Alignment of IL_93424.4 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
6

3
7
6
I

8
7

4
9
7
I

10
8


11
7
I

12
7

5
13
6
I

14
6

6
15
5
I

16
4

7
17
3
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_93424.4_Instance_1 IL_93424.4_IL_2QBG_054_C1417_G1581CGAAGCUAAG
IL_93424.4_Sequence_1 IL_93424.4_IL_2QBG_054_C_1417_G_1581CGAAG*CUAAGtrue100000.00
IL_93424.4_Instance_2 IL_93424.4_IL_3V2F_052_C1417_G1581CGAUGCUAAG
IL_93424.4_Sequence_2 IL_93424.4_IL_3V2F_052_C_1417_G_1581CGAUG*CUAAGtrue91001.04
IL_93424.4_Instance_3 IL_93424.4_IL_3V2F_049_C1376_G1355CGAAGCUAAG
IL_93424.4_Sequence_3 IL_93424.4_IL_3V2F_049_C_1376_G_1355CGAAG*CUAAGtrue100000.00
IL_93424.4_Instance_4 IL_93424.4_IL_2QBG_051_C1376_G1355CGAUGCUAAG
IL_93424.4_Sequence_4 IL_93424.4_IL_2QBG_051_C_1376_G_1355CGAUG*CUAAGtrue91001.04
IL_93424.4_Instance_5 IL_93424.4_IL_1S72_038_C1257_G1099CGAGAUUAAG
IL_93424.4_Sequence_5 IL_93424.4_IL_1S72_038_C_1257_G_1099CGAGA*UUAAGtrue75002.83
IL_93424.4_Instance_6 IL_93424.4_IL_2QBG_036_C1153_G1002CGAAGCUAAG
IL_93424.4_Sequence_6 IL_93424.4_IL_2QBG_036_C_1153_G_1002CGAAG*CUAAGtrue100000.00
IL_93424.4_Instance_7 IL_93424.4_IL_1S72_052_C1483_G1460CGAAAUGCUAAG
IL_93424.4_Sequence_7 IL_93424.4_IL_1S72_052_C_1483_G_1460CGAAAUG*CUAAGtrue66003.86
IL_93424.4_Instance_8 IL_93424.4_IL_4IOA_032_C1164_G1013CGAAGCUAAG
IL_93424.4_Sequence_8 IL_93424.4_IL_4IOA_032_C_1164_G_1013CGAAG*CUAAGtrue100000.00
IL_93424.4_Instance_9 IL_93424.4_IL_3V2F_036_C1153_G1002CGAAGCUAAG
IL_93424.4_Sequence_9 IL_93424.4_IL_3V2F_036_C_1153_G_1002CGAAG*CUAAGtrue100000.00
IL_93424.4_Instance_10 IL_93424.4_IL_3U5H_069_C1585_G1536CGAAAGCUAAG
IL_93424.4_Sequence_10 IL_93424.4_IL_3U5H_069_C_1585_G_1536CGAAAG*CUAAGtrue79002.33
IL_93424.4_Instance_11 IL_93424.4_IL_3U5H_126_A3127_U3107AGAAUAUUAU
IL_93424.4_Sequence_11 IL_93424.4_IL_3U5H_126_A_3127_U_3107AGAAU*AUUAUtrue78002.45
IL_93424.4_Instance_12 IL_93424.4_IL_4A1B_122_A3116_U3096AGAAUAUUAU
IL_93424.4_Sequence_12 IL_93424.4_IL_4A1B_122_A_3116_U_3096AGAAU*AUUAUtrue78002.45
IL_93424.4_Instance_13 IL_93424.4_IL_4A1B_067_C1610_G1562CAAAAGCUAAG
IL_93424.4_Sequence_13 IL_93424.4_IL_4A1B_067_C_1610_G_1562CAAAAG*CUAAGtrue61004.36
IL_93424.4_Instance_14 IL_93424.4_IL_2XXA_014_C31_G66CGAACCUAUAAG
IL_93424.4_Sequence_14 IL_93424.4_IL_2XXA_014_C31_G66CGAACCU*AUAAGtrue39006.83
IL_93424.4_Instance_15 IL_93424.4_IL_4IOA_053_U1431_A1597UGAUGCUAAA
IL_93424.4_Sequence_15 IL_93424.4_IL_4IOA_053_U_1431_A_1597UGAUG*CUAAAtrue86001.56
IL_93424.4_Instance_16 IL_93424.4_IL_1S72_092_U2724_G2758UGUACGGUAG
IL_93424.4_Sequence_16 IL_93424.4_IL_1S72_092_U_2724_G_2758UGUAC*GGUAGtrue52005.46
IL_93424.4_Instance_17 IL_93424.4_IL_3U5H_024_G725_C745GGGGUGCAC
IL_93424.4_Sequence_17 IL_93424.4_IL_3U5H_024_G725_C745GGGG*UGCACtrue34007.47
IL_93424.4_Instance_18 IL_93424.4_IL_3U5H_124_U3054_G3088UUUUUGCGAAG
IL_93424.4_Sequence_18 IL_93424.4_IL_3U5H_124_U_3054_G_3088UUUUUG*CGAAGtrue17009.33
IL_93424.4_Instance_19 IL_93424.4_IL_1X8W_006_U253_G220UGCAGCCAAG
IL_93424.4_Sequence_19 IL_93424.4_IL_1X8W_006_U253_G220UGCAG*CCAAGtrue73003.05
IL_93424.4_Instance_20 IL_93424.4_IL_4A1B_126_U3212_G3199UGACGGAAG
IL_93424.4_Sequence_20 IL_93424.4_IL_4A1B_126_U_3212_G_3199UGAC*GGAAGtrue59004.63
IL_93424.4_Instance_21 IL_93424.4_IL_3V2F_057_U1518_G1473UGGUAGAAG
IL_93424.4_Sequence_21 IL_93424.4_IL_3V2F_057_U_1518_G_1473UGGU*AGAAGtrue68003.66

