Alignment of HL_86880.4 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
3

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_86880.4_Instance_1 HL_86880.4_HL_4WF9_033_G1361_C1367GCUCGUC
HL_86880.4_Sequence_1 HL_86880.4_HL_4WF9_033_G_1361_C_1367GCUCGUCtrue100000.00
HL_86880.4_Instance_2 HL_86880.4_HL_4Y4O_135_G1324_C1330GGUCGUC
HL_86880.4_Sequence_2 HL_86880.4_HL_4Y4O_135_G_1324_C_1330GGUCGUCtrue97000.25
HL_86880.4_Instance_3 HL_86880.4_HL_7A0S_033_G1337_C1343GGUCGUC
HL_86880.4_Sequence_3 HL_86880.4_HL_7A0S_033_G_1337_C_1343GGUCGUCtrue97000.25
HL_86880.4_Instance_4 HL_86880.4_HL_4V9F_035_G1430_C1436GCUGAUC
HL_86880.4_Sequence_4 HL_86880.4_HL_4V9F_035_G_1430_C_1436GCUGAUCtrue78002.10
HL_86880.4_Instance_5 HL_86880.4_HL_5J7L_170_G1492_C1498GCAAAUC
HL_86880.4_Sequence_5 HL_86880.4_HL_5J7L_170_G_1492_C_1498GCAAAUCtrue93000.64
HL_86880.4_Instance_6 HL_86880.4_HL_5TBW_032_A1506_U1512AGCAGUU
HL_86880.4_Sequence_6 HL_86880.4_HL_5TBW_032_A_1506_U_1512AGCAGUUtrue78002.09
HL_86880.4_Instance_7 HL_86880.4_HL_4Y4O_139_G1492_C1498GCAAAUC
HL_86880.4_Sequence_7 HL_86880.4_HL_4Y4O_139_G_1492_C_1498GCAAAUCtrue93000.64
HL_86880.4_Instance_8 HL_86880.4_HL_5J7L_166_G1324_C1330GUUAAUC
HL_86880.4_Sequence_8 HL_86880.4_HL_5J7L_166_G_1324_C_1330GUUAAUCtrue80001.90
HL_86880.4_Instance_9 HL_86880.4_HL_5VJ9_003_G6_C11GACGAC
HL_86880.4_Sequence_9 HL_86880.4_HL_5VJ9_003_G6_C11GACGACtrue96000.36
HL_86880.4_Instance_10 HL_86880.4_HL_5NDI_002_G8_C13GACGAC
HL_86880.4_Sequence_10 HL_86880.4_HL_5NDI_002_G8_C13GACGACtrue96000.36
HL_86880.4_Instance_11 HL_86880.4_HL_5NDH_001_G6_C11GACGAC
HL_86880.4_Sequence_11 HL_86880.4_HL_5NDH_001_G6_C11GACGACtrue96000.36
HL_86880.4_Instance_12 HL_86880.4_HL_4Y4O_143_C1631_G1635CAAGAG
HL_86880.4_Sequence_12 HL_86880.4_HL_4Y4O_143_C_1631_G_1635CAAGAGtrue91000.89

Conserved interactions between motif group positions in HL_86880.4:
1 4 s33 
1 5 cWW 
2 3 s35 
3 4 s35 
4 5 s35 
JAR3D SCFG/MRF model for HL_86880.4:
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 [5] // Initial node G1361 - C1367 from junction 
BasepairNode | Deletion Probability [0.0000000035949991] | Pair Probability [[0.008815443,0.018353160,0.009996502,0.192294218,0.000000000],[0.015844115,0.008708069,0.193606842,0.011914381,0.000000000],[0.009910961,0.278185774,0.001899121,0.026132318,0.000000000],[0.180991745,0.012309084,0.021583371,0.009454896,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.333724057,0.663311039,0.002827001,0.000137903] | Left Letter Distribution [0.050000000,0.450000000,0.350000000,0.150000000,0.000000000] | Right Length Distribution [0.004131378,0.991530675,0.004131378,0.000206569] | Right Letter Distribution [0.321428571,0.035714286,0.035714286,0.607142857,0.000000000] | Left Index [1] | Right Index [5] // Basepair G1361 - C1367 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U1363:G1365
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.464285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.107142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.392857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1363
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.392857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.464285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.107142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1364
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.321428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.035714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.607142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1365
Sequences of instances from HL_86880.4:
> HL_86880.4 HL_4WF9_033 G 1361 C 1367
GCUCGUC
> HL_86880.4 HL_4Y4O_135 G 1324 C 1330
GGUCGUC
> HL_86880.4 HL_7A0S_033 G 1337 C 1343
GGUCGUC
> HL_86880.4 HL_4V9F_035 G 1430 C 1436
GCUGAUC
> HL_86880.4 HL_5J7L_170 G 1492 C 1498
GCAAAUC
> HL_86880.4 HL_5TBW_032 A 1506 U 1512
AGCAGUU
> HL_86880.4 HL_4Y4O_139 G 1492 C 1498
GCAAAUC
> HL_86880.4 HL_5J7L_166 G 1324 C 1330
GUUAAUC
> HL_86880.4 HL_5VJ9_003 G    6 C   11
GACGAC
> HL_86880.4 HL_5NDI_002 G    8 C   13
GACGAC
> HL_86880.4 HL_5NDH_001 G    6 C   11
GACGAC
> HL_86880.4 HL_4Y4O_143 C 1631 G 1635
CAAGAG