Alignment of IL_67623.1 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_67623.1
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:	1 1 I	2 2 1	3 2 I	4 3 2	5 3 I	6 3 3	7 3 I	8 3 4	9 3 I	10 3 5	11 3 I	12 3 6	13 4 I	14 5 7	15 5 I	16 5 8	17 6 I	18 7	19 6 I	20 5 9	21 5 I	22 5 10	23 5 I	24 5 11	25 5 I	26 5 12	27 4 I	28 3 13	29 2 I	30 2 14	31 1 I	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_67623.1_Instance_1 IL_67623.1,IL_4V9F_102,G21_C59		G		G		U		U		G		C		C		U				A		U		A		A		G		C
IL_67623.1_Sequence_1 IL_67623.14V9F_G21_C59		G		G		U		U		G		C		C		U		*		A		U		A		A		G		C		true	100	0	0	0.00

Conserved interactions between motif group positions in IL_67623.1:

1 14 cWW 
2 6 tSW 
2 7 s35 
2 10 s33 
2 13 bif 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
7 10 cWW 
8 9 cWW 
8 12 cSW 
9 10 s35 
9 11 perp 
10 12 cSH 
11 12 s35 
12 13 s35 
13 14 s35 
14 13 7BPh

JAR3D SCFG/MRF model for IL_67623.1:

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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.003861747,0.056298454,0.004397499,0.079872036,0.000000000],[0.006783263,0.026507815,0.080548829,0.005270297,0.000000000],[0.004348662,0.590132004,0.000828901,0.010618820,0.000000000],[0.078849827,0.038290418,0.009307874,0.004083553,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair G21 - C59 cWW 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [5] | Num Right Bases [1] | Left Index [2] | Right Index [13] | Norm Constant [0.378910815823155] // Cluster node 4V9F|1|9|G|22:4V9F|1|9|C|26 and 4V9F|1|9|G|58:4V9F|1|9|G|58
Interaction  | Interacting Bases [1,6] | Pair Probability [[0.286859111,0.207254157,0.003021830,0.003021830,0.000000000],[0.012680128,0.008875223,0.003021830,0.003021830,0.000000000],[0.003021830,0.003021830,0.312083968,0.142029115,0.000000000],[0.003021830,0.003021830,0.003021830,0.003021830,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|G|22 - 4V9F|1|9|G|58 bif 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.007482036,0.007482036,0.007482036,0.007482036,0.000000000],[0.007482036,0.007482036,0.137146856,0.007482036,0.000000000],[0.007482036,0.758104634,0.007482036,0.007482036,0.000000000],[0.007482036,0.007482036,0.007482036,0.007482036,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|G|22 - 4V9F|1|9|C|26 tSW 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|U|23
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|U|24
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|9|G|25
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [12] // Initial node 4V9F|1|9|C|27 - 4V9F|1|9|A|57 from node 
ClusterNode  | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [2] | Num Right Bases [4] | Left Index [7] | Right Index [12] | Norm Constant [0.022107374884817] // Cluster node 4V9F|1|9|C|27:4V9F|1|9|U|28 and 4V9F|1|9|A|54:4V9F|1|9|A|57
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|U|28 - 4V9F|1|9|A|54 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.016630886,0.015189662,0.044428677,0.019126085,0.000000000],[0.016667847,0.013061754,0.024870209,0.386769861,0.000000000],[0.046942534,0.023961968,0.003768689,0.016732811,0.000000000],[0.020361889,0.319807982,0.018277361,0.013401785,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|C|27 - 4V9F|1|9|U|55 cWW 
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.180519376,0.017157494,0.024883181,0.007207709,0.000000000],[0.173124567,0.013878938,0.001921253,0.007559536,0.000000000],[0.178058238,0.001921253,0.155093256,0.006042475,0.000000000],[0.202026315,0.014064519,0.009451832,0.007090057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|U|28 - 4V9F|1|9|A|57 cSW 
Interaction  | Interacting Bases [4,6] | Pair Probability [[0.113280636,0.107289768,0.005483455,0.015299062,0.000000000],[0.110644042,0.103542883,0.001177205,0.009856998,0.000000000],[0.010048060,0.001177205,0.099171378,0.096370483,0.000000000],[0.127621474,0.101020887,0.001177205,0.096839258,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|9|U|55 - 4V9F|1|9|A|57 cSH 
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 4V9F|1|9|A|56
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [8] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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_67623.1:> IL_67623.1 4V9F G 21 C 59 GGUUGCCU*AUAAGC