Alignment of IL_92027.3 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
3

2
5
4
I

6
5


7
4
I

8
3

3
9
3
I

10
3

4
11
3
I

12
3

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_92027.3_Instance_1 IL_92027.3_IL_1S03_007_G37_C15GUAAAC
IL_92027.3_Sequence_1 IL_92027.3_IL_1S03_007_G37_C15GU*AAACtrue94000.60
IL_92027.3_Instance_2 IL_92027.3_IL_1FJG_025_G597_C643GUAUAC
IL_92027.3_Sequence_2 IL_92027.3_IL_1FJG_025_G597_C643GU*AUACtrue89001.09
IL_92027.3_Instance_3 IL_92027.3_IL_1I6U_004_G12_C27GUAUAC
IL_92027.3_Sequence_3 IL_92027.3_IL_1I6U_004_G12_C27GU*AUACtrue89001.09
IL_92027.3_Instance_4 IL_92027.3_IL_2AW7_032_G597_C643GUAUAC
IL_92027.3_Sequence_4 IL_92027.3_IL_2AW7_032_G597_C643GU*AUACtrue89001.09
IL_92027.3_Instance_5 IL_92027.3_IL_3U5F_040_A746_U805ACGAAU
IL_92027.3_Sequence_5 IL_92027.3_IL_3U5F_040_A746_U805AC*GAAUtrue97000.29
IL_92027.3_Instance_6 IL_92027.3_IL_1S72_101_C29_G53CCGAAG
IL_92027.3_Sequence_6 IL_92027.3_IL_1S72_101_C29_G53CC*GAAGtrue100000.00
IL_92027.3_Instance_7 IL_92027.3_IL_4IOA_068_C1876_G1841CCGAAG
IL_92027.3_Sequence_7 IL_92027.3_IL_4IOA_068_C_1876_G_1841CC*GAAGtrue100000.00
IL_92027.3_Instance_8 IL_92027.3_IL_4A1C_006_C28_G51CCGAAG
IL_92027.3_Sequence_8 IL_92027.3_IL_4A1C_006_C28_G51CC*GAAGtrue100000.00
IL_92027.3_Instance_9 IL_92027.3_IL_4A1B_019_U469_A510UCGAAA
IL_92027.3_Sequence_9 IL_92027.3_IL_4A1B_019_U469_A510UC*GAAAtrue96000.33
IL_92027.3_Instance_10 IL_92027.3_IL_1S72_068_A1934_U1905ACGUAU
IL_92027.3_Sequence_10 IL_92027.3_IL_1S72_068_A_1934_U_1905AC*GUAUtrue92000.77
IL_92027.3_Instance_11 IL_92027.3_IL_1U9S_005_G161_C139GGCAGC
IL_92027.3_Sequence_11 IL_92027.3_IL_1U9S_005_G161_C139GG*CAGCtrue67003.12
IL_92027.3_Instance_12 IL_92027.3_IL_3U5H_091_C2245_G2199CGCCAG
IL_92027.3_Sequence_12 IL_92027.3_IL_3U5H_091_C_2245_G_2199CG*CCAGtrue84001.49
IL_92027.3_Instance_13 IL_92027.3_IL_1U9S_002_C228_G115CCGAAAG
IL_92027.3_Sequence_13 IL_92027.3_IL_1U9S_002_C228_G115CC*GAAAGtrue63003.54
IL_92027.3_Instance_14 IL_92027.3_IL_3Q1Q_005_C126_G151CGCAAG
IL_92027.3_Sequence_14 IL_92027.3_IL_3Q1Q_005_C126_G151CG*CAAGtrue94000.53
IL_92027.3_Instance_15 IL_92027.3_IL_1U9S_004_C133_G167CGCAAG
IL_92027.3_Sequence_15 IL_92027.3_IL_1U9S_004_C133_G167CG*CAAGtrue94000.53
IL_92027.3_Instance_16 IL_92027.3_IL_3TZR_001_G110_C58GCGAACUAC
IL_92027.3_Sequence_16 IL_92027.3_IL_3TZR_001_G110_C58GC*GAACUACtrue32006.43
IL_92027.3_Instance_17 IL_92027.3_IL_2QBG_074_C1893_G1849CCGAAG
IL_92027.3_Sequence_17 IL_92027.3_IL_2QBG_074_C_1893_G_1849CC*GAAGtrue100000.00

