Alignment of IL_55938.4 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
4
I

8
5

4
9
5
I

10
6


11
5
I

12
5

5
13
4
I

14
3

6
15
2
I

16
2

7
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_55938.4_Instance_1 IL_55938.4_IL_4A1B_038_G894_C915GAUAUUC
IL_55938.4_Sequence_1 IL_55938.4_IL_4A1B_038_G894_C915GAUA*UUCtrue74002.49
IL_55938.4_Instance_2 IL_55938.4_IL_3V2F_022_G738_C758GGUGCUC
IL_55938.4_Sequence_2 IL_55938.4_IL_3V2F_022_G738_C758GGUG*CUCtrue100000.00
IL_55938.4_Instance_3 IL_55938.4_IL_4IOA_018_G751_C771GGUGCUC
IL_55938.4_Sequence_3 IL_55938.4_IL_4IOA_018_G751_C771GGUG*CUCtrue100000.00
IL_55938.4_Instance_4 IL_55938.4_IL_1S72_029_G830_C851GUUGCUC
IL_55938.4_Sequence_4 IL_55938.4_IL_1S72_029_G830_C851GUUG*CUCtrue98000.18
IL_55938.4_Instance_5 IL_55938.4_IL_3U5H_033_G869_C890GGUUAUC
IL_55938.4_Sequence_5 IL_55938.4_IL_3U5H_033_G869_C890GGUU*AUCtrue97000.26
IL_55938.4_Instance_6 IL_55938.4_IL_3U5F_014_U259_A206UUUUCGUA
IL_55938.4_Sequence_6 IL_55938.4_IL_3U5F_014_U259_A206UUUUC*GUAtrue81001.84
IL_55938.4_Instance_7 IL_55938.4_IL_1S72_082_G2524_C2496GGCUUGUC
IL_55938.4_Sequence_7 IL_55938.4_IL_1S72_082_G_2524_C_2496GGCUU*GUCtrue69002.94
IL_55938.4_Instance_8 IL_55938.4_IL_3V2F_091_G2489_C2461GGUUUAUC
IL_55938.4_Sequence_8 IL_55938.4_IL_3V2F_091_G_2489_C_2461GGUUU*AUCtrue84001.54
IL_55938.4_Instance_9 IL_55938.4_IL_4BPP_014_U256_A201UGAUCGUA
IL_55938.4_Sequence_9 IL_55938.4_IL_4BPP_014_U256_A201UGAUC*GUAtrue83001.66
IL_55938.4_Instance_10 IL_55938.4_IL_3U5H_061_G1262_C1277GAGUGCUC
IL_55938.4_Sequence_10 IL_55938.4_IL_3U5H_061_G_1262_C_1277GAGUG*CUCtrue68003.04
IL_55938.4_Instance_11 IL_55938.4_IL_4A1B_109_U2846_G2818UUUUUGUG
IL_55938.4_Sequence_11 IL_55938.4_IL_4A1B_109_U_2846_G_2818UUUUU*GUGtrue63003.47
IL_55938.4_Instance_12 IL_55938.4_IL_3U5H_111_U2858_G2830UUUUUGUG
IL_55938.4_Sequence_12 IL_55938.4_IL_3U5H_111_U_2858_G_2830UUUUU*GUGtrue63003.47
IL_55938.4_Instance_13 IL_55938.4_IL_1S72_003_C440_G41CAACGCG
IL_55938.4_Sequence_13 IL_55938.4_IL_1S72_003_C440_G41CAAC*GCGtrue81001.80
IL_55938.4_Instance_14 IL_55938.4_IL_2QBZ_004_C33_G151CUCCGUG
IL_55938.4_Sequence_14 IL_55938.4_IL_2QBZ_004_C33_G151CUCC*GUGtrue64003.40
IL_55938.4_Instance_15 IL_55938.4_IL_3V2F_003_C433_G44CUCCGAG
IL_55938.4_Sequence_15 IL_55938.4_IL_3V2F_003_C433_G44CUCC*GAGtrue65003.32
IL_55938.4_Instance_16 IL_55938.4_IL_3P49_006_C34_G53CGAAGCAG
IL_55938.4_Sequence_16 IL_55938.4_IL_3P49_006_C34_G53CGAAG*CAGtrue47004.99
IL_55938.4_Instance_17 IL_55938.4_IL_3P49_009_C109_G144CGAAGCAG
IL_55938.4_Sequence_17 IL_55938.4_IL_3P49_009_C109_G144CGAAG*CAGtrue47004.99
IL_55938.4_Instance_18 IL_55938.4_IL_1XJR_001_C9_G41CCGAGCAG
IL_55938.4_Sequence_18 IL_55938.4_IL_1XJR_001_C9_G41CCGAG*CAGtrue50004.80

