Alignment of IL_58291.4 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
4
I

6
5

3
7
6
I

8
7

4
9
7
I

10
8


11
7
I

12
7

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_58291.4_Instance_1 IL_58291.4_IL_4BPP_042_C940_G844CAUUAG
IL_58291.4_Sequence_1 IL_58291.4_IL_4BPP_042_C940_G844CAUU*AGtrue88001.14
IL_58291.4_Instance_2 IL_58291.4_IL_3U5F_045_C962_G866CAUUAG
IL_58291.4_Sequence_2 IL_58291.4_IL_3U5F_045_C962_G866CAUU*AGtrue88001.14
IL_58291.4_Instance_3 IL_58291.4_IL_1S72_008_C245_G266CGAAUG
IL_58291.4_Sequence_3 IL_58291.4_IL_1S72_008_C245_G266CGAA*UGtrue64003.37
IL_58291.4_Instance_4 IL_58291.4_IL_3V2F_047_G1310_C1604GGUUAC
IL_58291.4_Sequence_4 IL_58291.4_IL_3V2F_047_G_1310_C_1604GGUU*ACtrue100000.00
IL_58291.4_Instance_5 IL_58291.4_IL_4IOA_022_U857_G945UGUUAG
IL_58291.4_Sequence_5 IL_58291.4_IL_4IOA_022_U857_G945UGUU*AGtrue87001.28
IL_58291.4_Instance_6 IL_58291.4_IL_1NTB_003_C15_G111CUUCGG
IL_58291.4_Sequence_6 IL_58291.4_IL_1NTB_003_C15_G111CUUC*GGtrue69002.90
IL_58291.4_Instance_7 IL_58291.4_IL_4A1B_065_G1518_C1860GGUUAC
IL_58291.4_Sequence_7 IL_58291.4_IL_4A1B_065_G_1518_C_1860GGUU*ACtrue100000.00
IL_58291.4_Instance_8 IL_58291.4_IL_1S72_050_G1416_C1679GGUUAC
IL_58291.4_Sequence_8 IL_58291.4_IL_1S72_050_G_1416_C_1679GGUU*ACtrue100000.00
IL_58291.4_Instance_9 IL_58291.4_IL_3U5H_067_G1492_C1836GGUUAC
IL_58291.4_Sequence_9 IL_58291.4_IL_3U5H_067_G_1492_C_1836GGUU*ACtrue100000.00
IL_58291.4_Instance_10 IL_58291.4_IL_4IOA_048_G1323_C1620GGUUAC
IL_58291.4_Sequence_10 IL_58291.4_IL_4IOA_048_G_1323_C_1620GGUU*ACtrue100000.00

Conserved interactions between motif group positions in IL_58291.4:
1 2 s35 
1 4 s35 
1 6 cWW 
3 4 s53 
3 5 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
3 2 7BR
4 2 7BR
JAR3D SCFG/MRF model for IL_58291.4:
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 [6] // Initial node C940 - G844 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009654467,0.017382325,0.011239422,0.164655864,0.000000000],[0.045073158,0.008564718,0.216916730,0.012934053,0.000000000],[0.011258298,0.226039685,0.002121174,0.023042289,0.000000000],[0.165191753,0.012837436,0.063061178,0.010027450,0.000000000],[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 C940 - G844 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.208333333,0.041666667,0.625000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [5] // Fixed node on left
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
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.105769231,0.009615385,0.009615385,0.875000000,0.000000000] | Position [1] | Left Index [3] | Right Index [5] // Fixed node on left
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 [4] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.005775413,0.013436787,0.006224462,0.139814675,0.000000000],[0.014288816,0.005736381,0.135084521,0.007289412,0.000000000],[0.004464821,0.086521219,0.000958184,0.010718856,0.000000000],[0.472864381,0.019345217,0.051729227,0.025747629,0.000000000],[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 U943 - A843 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_58291.4:
> IL_58291.4 IL_4BPP_042 C  940 G  844
CAUU*AG
> IL_58291.4 IL_3U5F_045 C  962 G  866
CAUU*AG
> IL_58291.4 IL_1S72_008 C  245 G  266
CGAA*UG
> IL_58291.4 IL_3V2F_047 G 1310 C 1604
GGUU*AC
> IL_58291.4 IL_4IOA_022 U  857 G  945
UGUU*AG
> IL_58291.4 IL_1NTB_003 C   15 G  111
CUUC*GG
> IL_58291.4 IL_4A1B_065 G 1518 C 1860
GGUU*AC
> IL_58291.4 IL_1S72_050 G 1416 C 1679
GGUU*AC
> IL_58291.4 IL_3U5H_067 G 1492 C 1836
GGUU*AC
> IL_58291.4 IL_4IOA_048 G 1323 C 1620
GGUU*AC