Alignment of IL_34363.2 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
2
I

6
2

3
7
2
I

8
2

4
9
2
I

10
2

5
11
3
I

12
4

6
13
5
I

14
6

7
15
6
I

16
7

8
17
7
I

18
8


19
7
I

20
7

9
21
6
I

22
6

10
23
3
I

24
2

11
25
2
I

26
2

12
27
2
I

28
2

13
29
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_34363.2_Instance_1 IL_34363.2_IL_1S72_043_C1147_G1216CCUAGACAGCCGAG
IL_34363.2_Sequence_1 IL_34363.2_IL_1S72_043_C_1147_G_1216CCUAGACAG*CCGAGtrue99000.16
IL_34363.2_Instance_2 IL_34363.2_IL_3U5H_059_U1218_A1287UCUAGACAGCCGAA
IL_34363.2_Sequence_2 IL_34363.2_IL_3U5H_059_U_1218_A_1287UCUAGACAG*CCGAAtrue97000.62
IL_34363.2_Instance_3 IL_34363.2_IL_2QBG_042_C1043_G1112CCCAGACAGUCGAG
IL_34363.2_Sequence_3 IL_34363.2_IL_2QBG_042_C_1043_G_1112CCCAGACAG*UCGAGtrue97000.68
IL_34363.2_Instance_4 IL_34363.2_IL_4IOA_039_C1054_G1123CAUAGACAGUCGAG
IL_34363.2_Sequence_4 IL_34363.2_IL_4IOA_039_C_1054_G_1123CAUAGACAG*UCGAGtrue100000.00

Conserved interactions between motif group positions in IL_34363.2:
1 2 s35 
1 5 cSS 
1 13 cWW 
2 12 tSS 
2 13 s55 
3 4 s55 
3 12 s53 
4 11 s33 
4 12 tSH 
5 6 s35 
5 11 tHS 
5 12 s55 
5 13 tSS 
6 7 s35 
7 8 s35 
7 10 bif 
8 9 cWW 
9 10 s35 
10 11 s35 
12 13 cSS 
11 5 6BPh
12 2 6BR
11 4 6BR
JAR3D SCFG/MRF model for IL_34363.2:
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 [13] // Initial node C1147 - G1216 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000001940553474955695100000000000000000000000] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [13] | Norm Constant [0.000558380037188] // Cluster node C1147:A1152 and G1214:G1216
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.042875527,0.043256990,0.400078329,0.046604180,0.000000000],[0.049976915,0.045339634,0.003616168,0.044897183,0.000000000],[0.000516595,0.000516595,0.017519574,0.000516595,0.000000000],[0.002459961,0.000516595,0.300792562,0.000516595,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1152 - G1214 tHS 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.107954545,0.054632867,0.054632867,0.054632867,0.000000000],[0.127185315,0.054632867,0.054632867,0.054632867,0.000000000],[0.054632867,0.054632867,0.054632867,0.054632867,0.000000000],[0.054632867,0.054632867,0.054632867,0.054632867,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1148 - A1215 tSS 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.185166390,0.043167026,0.000446204,0.002124765,0.000000000],[0.186813816,0.039161625,0.000446204,0.000446204,0.000000000],[0.261563424,0.000446204,0.002161764,0.037115194,0.000000000],[0.201269312,0.038779462,0.000446204,0.000446204,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1151 - A1215 tSH 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.009613617,0.017593128,0.010983027,0.192350441,0.000000000],[0.021287894,0.008639455,0.234523700,0.012787711,0.000000000],[0.011096459,0.200570476,0.002109537,0.023296342,0.000000000],[0.204768830,0.012284769,0.027115440,0.010979173,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1147 - G1216 cWW 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.204273875,0.182392691,0.228460848,0.175009089,0.000000000],[0.001996147,0.001996147,0.001996147,0.001996147,0.000000000],[0.010954656,0.012643890,0.019492821,0.150802954,0.000000000],[0.001996147,0.001996147,0.001996147,0.001996147,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1152 - G1216 tSS 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.056456460,0.057489227,0.055785276,0.056733612,0.000000000],[0.136969236,0.057810615,0.007079764,0.053147720,0.000000000],[0.060169857,0.061092715,0.055484166,0.061453996,0.000000000],[0.111667921,0.056875119,0.054584017,0.057200297,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1147 - A1152 cSS 
Interaction  | Interacting Bases [7,8] | Pair Probability [[0.195141897,0.160173003,0.197628067,0.154493037,0.000000000],[0.029233204,0.029516469,0.003600697,0.030054980,0.000000000],[0.029730386,0.030050892,0.013725809,0.030122553,0.000000000],[0.029973668,0.007433790,0.028524377,0.030597170,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1215 - G1216 cSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.583333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U1149
Insertion    | Location [3] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // Initial node C1153 - C1213 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left
InitialNode  | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [7] | Right Index [10] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.018665872,0.615612422,0.004897383,0.004897383,0.000000000],[0.021553581,0.253036378,0.004897383,0.004897383,0.000000000],[0.004897383,0.004897383,0.018574216,0.004897383,0.000000000],[0.004897383,0.004897383,0.023583701,0.004897383,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Basepair A1154 - C1213 bif 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.013091073,0.162345844,0.013424526,0.116783626,0.000000000],[0.015534003,0.009786201,0.120926247,0.014071788,0.000000000],[0.013182666,0.146362737,0.002747701,0.202112848,0.000000000],[0.112925662,0.015211513,0.019098011,0.022395553,0.000000000],[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 [8] | Right Index [9] // Basepair G1155 - C1212 cWW 
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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_34363.2:
> IL_34363.2 IL_1S72_043 C 1147 G 1216
CCUAGACAG*CCGAG
> IL_34363.2 IL_3U5H_059 U 1218 A 1287
UCUAGACAG*CCGAA
> IL_34363.2 IL_2QBG_042 C 1043 G 1112
CCCAGACAG*UCGAG
> IL_34363.2 IL_4IOA_039 C 1054 G 1123
CAUAGACAG*UCGAG