Alignment of HL_77436.5 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
4

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
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Alignment
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HL_77436.5_Instance_1 HL_77436.5,HL_8CRE_219,C1294_G1301CUUAAUUG
HL_77436.5_Sequence_1 HL_77436.58CRE_C_1294_G_1301CUUAAUUGtrue97000.27
HL_77436.5_Instance_2 HL_77436.5,HL_8P9A_218,C1309_G1316CUUAAUUG
HL_77436.5_Sequence_2 HL_77436.58P9A_C_1309_G_1316CUUAAUUGtrue97000.27
HL_77436.5_Instance_3 HL_77436.5,HL_8CRE_023,C1072_G1079CUUAAUUG
HL_77436.5_Sequence_3 HL_77436.58CRE_C_1072_G_1079CUUAAUUGtrue97000.27
HL_77436.5_Instance_4 HL_77436.5,HL_8P9A_136,C1076_G1083CUUAAUUG
HL_77436.5_Sequence_4 HL_77436.58P9A_C_1076_G_1083CUUAAUUGtrue97000.27
HL_77436.5_Instance_5 HL_77436.5,HL_4LFB_025,G1089_C1096GUUAAGUC
HL_77436.5_Sequence_5 HL_77436.54LFB_G_1089_C_1096GUUAAGUCtrue100000.00
HL_77436.5_Instance_6 HL_77436.5,HL_5J7L_024,G1089_C1096GUUAAGUC
HL_77436.5_Sequence_6 HL_77436.55J7L_G_1089_C_1096GUUAAGUCtrue100000.00
HL_77436.5_Instance_7 HL_77436.5,HL_8P9A_120,U278_G287UUUGGGAAUG
HL_77436.5_Sequence_7 HL_77436.58P9A_U278_G287UUUGGGAAUGtrue26007.19
HL_77436.5_Instance_8 HL_77436.5,HL_8CRE_008,U278_G287UUUGGGAAUG
HL_77436.5_Sequence_8 HL_77436.58CRE_U278_G287UUUGGGAAUGtrue26007.19
HL_77436.5_Instance_9 HL_77436.5,HL_3R4F_001,A24_U31AUUGAGUU
HL_77436.5_Sequence_9 HL_77436.53R4F_A24_U31AUUGAGUUtrue90000.99
HL_77436.5_Instance_10 HL_77436.5,HL_3K0J_002,G66_C73GAUAAUGC
HL_77436.5_Sequence_10 HL_77436.53K0J_G66_C73GAUAAUGCtrue80001.90
HL_77436.5_Instance_11 HL_77436.5,HL_7TZS_002,G66_C73GAUAAUGC
HL_77436.5_Sequence_11 HL_77436.57TZS_G66_C73GAUAAUGCtrue80001.90
HL_77436.5_Instance_12 HL_77436.5,HL_3D2V_002,G54_C61GGUAAUGC
HL_77436.5_Sequence_12 HL_77436.53D2V_G54_C61GGUAAUGCtrue77002.19
HL_77436.5_Instance_13 HL_77436.5,HL_8CRE_196,G241_C248GAUGAUUC
HL_77436.5_Sequence_13 HL_77436.58CRE_G241_C248GAUGAUUCtrue76002.31
HL_77436.5_Instance_14 HL_77436.5,HL_8P9A_195,G243_C250GAUGAUUC
HL_77436.5_Sequence_14 HL_77436.58P9A_G243_C250GAUGAUUCtrue76002.31
HL_77436.5_Instance_15 HL_77436.5,HL_4V9F_039,C1594_G1600CGUAAUG
HL_77436.5_Sequence_15 HL_77436.54V9F_C_1594_G_1600CGUAAUGtrue96000.40
HL_77436.5_Instance_16 HL_77436.5,HL_3IVK_005,G92_C99GUUAAAAC
HL_77436.5_Sequence_16 HL_77436.53IVK_G92_C99GUUAAAACtrue76002.34
HL_77436.5_Instance_17 HL_77436.5,HL_1QTQ_002,A931_U939AUUCUGAUU
HL_77436.5_Sequence_17 HL_77436.51QTQ_A931_U939AUUCUGAUUtrue49004.96
HL_77436.5_Instance_18 HL_77436.5,HL_4JYZ_002,U931_A939UUUUUGAUA
HL_77436.5_Sequence_18 HL_77436.54JYZ_U931_A939UUUUUGAUAtrue57004.14
HL_77436.5_Instance_19 HL_77436.5,HL_4WF9_019,C654_G662CAGUAAAUG
HL_77436.5_Sequence_19 HL_77436.54WF9_C654_G662CAGUAAAUGtrue34006.39
HL_77436.5_Instance_20 HL_77436.5,HL_4V9F_049,C1916_G1923CGUACAAG
HL_77436.5_Sequence_20 HL_77436.54V9F_C_1916_G_1923CGUACAAGtrue49004.98
HL_77436.5_Instance_21 HL_77436.5,HL_2D6F_005,G931_C939GCUUUGGAC
HL_77436.5_Sequence_21 HL_77436.52D6F_G931_C939GCUUUGGACtrue23007.51
HL_77436.5_Instance_22 HL_77436.5,HL_5CCB_003,G53_C61GUUCAAGUC
HL_77436.5_Sequence_22 HL_77436.55CCB_G53_C61GUUCAAGUCtrue67003.17
HL_77436.5_Instance_23 HL_77436.5,HL_7A0S_029,C1103_G1110CGUAAUAG
HL_77436.5_Sequence_23 HL_77436.57A0S_C_1103_G_1110CGUAAUAGtrue74002.57

Conserved interactions between motif group positions in HL_77436.5:
1 2 s35 
1 7 cWW 
2 3 s35 
2 6 cWW 
2 7 s55 
3 6 s55 
4 5 s35 
5 6 s35 
6 7 s35
JAR3D SCFG/MRF model for HL_77436.5:
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 [7] // Initial node
