Alignment of IL_94430.5 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
2

2
5
3
I

6
4

3
7
4
I

8
5


9
4
I

10
4

4
11
3
I

12
2

5
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_94430.5_Instance_1 IL_94430.5_IL_3Q1Q_003_G103_C210GACAGCC
IL_94430.5_Sequence_1 IL_94430.5_IL_3Q1Q_003_G103_C210GACAG*CCtrue78002.11
IL_94430.5_Instance_2 IL_94430.5_IL_2AW7_007_U70_A98UAACGA
IL_94430.5_Sequence_2 IL_94430.5_IL_2AW7_007_U70_A98UAAC*GAtrue86001.29
IL_94430.5_Instance_3 IL_94430.5_IL_3U5H_145_G49_C29GUAGCC
IL_94430.5_Sequence_3 IL_94430.5_IL_3U5H_145_G49_C29GUAG*CCtrue88001.11
IL_94430.5_Instance_4 IL_94430.5_IL_4IOA_106_G53_C33GUCGCC
IL_94430.5_Sequence_4 IL_94430.5_IL_4IOA_106_G53_C33GUCG*CCtrue67003.14
IL_94430.5_Instance_5 IL_94430.5_IL_2QBG_072_C1837_G1903CCGGCG
IL_94430.5_Sequence_5 IL_94430.5_IL_2QBG_072_C_1837_G_1903CCGG*CGtrue91000.83
IL_94430.5_Instance_6 IL_94430.5_IL_1S72_066_C1893_G1944CCAGCG
IL_94430.5_Sequence_6 IL_94430.5_IL_1S72_066_C_1893_G_1944CCAG*CGtrue96000.41
IL_94430.5_Instance_7 IL_94430.5_IL_4BPP_040_G785_C731GAAUAC
IL_94430.5_Sequence_7 IL_94430.5_IL_4BPP_040_G785_C731GAAU*ACtrue93000.64
IL_94430.5_Instance_8 IL_94430.5_IL_2AW7_046_G993_C1045GACAUAC
IL_94430.5_Sequence_8 IL_94430.5_IL_2AW7_046_G993_C_1045GACAU*ACtrue75002.42
IL_94430.5_Instance_9 IL_94430.5_IL_4IOA_066_C1829_G1886CCGGCG
IL_94430.5_Sequence_9 IL_94430.5_IL_4IOA_066_C_1829_G_1886CCGG*CGtrue91000.83
IL_94430.5_Instance_10 IL_94430.5_IL_1FJG_039_G993_C1045GACAUAC
IL_94430.5_Sequence_10 IL_94430.5_IL_1FJG_039_G993_C_1045GACAU*ACtrue75002.42
IL_94430.5_Instance_11 IL_94430.5_IL_3V2F_068_C1837_G1903CCGGCG
IL_94430.5_Sequence_11 IL_94430.5_IL_3V2F_068_C_1837_G_1903CCGG*CGtrue91000.83
IL_94430.5_Instance_12 IL_94430.5_IL_4A1B_086_C2191_G2241CCAGCG
IL_94430.5_Sequence_12 IL_94430.5_IL_4A1B_086_C_2191_G_2241CCAG*CGtrue96000.41
IL_94430.5_Instance_13 IL_94430.5_IL_3V2F_055_G1448_C1463GAGCC
IL_94430.5_Sequence_13 IL_94430.5_IL_3V2F_055_G_1448_C_1463GAG*CCtrue100000.00
IL_94430.5_Instance_14 IL_94430.5_IL_3V2F_032_U877_A899UAGCA
IL_94430.5_Sequence_14 IL_94430.5_IL_3V2F_032_U877_A899UAG*CAtrue93000.64
IL_94430.5_Instance_15 IL_94430.5_IL_4GMA_001_A7_U177AGCGU
IL_94430.5_Sequence_15 IL_94430.5_IL_4GMA_001_A7_U177AGC*GUtrue78002.12
IL_94430.5_Instance_16 IL_94430.5_IL_2XXA_013_G68_C29GAUGC
IL_94430.5_Sequence_16 IL_94430.5_IL_2XXA_013_G68_C29GAU*GCtrue82001.68

Conserved interactions between motif group positions in IL_94430.5:
1 5 cWW 
2 3 s35 
2 5 cWS 
3 4 cWW 
4 5 s35 
JAR3D SCFG/MRF model for IL_94430.5:
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 G103 - C210 from junction 
ClusterNode  | Deletion Probability [0.0000000008620170] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [5] | Norm Constant [0.255107818202131] // Cluster node G103:A106 and C210:C210
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.008749015,0.017415315,0.010011712,0.181140724,0.000000000],[0.017067831,0.007609293,0.225669046,0.011363249,0.000000000],[0.009988146,0.252552013,0.001890595,0.022784617,0.000000000],[0.190022474,0.011467899,0.022392238,0.009875835,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G103 - C210 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.164033804,0.235204347,0.156292787,0.135327736,0.000000000],[0.015108920,0.030878952,0.013650815,0.013448497,0.000000000],[0.011525639,0.041331922,0.102393924,0.054059290,0.000000000],[0.006916998,0.007800792,0.005725395,0.006300183,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A106 - C210 cWS 
Insertion    | Location [1] | Length Distribution [0.250349596,0.560713176,0.188238036,0.000670059,0.000029133] | Letter Distribution [0.323529412,0.500000000,0.029411765,0.147058824,0.000000000]// Insertion after nucleotide 1, 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 [3] | Right Index [4] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008923836,0.017437847,0.010242436,0.163781264,0.000000000],[0.033196525,0.008016118,0.189841314,0.011490510,0.000000000],[0.010199220,0.261168283,0.001966599,0.022517066,0.000000000],[0.190863191,0.011674884,0.048704589,0.009976317,0.000000000],[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 G107 - C209 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_94430.5:
> IL_94430.5 IL_3Q1Q_003 G  103 C  210
GACAG*CC
> IL_94430.5 IL_2AW7_007 U   70 A   98
UAAC*GA
> IL_94430.5 IL_3U5H_145 G   49 C   29
GUAG*CC
> IL_94430.5 IL_4IOA_106 G   53 C   33
GUCG*CC
> IL_94430.5 IL_2QBG_072 C 1837 G 1903
CCGG*CG
> IL_94430.5 IL_1S72_066 C 1893 G 1944
CCAG*CG
> IL_94430.5 IL_4BPP_040 G  785 C  731
GAAU*AC
> IL_94430.5 IL_2AW7_046 G  993 C 1045
GACAU*AC
> IL_94430.5 IL_4IOA_066 C 1829 G 1886
CCGG*CG
> IL_94430.5 IL_1FJG_039 G  993 C 1045
GACAU*AC
> IL_94430.5 IL_3V2F_068 C 1837 G 1903
CCGG*CG
> IL_94430.5 IL_4A1B_086 C 2191 G 2241
CCAG*CG
> IL_94430.5 IL_3V2F_055 G 1448 C 1463
GAG*CC
> IL_94430.5 IL_3V2F_032 U  877 A  899
UAG*CA
> IL_94430.5 IL_4GMA_001 A    7 U  177
AGC*GU
> IL_94430.5 IL_2XXA_013 G   68 C   29
GAU*GC