Alignment of IL_17212.2 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


9
4
I

10
4

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_17212.2_Instance_1 IL_17212.2_IL_4IOA_043_A1260_U1212AGUGCGU
IL_17212.2_Sequence_1 IL_17212.2_IL_4IOA_043_A_1260_U_1212AGUG*CGUtrue95000.46
IL_17212.2_Instance_2 IL_17212.2_IL_3V2F_042_A1247_U1198AGUGCGU
IL_17212.2_Sequence_2 IL_17212.2_IL_3V2F_042_A_1247_U_1198AGUG*CGUtrue95000.46
IL_17212.2_Instance_3 IL_17212.2_IL_1S72_046_G1351_C1303GACGCGC
IL_17212.2_Sequence_3 IL_17212.2_IL_1S72_046_G_1351_C_1303GACG*CGCtrue80001.88
IL_17212.2_Instance_4 IL_17212.2_IL_3U5H_062_A1428_U1378AGUGCGU
IL_17212.2_Sequence_4 IL_17212.2_IL_3U5H_062_A_1428_U_1378AGUG*CGUtrue95000.46
IL_17212.2_Instance_5 IL_17212.2_IL_2QBG_045_A1247_U1198AGUGCGU
IL_17212.2_Sequence_5 IL_17212.2_IL_2QBG_045_A_1247_U_1198AGUG*CGUtrue95000.46
IL_17212.2_Instance_6 IL_17212.2_IL_3V2F_030_A870_U907AUAUGU
IL_17212.2_Sequence_6 IL_17212.2_IL_3V2F_030_A870_U907AUA*UGUtrue100000.00
IL_17212.2_Instance_7 IL_17212.2_IL_3U5H_052_U1123_A1135UUUAGA
IL_17212.2_Sequence_7 IL_17212.2_IL_3U5H_052_U_1123_A_1135UUU*AGAtrue99000.14
IL_17212.2_Instance_8 IL_17212.2_IL_4J39_001_G9_C11GCCGCC
IL_17212.2_Sequence_8 IL_17212.2_IL_4J39_001_G9_C11GCC*GCCtrue74002.47
IL_17212.2_Instance_9 IL_17212.2_IL_2ZI0_001_U9_A11UUAUUA
IL_17212.2_Sequence_9 IL_17212.2_IL_2ZI0_001_U9_A11UUA*UUAtrue73002.54
IL_17212.2_Instance_10 IL_17212.2_IL_3V2F_025_C844_G934CGCGGAG
IL_17212.2_Sequence_10 IL_17212.2_IL_3V2F_025_C844_G934CGC*GGAGtrue42005.48
IL_17212.2_Instance_11 IL_17212.2_IL_4ERD_003_U119_A148UCGACGGA
IL_17212.2_Sequence_11 IL_17212.2_IL_4ERD_003_U119_A148UCGAC*GGAtrue53004.43

Conserved interactions between motif group positions in IL_17212.2:
1 2 s35 
1 6 cWW 
2 5 cSW 
3 4 cWW 
3 5 s55 
4 5 s35 
5 6 s35 
JAR3D SCFG/MRF model for IL_17212.2:
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 A1260 - U1212 from junction 
BasepairNode | Deletion Probability [0.0000021781539185] | Pair Probability [[0.008689929,0.020160253,0.009504388,0.235118271,0.000000000],[0.019137928,0.008395256,0.190661991,0.010272581,0.000000000],[0.009489195,0.200405405,0.001975739,0.024126020,0.000000000],[0.215665956,0.010339743,0.023110977,0.012946368,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.543801687,0.453920502,0.002175207,0.000102604] | Left Letter Distribution [0.214285714,0.071428571,0.642857143,0.071428571,0.000000000] | 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 A1260 - U1212 cWW 
BasepairNode | Deletion Probability [0.0000055822185641] | Pair Probability [[0.015307233,0.014152753,0.062571942,0.012015483,0.000000000],[0.014890737,0.034347499,0.320439627,0.014761469,0.000000000],[0.034150702,0.012767370,0.017416671,0.009480468,0.000000000],[0.017109969,0.013608308,0.374787559,0.032192212,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.904400732,0.004522004,0.090645619,0.000411091,0.000020555] | Left Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Right Length Distribution [0.904811823,0.094550986,0.000616637,0.000020555] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [2] | Right Index [5] // Basepair U1262 - G1211 cSW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009079395,0.018751861,0.010311537,0.200254787,0.000000000],[0.017793342,0.008009199,0.216258756,0.011613886,0.000000000],[0.010285326,0.235466898,0.001975452,0.024095549,0.000000000],[0.190387789,0.011730064,0.023113053,0.010873107,0.000000000],[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 [3] | Right Index [4] // Basepair G1263 - C1210 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_17212.2:
> IL_17212.2 IL_4IOA_043 A 1260 U 1212
AGUG*CGU
> IL_17212.2 IL_3V2F_042 A 1247 U 1198
AGUG*CGU
> IL_17212.2 IL_1S72_046 G 1351 C 1303
GACG*CGC
> IL_17212.2 IL_3U5H_062 A 1428 U 1378
AGUG*CGU
> IL_17212.2 IL_2QBG_045 A 1247 U 1198
AGUG*CGU
> IL_17212.2 IL_3V2F_030 A  870 U  907
AUA*UGU
> IL_17212.2 IL_3U5H_052 U 1123 A 1135
UUU*AGA
> IL_17212.2 IL_4J39_001 G    9 C   11
GCC*GCC
> IL_17212.2 IL_2ZI0_001 U    9 A   11
UUA*UUA
> IL_17212.2 IL_3V2F_025 C  844 G  934
CGC*GGAG
> IL_17212.2 IL_4ERD_003 U  119 A  148
UCGAC*GGA