BasepairNode | Deletion Probability [0.0000061358665091] | Pair Probability [[0.008066330,0.015469919,0.009260495,0.170670750,0.000000000],[0.035887225,0.009303818,0.222677048,0.011068784,0.000000000],[0.009273472,0.239075942,0.001815365,0.022145087,0.000000000],[0.165591251,0.011031447,0.059862661,0.008800407,0.000000000],[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 [0.737595604,0.261730513,0.000645608,0.000028275] | Right Letter Distribution [0.062500000,0.062500000,0.437500000,0.437500000,0.000000000] | Left Index [1] | Right Index [7] // Basepair C1294 - G1301 cWW 
BasepairNode | Deletion Probability [0.0000007723675157] | Pair Probability [[0.011449859,0.197962169,0.010491671,0.090384015,0.000000000],[0.042730708,0.015397374,0.016524302,0.011534441,0.000000000],[0.038985482,0.016446721,0.003188189,0.067460065,0.000000000],[0.031421182,0.012319220,0.047270663,0.386433940,0.000000000],[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 [0.520859338,0.391139080,0.001092778,0.086710974,0.000188410,0.000009420] | Right Letter Distribution [0.382352941,0.029411765,0.323529412,0.264705882,0.000000000] | Left Index [2] | Right Index [6] // Basepair U1295 - U1300 cWW 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U1296:A1298
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.020000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.020000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.060000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.900000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1296
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.260000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.140000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1297
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.780000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.020000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.140000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.060000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1298
Insertion    | Location [1] | Length Distribution [0.780835411,0.175226102,0.043820664,0.000113110,0.000004713] | Letter Distribution [0.312500000,0.187500000,0.062500000,0.437500000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1
Insertion    | Location [2] | Length Distribution [0.824271904,0.175242620,0.000466622,0.000018853] | Letter Distribution [0.416666667,0.083333333,0.416666667,0.083333333,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2
Sequences of instances from HL_77436.5:
> HL_77436.5  8CRE C 1294 G 1301
CUUAAUUG
> HL_77436.5  8P9A C 1309 G 1316
CUUAAUUG
> HL_77436.5  8CRE C 1072 G 1079
CUUAAUUG
> HL_77436.5  8P9A C 1076 G 1083
CUUAAUUG
> HL_77436.5  4LFB G 1089 C 1096
GUUAAGUC
> HL_77436.5  5J7L G 1089 C 1096
GUUAAGUC
> HL_77436.5  8P9A U  278 G  287
UUUGGGAAUG
> HL_77436.5  8CRE U  278 G  287
UUUGGGAAUG
> HL_77436.5  3R4F A   24 U   31
AUUGAGUU
> HL_77436.5  3K0J G   66 C   73
GAUAAUGC
> HL_77436.5  7TZS G   66 C   73
GAUAAUGC
> HL_77436.5  3D2V G   54 C   61
GGUAAUGC
> HL_77436.5  8CRE G  241 C  248
GAUGAUUC
> HL_77436.5  8P9A G  243 C  250
GAUGAUUC
> HL_77436.5  4V9F C 1594 G 1600
CGUAAUG
> HL_77436.5  3IVK G   92 C   99
GUUAAAAC
> HL_77436.5  1QTQ A  931 U  939
AUUCUGAUU
> HL_77436.5  4JYZ U  931 A  939
UUUUUGAUA
> HL_77436.5  4WF9 C  654 G  662
CAGUAAAUG
> HL_77436.5  4V9F C 1916 G 1923
CGUACAAG
> HL_77436.5  2D6F G  931 C  939
GCUUUGGAC
> HL_77436.5  5CCB G   53 C   61
GUUCAAGUC
> HL_77436.5  7A0S C 1103 G 1110
CGUAAUAG