Conserved interactions between motif group positions in IL_92027.3:
1 2 s35 
1 6 cWW 
2 3 cWW 
2 5 cSW 
3 4 s35 
4 5 cSH 
5 6 s35 
JAR3D SCFG/MRF model for IL_92027.3:
Character Definition | A,C,G,U,* // Define characters here
InitialNode  | 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 [1] | Right Index [6] // Initial node G37 - C15 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008668452,0.016988087,0.009924636,0.188219101,0.000000000],[0.017131643,0.007544544,0.250353907,0.011380325,0.000000000],[0.009939034,0.232642761,0.001874181,0.022305022,0.000000000],[0.179374627,0.011316366,0.022479125,0.009858189,0.000000000],[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 G37 - C15 cWW 
ClusterNode  | Deletion Probability [0.0000000001763743] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [5] | Norm Constant [0.094752302846867] // Cluster node U38:U38 and A12:A14
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.008590864,0.016331836,0.009816266,0.171008313,0.000000000],[0.018142150,0.007634138,0.258662220,0.011276526,0.000000000],[0.009857818,0.214012712,0.001875006,0.021485688,0.000000000],[0.207140253,0.011092461,0.023320816,0.009752934,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U38 - A12 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.148845005,0.016642779,0.008840780,0.006304384,0.000000000],[0.259403036,0.012911978,0.009864416,0.006983616,0.000000000],[0.184512997,0.013990132,0.108087970,0.005348851,0.000000000],[0.190360302,0.014390467,0.007769248,0.005744039,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U38 - A14 cSW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.213394359,0.097711652,0.029298823,0.008073800,0.000000000],[0.081617278,0.055476529,0.001516816,0.058595049,0.000000000],[0.006792689,0.077315958,0.022342735,0.056169929,0.000000000],[0.131754900,0.103459442,0.001516816,0.054963226,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A13 - A14 cSH 
Insertion    | Location [3] | Length Distribution [0.879505504,0.061208480,0.000474150,0.058630827,0.000172418,0.000008621] | Letter Distribution [0.416666667,0.250000000,0.083333333,0.250000000,0.000000000]// Insertion after nucleotide 4, position 3 in cluster node
InitialNode  | 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 [3] | Right Index [2] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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_92027.3:
> IL_92027.3 IL_1S03_007 G   37 C   15
GU*AAAC
> IL_92027.3 IL_1FJG_025 G  597 C  643
GU*AUAC
> IL_92027.3 IL_1I6U_004 G   12 C   27
GU*AUAC
> IL_92027.3 IL_2AW7_032 G  597 C  643
GU*AUAC
> IL_92027.3 IL_3U5F_040 A  746 U  805
AC*GAAU
> IL_92027.3 IL_1S72_101 C   29 G   53
CC*GAAG
> IL_92027.3 IL_4IOA_068 C 1876 G 1841
CC*GAAG
> IL_92027.3 IL_4A1C_006 C   28 G   51
CC*GAAG
> IL_92027.3 IL_4A1B_019 U  469 A  510
UC*GAAA
> IL_92027.3 IL_1S72_068 A 1934 U 1905
AC*GUAU
> IL_92027.3 IL_1U9S_005 G  161 C  139
GG*CAGC
> IL_92027.3 IL_3U5H_091 C 2245 G 2199
CG*CCAG
> IL_92027.3 IL_1U9S_002 C  228 G  115
CC*GAAAG
> IL_92027.3 IL_3Q1Q_005 C  126 G  151
CG*CAAG
> IL_92027.3 IL_1U9S_004 C  133 G  167
CG*CAAG
> IL_92027.3 IL_3TZR_001 G  110 C   58
GC*GAACUAC
> IL_92027.3 IL_2QBG_074 C 1893 G 1849
CC*GAAG