Conserved interactions between motif group positions in IL_93424.4:
1 2 s35 
1 9 cWW 
2 6 s33 
2 7 s33 
2 8 tSH 
2 9 s55 
3 4 s35 
3 6 tHW 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35 
8 9 s35 
2 7 6BPh
8 2 6BR
JAR3D SCFG/MRF model for IL_93424.4:
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 [9] // Initial node C1417 - G1581 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008962558,0.014859592,0.010393278,0.150315095,0.000000000],[0.076913212,0.008817731,0.243398715,0.011987446,0.000000000],[0.010528894,0.148385406,0.002088945,0.018854073,0.000000000],[0.143605439,0.011357816,0.129384680,0.010147120,0.000000000],[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 [9] // Basepair C1417 - G1581 cWW 
BasepairNode | Deletion Probability [0.0000147294218142] | Pair Probability [[0.059544634,0.053787320,0.000584169,0.003300211,0.000000000],[0.037422832,0.037770072,0.000443210,0.000443210,0.000000000],[0.452776205,0.002961509,0.014438148,0.244674219,0.000000000],[0.052405994,0.038561849,0.000443210,0.000443210,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.902527688,0.097127447,0.000333558,0.000011307] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair G1418 - A1580 tSH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.760869565,0.065217391,0.021739130,0.152173913,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [3] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000000741983018] | Pair Probability [[0.021051522,0.043854046,0.031539389,0.565466781,0.000000000],[0.004414998,0.050217320,0.004414998,0.004414998,0.000000000],[0.021656535,0.029306072,0.078793737,0.054465806,0.000000000],[0.004414998,0.004414998,0.034156873,0.047416927,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.191104012,0.616996179,0.096534053,0.095117422,0.000237046,0.000011288] | Left Letter Distribution [0.620000000,0.100000000,0.060000000,0.220000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A1419 - U1578 tHW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008622968,0.028889233,0.009691427,0.168375221,0.000000000],[0.015965643,0.007442493,0.182909660,0.010737626,0.000000000],[0.009614004,0.276828393,0.001864995,0.043338082,0.000000000],[0.193378178,0.011086787,0.020653500,0.010601790,0.000000000],[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 [4] | Right Index [5] // Basepair G1421 - C1577 cWW 
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_93424.4:
> IL_93424.4 IL_2QBG_054 C 1417 G 1581
CGAAG*CUAAG
> IL_93424.4 IL_3V2F_052 C 1417 G 1581
CGAUG*CUAAG
> IL_93424.4 IL_3V2F_049 C 1376 G 1355
CGAAG*CUAAG
> IL_93424.4 IL_2QBG_051 C 1376 G 1355
CGAUG*CUAAG
> IL_93424.4 IL_1S72_038 C 1257 G 1099
CGAGA*UUAAG
> IL_93424.4 IL_2QBG_036 C 1153 G 1002
CGAAG*CUAAG
> IL_93424.4 IL_1S72_052 C 1483 G 1460
CGAAAUG*CUAAG
> IL_93424.4 IL_4IOA_032 C 1164 G 1013
CGAAG*CUAAG
> IL_93424.4 IL_3V2F_036 C 1153 G 1002
CGAAG*CUAAG
> IL_93424.4 IL_3U5H_069 C 1585 G 1536
CGAAAG*CUAAG
> IL_93424.4 IL_3U5H_126 A 3127 U 3107
AGAAU*AUUAU
> IL_93424.4 IL_4A1B_122 A 3116 U 3096
AGAAU*AUUAU
> IL_93424.4 IL_4A1B_067 C 1610 G 1562
CAAAAG*CUAAG
> IL_93424.4 IL_2XXA_014 C   31 G   66
CGAACCU*AUAAG
> IL_93424.4 IL_4IOA_053 U 1431 A 1597
UGAUG*CUAAA
> IL_93424.4 IL_1S72_092 U 2724 G 2758
UGUAC*GGUAG
> IL_93424.4 IL_3U5H_024 G  725 C  745
GGGG*UGCAC
> IL_93424.4 IL_3U5H_124 U 3054 G 3088
UUUUUG*CGAAG
> IL_93424.4 IL_1X8W_006 U  253 G  220
UGCAG*CCAAG
> IL_93424.4 IL_4A1B_126 U 3212 G 3199
UGAC*GGAAG
> IL_93424.4 IL_3V2F_057 U 1518 G 1473
UGGU*AGAAG