Alignment of IL_26793.1 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
6


9
5
I

10
5

4
11
2
I

12
2

5
13
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_26793.1_Instance_1 IL_26793.1,IL_7ZO1_005,G5_C15GAGCC
IL_26793.1_Sequence_1 IL_26793.17ZO1_G5_C15GAG*CCtrue100000.00
IL_26793.1_Instance_2 IL_26793.1,IL_8CRE_091,C2182_G2216CUGCG
IL_26793.1_Sequence_2 IL_26793.18CRE_C_2182_G_2216CUG*CGtrue80001.91
IL_26793.1_Instance_3 IL_26793.1,IL_7A0S_054,A1463_U1478AAGCU
IL_26793.1_Sequence_3 IL_26793.17A0S_A_1463_U_1478AAG*CUtrue100000.00
IL_26793.1_Instance_4 IL_26793.1,IL_5J7L_269,G926_C851GAAUC
IL_26793.1_Sequence_4 IL_26793.15J7L_G926_C851GAA*UCtrue96000.36
IL_26793.1_Instance_5 IL_26793.1,IL_9DFE_091,C2498_G2454CCUAG
IL_26793.1_Sequence_5 IL_26793.19DFE_C_2498_G_2454CCU*AGtrue92000.80
IL_26793.1_Instance_6 IL_26793.1,IL_5J7L_044,G1041_C999GAGCC
IL_26793.1_Sequence_6 IL_26793.15J7L_G_1041_C999GAG*CCtrue100000.00
IL_26793.1_Instance_7 IL_26793.1,IL_4V9F_081,U2436_A2455UAGCA
IL_26793.1_Sequence_7 IL_26793.14V9F_U_2436_A_2455UAG*CAtrue99000.05
IL_26793.1_Instance_8 IL_26793.1,IL_7A0S_083,C2477_G2433CCUAG
IL_26793.1_Sequence_8 IL_26793.17A0S_C_2477_G_2433CCU*AGtrue92000.80
IL_26793.1_Instance_9 IL_26793.1,IL_4WF9_089,C2525_G2481CCUAG
IL_26793.1_Sequence_9 IL_26793.14WF9_C_2525_G_2481CCU*AGtrue92000.80
IL_26793.1_Instance_10 IL_26793.1,IL_5J7L_391,C2498_G2454CCUAG
IL_26793.1_Sequence_10 IL_26793.15J7L_C_2498_G_2454CCU*AGtrue92000.80
IL_26793.1_Instance_11 IL_26793.1,IL_5J7L_032,A746_U659AAGCU
IL_26793.1_Sequence_11 IL_26793.15J7L_A746_U659AAG*CUtrue100000.00
IL_26793.1_Instance_12 IL_26793.1,IL_8CRE_038,U1107_A966UAGCA
IL_26793.1_Sequence_12 IL_26793.18CRE_U_1107_A966UAG*CAtrue99000.05
IL_26793.1_Instance_13 IL_26793.1,IL_8P9A_263,U1111_A970UAGCA
IL_26793.1_Sequence_13 IL_26793.18P9A_U_1111_A970UAG*CAtrue99000.05
IL_26793.1_Instance_14 IL_26793.1,IL_7KGA_006,A37_U16ACUAU
IL_26793.1_Sequence_14 IL_26793.17KGA_A37_U16ACU*AUtrue91000.84
IL_26793.1_Instance_15 IL_26793.1,IL_9DFE_057,G1448_C1463GAGCC
IL_26793.1_Sequence_15 IL_26793.19DFE_G_1448_C_1463GAG*CCtrue100000.00
IL_26793.1_Instance_16 IL_26793.1,IL_5VSU_003,A75_U70AAGCU
IL_26793.1_Sequence_16 IL_26793.15VSU_A75_U70AAG*CUtrue100000.00

Conserved interactions between motif group positions in IL_26793.1:
1 2 s35 
1 5 cWW 
2 3 s35 
2 5 s55 
3 4 cWW 
4 5 s35
JAR3D SCFG/MRF model for IL_26793.1:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008290378,0.016886634,0.009262512,0.210600594,0.000000000],[0.016815519,0.008494092,0.220317059,0.010807783,0.000000000],[0.009268229,0.211509385,0.001819252,0.027829594,0.000000000],[0.201679001,0.010816696,0.026359189,0.009244083,0.000000000],[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 [5] // Basepair G5 - C15 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.305555556,0.027777778,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left for 7ZO1|1|A|A|6
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 [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008341991,0.017171409,0.009359466,0.184423873,0.000000000],[0.016416333,0.008473653,0.176375408,0.010904732,0.000000000],[0.009296067,0.265271130,0.001822107,0.023966880,0.000000000],[0.219272777,0.011034030,0.028802589,0.009067555,0.000000000],[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 G7 - C14 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_26793.1:
> IL_26793.1  7ZO1 G    5 C   15
GAG*CC
> IL_26793.1  8CRE C 2182 G 2216
CUG*CG
> IL_26793.1  7A0S A 1463 U 1478
AAG*CU
> IL_26793.1  5J7L G  926 C  851
GAA*UC
> IL_26793.1  9DFE C 2498 G 2454
CCU*AG
> IL_26793.1  5J7L G 1041 C  999
GAG*CC
> IL_26793.1  4V9F U 2436 A 2455
UAG*CA
> IL_26793.1  7A0S C 2477 G 2433
CCU*AG
> IL_26793.1  4WF9 C 2525 G 2481
CCU*AG
> IL_26793.1  5J7L C 2498 G 2454
CCU*AG
> IL_26793.1  5J7L A  746 U  659
AAG*CU
> IL_26793.1  8CRE U 1107 A  966
UAG*CA
> IL_26793.1  8P9A U 1111 A  970
UAG*CA
> IL_26793.1  7KGA A   37 U   16
ACU*AU
> IL_26793.1  9DFE G 1448 C 1463
GAG*CC
> IL_26793.1  5VSU A   75 U   70
AAG*CU