Alignment of IL_14368.1 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
4
I

6
5

3
7
5
I

8
5

4
9
6
I

10
7


11
6
I

12
5

5
13
2
I

14
2

6
15
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_14368.1_Instance_1 IL_14368.1,IL_5VCI_003,C8_G5CUAAUG
IL_14368.1_Sequence_1 IL_14368.15VCI_C8_G5CUAA*UGtrue100000.00
IL_14368.1_Instance_2 IL_14368.1,IL_4PCJ_003,C8_G28CUAAUG
IL_14368.1_Sequence_2 IL_14368.14PCJ_C8_G28CUAA*UGtrue100000.00
IL_14368.1_Instance_3 IL_14368.1,IL_5XTM_005,C41_G6CUAAUG
IL_14368.1_Sequence_3 IL_14368.15XTM_C41_G6CUAA*UGtrue100000.00
IL_14368.1_Instance_4 IL_14368.1,IL_1U6B_009,C147_G163CUAAUG
IL_14368.1_Sequence_4 IL_14368.11U6B_C147_G163CUAA*UGtrue100000.00
IL_14368.1_Instance_5 IL_14368.1,IL_5DCV_006,C45_G6CUAAUG
IL_14368.1_Sequence_5 IL_14368.15DCV_C45_G6CUAA*UGtrue100000.00
IL_14368.1_Instance_6 IL_14368.1,IL_7VTI_002,G5_U31GAGCAUU
IL_14368.1_Sequence_6 IL_14368.17VTI_G5_U31GAGCA*UUtrue26007.70

Conserved interactions between motif group positions in IL_14368.1:
1 2 s35 
1 6 cWW 
2 3 s35 
2 6 s55 
3 4 cSH 
3 5 tSH 
4 5 cWW
JAR3D SCFG/MRF model for IL_14368.1:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010187606,0.061327314,0.011087687,0.172971723,0.000000000],[0.018460196,0.009839639,0.220587306,0.013368761,0.000000000],[0.011137225,0.169507099,0.002196073,0.080283893,0.000000000],[0.167339440,0.013178161,0.023776616,0.014751262,0.000000000],[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 [6] // Basepair C8 - G5 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.187500000,0.062500000,0.062500000,0.687500000,0.000000000] | Position [1] | Left Index [2] | Right Index [5] // Fixed node on left for 5VCI|1|A|U|9
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 [5] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000493232005] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.020921021768211] // Cluster node 5VCI|1|A|A|10:5VCI|1|A|A|11 and 5VCI|1|B|U|4:5VCI|1|B|U|4
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.029167032,0.025707784,0.003594886,0.381883230,0.000000000],[0.021420106,0.018778763,0.003594886,0.003594886,0.000000000],[0.053873187,0.003594886,0.286180329,0.074524582,0.000000000],[0.053663672,0.033231998,0.003594886,0.003594886,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|A|10 - 5VCI|1|B|U|4 tSH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.008932627,0.021179957,0.009540239,0.253016483,0.000000000],[0.016857107,0.009218740,0.186838956,0.009967940,0.000000000],[0.009521668,0.189261136,0.001964127,0.051205712,0.000000000],[0.188626503,0.010612004,0.022144213,0.011112588,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|A|11 - 5VCI|1|B|U|4 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.159101612,0.101642687,0.005091781,0.012804749,0.000000000],[0.102869672,0.096130391,0.001119318,0.007905053,0.000000000],[0.035862729,0.001119318,0.093002231,0.090231618,0.000000000],[0.107710274,0.094047641,0.001119318,0.090241608,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5VCI|1|A|A|10 - 5VCI|1|A|A|11 cSH 
Insertion    | Location [1] | Length Distribution [0.826344012,0.171868555,0.001718686,0.000068747] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node
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 [5] | Right Index [4] // New Initial node after Cluster
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_14368.1:
> IL_14368.1  5VCI C    8 G    5
CUAA*UG
> IL_14368.1  4PCJ C    8 G   28
CUAA*UG
> IL_14368.1  5XTM C   41 G    6
CUAA*UG
> IL_14368.1  1U6B C  147 G  163
CUAA*UG
> IL_14368.1  5DCV C   45 G    6
CUAA*UG
> IL_14368.1  7VTI G    5 U   31
GAGCA*UU