Alignment of IL_03109.3 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
2

2
5
2
I

6
2

3
7
2
I

8
2

4
9
2
I

10
2

5
11
3
I

12
4


13
3
I

14
2

6
15
2
I

16
2

7
17
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
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distance
Alignment
score
deficit
IL_03109.3_Instance_1 IL_03109.3,IL_8P9A_397,C443_G461CCAAUAG
IL_03109.3_Sequence_1 IL_03109.38P9A_C443_G461CCAAU*AGtrue100000.00
IL_03109.3_Instance_2 IL_03109.3,IL_8CRE_414,C441_G459CCAAUAG
IL_03109.3_Sequence_2 IL_03109.38CRE_C441_G459CCAAU*AGtrue100000.00
IL_03109.3_Instance_3 IL_03109.3,IL_5J7L_018,A371_U390ACAAUAU
IL_03109.3_Sequence_3 IL_03109.35J7L_A371_U390ACAAU*AUtrue97000.26
IL_03109.3_Instance_4 IL_03109.3,IL_4LFB_015,G371_C390GCAAUAC
IL_03109.3_Sequence_4 IL_03109.34LFB_G371_C390GCAAU*ACtrue88001.09
IL_03109.3_Instance_5 IL_03109.3,IL_4LFB_013,U304_G293UGGCCGG
IL_03109.3_Sequence_5 IL_03109.34LFB_U304_G293UGGCC*GGtrue51004.69
IL_03109.3_Instance_6 IL_03109.3,IL_5J7L_016,U304_G293UGACCGG
IL_03109.3_Sequence_6 IL_03109.35J7L_U304_G293UGACC*GGtrue64003.44

Conserved interactions between motif group positions in IL_03109.3:
1 2 s35 
1 3 cSH 
1 7 cWW 
2 4 cSH 
2 6 tWH 
2 7 s55 
3 4 s35 
4 5 s35 
4 7 cWS 
5 6 cWW 
6 7 s35
JAR3D SCFG/MRF model for IL_03109.3:
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 [7] // Initial node
ClusterNode  | Deletion Probability [0.000000000000000078125000000000012233710187403301545271878291] | Num Left Bases [5] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.001636750906250] // Cluster node 8P9A|1|sR|C|443:8P9A|1|sR|U|447 and 8P9A|1|sR|A|460:8P9A|1|sR|G|461
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.028150634,0.003288854,0.094083918,0.003288854,0.000000000],[0.366621280,0.023961426,0.003288854,0.003288854,0.000000000],[0.003288854,0.011482329,0.093366750,0.030315993,0.000000000],[0.033073764,0.003288854,0.014786757,0.284424024,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|C|444 - 8P9A|1|sR|A|460 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.008854514,0.016740477,0.009873999,0.189704501,0.000000000],[0.020645154,0.009422516,0.212263396,0.011508821,0.000000000],[0.009925891,0.189884907,0.001981704,0.022312113,0.000000000],[0.233465652,0.010917253,0.042775962,0.009723142,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|U|447 - 8P9A|1|sR|A|460 cWW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.009715992,0.016751901,0.011463867,0.150175329,0.000000000],[0.109095859,0.015147973,0.163183771,0.013358213,0.000000000],[0.011580780,0.151529457,0.002393189,0.025059826,0.000000000],[0.155547819,0.012950151,0.140954472,0.011091400,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|C|443 - 8P9A|1|sR|G|461 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.185853659,0.192148415,0.206960133,0.192369274,0.000000000],[0.014963268,0.012531621,0.065744759,0.012571448,0.000000000],[0.018853431,0.001953205,0.059899549,0.009144432,0.000000000],[0.006976870,0.007386555,0.005785039,0.006858342,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|A|446 - 8P9A|1|sR|G|461 cWS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.107772906,0.092207144,0.004875680,0.025481989,0.000000000],[0.120021076,0.089879740,0.001039542,0.008292878,0.000000000],[0.046607768,0.001039542,0.085361082,0.069630866,0.000000000],[0.136501855,0.088688263,0.039061268,0.083538401,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|C|443 - 8P9A|1|sR|A|445 cSH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.100165751,0.095527635,0.005188632,0.033823675,0.000000000],[0.146725533,0.094547687,0.001089897,0.009192068,0.000000000],[0.009640247,0.064881451,0.088966332,0.065593146,0.000000000],[0.102438069,0.093686988,0.001089897,0.087442992,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|C|444 - 8P9A|1|sR|A|446 cSH 
InitialNode  | Left Length Distribution [0.991157722,0.008431010,0.000411269] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991157722,0.008431010,0.000411269] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_03109.3:
> IL_03109.3  8P9A C  443 G  461
CCAAU*AG
> IL_03109.3  8CRE C  441 G  459
CCAAU*AG
> IL_03109.3  5J7L A  371 U  390
ACAAU*AU
> IL_03109.3  4LFB G  371 C  390
GCAAU*AC
> IL_03109.3  4LFB U  304 G  293
UGGCC*GG
> IL_03109.3  5J7L U  304 G  293
UGACC*GG