Alignment of IL_41756.4 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:		1
1
I

2
2

1
3
2
I

4
3

2
5
3
I

6
4

3
7
4
I

8
5

4
9
5
I

10
5

5
11
6
I

12
7

6
13
7
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14
8

7
15
9
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16
10

8
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10
I

18
11


19
10
I

20
10

9
21
7
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22
7

10
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6
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24
5

11
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4
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26
4

12
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3
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28
3

13
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2
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30
2

14
31
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_41756.4_Instance_1 IL_41756.4,IL_8P9A_428,G1111_C1134GGAGUAUGUGAAAC
IL_41756.4_Sequence_1 IL_41756.48P9A_G_1111_C_1134GGAGUAUG*UGAAACtrue100000.00
IL_41756.4_Instance_2 IL_41756.4,IL_8CRE_442,G1096_C1119GGAGUAUGUGAAAC
IL_41756.4_Sequence_2 IL_41756.48CRE_G_1096_C_1119GGAGUAUG*UGAAACtrue100000.00
IL_41756.4_Instance_3 IL_41756.4,IL_4LFB_034,G887_C910GGAGUACGUGAAAC
IL_41756.4_Sequence_3 IL_41756.44LFB_G887_C910GGAGUACG*UGAAACtrue100000.00
IL_41756.4_Instance_4 IL_41756.4,IL_5J7L_038,G887_C910GGAGUACGUAAAAC
IL_41756.4_Sequence_4 IL_41756.45J7L_G887_C910GGAGUACG*UAAAACtrue97000.59

Conserved interactions between motif group positions in IL_41756.4:
1 2 s35 
1 14 cWW 
2 3 s33 
2 12 s33 
2 13 tSH 
2 14 s55 
3 4 s55 
3 5 s55 
3 11 s53 
3 12 tHH 
4 5 cSH 
4 10 s33 
5 6 s35 
5 10 s33 
5 11 tWH 
6 7 s35 
6 10 tHS 
6 11 s55 
7 8 s35 
8 9 cWW 
9 10 s35 
11 12 s35 
12 13 s35 
13 14 s35 
10 5 6BPh
4 11 6BPh
3 12 6BPh
14 13 7BPh
13 2 6BR
6 10 6BR
JAR3D SCFG/MRF model for IL_41756.4:
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 [14] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.003750350,0.054674460,0.004270648,0.077568035,0.000000000],[0.006587592,0.025743166,0.078225305,0.005118269,0.000000000],[0.004223220,0.601955120,0.000804991,0.010312508,0.000000000],[0.076575313,0.037185886,0.009039378,0.003965758,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair G1111 - C1134 cWW 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.110577593,0.117061285,0.001327410,0.006256089,0.000000000],[0.111399105,0.116790218,0.001327410,0.001327410,0.000000000],[0.171202567,0.001327410,0.006489287,0.112665566,0.000000000],[0.123434124,0.116159705,0.001327410,0.001327410,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair G1112 - A1133 tSH 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.442799386,0.324831327,0.019385716,0.019778053,0.000000000],[0.050816783,0.000577625,0.049242991,0.005488648,0.000000000],[0.002879881,0.048613671,0.001441753,0.000577625,0.000000000],[0.003923273,0.028488016,0.000577625,0.000577625,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // Basepair A1113 - A1132 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [11] | Norm Constant [0.269832767432214] // Cluster node 8P9A|1|sR|G|1114:8P9A|1|sR|U|1115 and 8P9A|1|sR|A|1131:8P9A|1|sR|A|1131
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018414538,0.004075167,0.019126511,0.004075167,0.000000000],[0.040981170,0.328380556,0.004075167,0.004075167,0.000000000],[0.004075167,0.009768444,0.030991298,0.018124938,0.000000000],[0.445978203,0.004075167,0.023643628,0.040139714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|U|1115 - 8P9A|1|sR|A|1131 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.030507812,0.031086061,0.001709208,0.030379978,0.000000000],[0.022776075,0.034323944,0.000378448,0.030443666,0.000000000],[0.186583170,0.002649134,0.227599663,0.303374889,0.000000000],[0.030981169,0.030795185,0.000378448,0.036033152,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|G|1114 - 8P9A|1|sR|U|1115 cSH 
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.174590976,0.050781800,0.314754513,0.052967675,0.000000000],[0.049529943,0.041486312,0.002890767,0.050817093,0.000000000],[0.001714182,0.000575619,0.014852767,0.000575619,0.000000000],[0.009918595,0.000575619,0.233392901,0.000575619,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // Basepair A1116 - G1130 tHS 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left for 8P9A|1|sR|U|1117
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [8] | Right Index [9] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.015535214,0.291177596,0.014042294,0.082956205,0.000000000],[0.013458861,0.012543449,0.035731204,0.014127935,0.000000000],[0.013741462,0.040763683,0.003181999,0.356661451,0.000000000],[0.035874902,0.015432038,0.014121064,0.040650641,0.000000000],[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 [8] | Right Index [9] // Basepair G1118 - U1129 cWW 
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_41756.4:
> IL_41756.4  8P9A G 1111 C 1134
GGAGUAUG*UGAAAC
> IL_41756.4  8CRE G 1096 C 1119
GGAGUAUG*UGAAAC
> IL_41756.4  4LFB G  887 C  910
GGAGUACG*UGAAAC
> IL_41756.4  5J7L G  887 C  910
GGAGUACG*UAAAAC