Conserved interactions between motif group positions in IL_55938.4:
1 2 s35 
1 7 cWW 
2 3 cSH 
3 4 s35 
3 6 cWW 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35 
JAR3D SCFG/MRF model for IL_55938.4:
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 [7] // Initial node G894 - C915 from junction 
BasepairNode | Deletion Probability [0.0000135111498549] | Pair Probability [[0.008932872,0.016290939,0.010331188,0.153396411,0.000000000],[0.045391698,0.008156512,0.215817026,0.011782149,0.000000000],[0.010352346,0.232691981,0.001990992,0.021205394,0.000000000],[0.171676602,0.011675089,0.070593401,0.009715400,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.886338815,0.113215093,0.000430710,0.000015382] | Left Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | 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 [7] // Basepair G894 - C915 cWW 
ClusterNode  | Deletion Probability [0.0000000117080752] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [6] | Norm Constant [0.334293237869045] // Cluster node A895:U896 and U914:U914
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.058992769,0.156320290,0.012890526,0.031035873,0.000000000],[0.031742405,0.016837534,0.019466934,0.029412503,0.000000000],[0.012640957,0.019827790,0.004057590,0.041315015,0.000000000],[0.026061957,0.015427032,0.016516928,0.507453895,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U896 - U914 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.101544766,0.094028770,0.005043888,0.018571486,0.000000000],[0.103752614,0.100300448,0.001088231,0.101311333,0.000000000],[0.036651732,0.005055117,0.008908682,0.162632283,0.000000000],[0.014736849,0.109801903,0.001088231,0.135483665,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A895 - U896 cSH 
Insertion    | Location [1] | Length Distribution [0.554488312,0.444143909,0.001306306,0.000061473] | Letter Distribution [0.350000000,0.150000000,0.150000000,0.350000000,0.000000000]// Insertion after nucleotide 2, position 1 in cluster node
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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009030986,0.016350867,0.010422527,0.155516523,0.000000000],[0.059754563,0.008559478,0.198415479,0.011808726,0.000000000],[0.010459788,0.215045531,0.002057107,0.020817135,0.000000000],[0.165266294,0.011623489,0.094677147,0.010194359,0.000000000],[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 A897 - U913 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_55938.4:
> IL_55938.4 IL_4A1B_038 G  894 C  915
GAUA*UUC
> IL_55938.4 IL_3V2F_022 G  738 C  758
GGUG*CUC
> IL_55938.4 IL_4IOA_018 G  751 C  771
GGUG*CUC
> IL_55938.4 IL_1S72_029 G  830 C  851
GUUG*CUC
> IL_55938.4 IL_3U5H_033 G  869 C  890
GGUU*AUC
> IL_55938.4 IL_3U5F_014 U  259 A  206
UUUUC*GUA
> IL_55938.4 IL_1S72_082 G 2524 C 2496
GGCUU*GUC
> IL_55938.4 IL_3V2F_091 G 2489 C 2461
GGUUU*AUC
> IL_55938.4 IL_4BPP_014 U  256 A  201
UGAUC*GUA
> IL_55938.4 IL_3U5H_061 G 1262 C 1277
GAGUG*CUC
> IL_55938.4 IL_4A1B_109 U 2846 G 2818
UUUUU*GUG
> IL_55938.4 IL_3U5H_111 U 2858 G 2830
UUUUU*GUG
> IL_55938.4 IL_1S72_003 C  440 G   41
CAAC*GCG
> IL_55938.4 IL_2QBZ_004 C   33 G  151
CUCC*GUG
> IL_55938.4 IL_3V2F_003 C  433 G   44
CUCC*GAG
> IL_55938.4 IL_3P49_006 C   34 G   53
CGAAG*CAG
> IL_55938.4 IL_3P49_009 C  109 G  144
CGAAG*CAG
> IL_55938.4 IL_1XJR_001 C    9 G   41
CCGAG*CAG