G 1873 C 1921 GAAG*CC > IL_68140.4 4V9F G 1902 C 1935 GUAU*AC > IL_68140.4 1U9S C 164 G 134 CAAG*CG > IL_68140.4 1U9S G 111 C 229 GAAAG*CC