Alignment of IL_65553.8 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_65553.8
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
4
I

14
5

7
15
5
I

16
6


17
5
I

18
5

8
19
4
I

20
4

9
21
3
I

22
2

10
23
2
I

24
2

11
25
2
I

26
2

12
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_65553.8_Instance_1 IL_65553.8_IL_3GX5_002_C31_G21CGACGAAAUGGAG
IL_65553.8_Sequence_1 IL_65553.8_IL_3GX5_002_C31_G21CGACGAAA*UGGAGtrue95000.94
IL_65553.8_Instance_2 IL_65553.8_IL_3V7E_006_C231_G221CGAUGAAAUGGAG
IL_65553.8_Sequence_2 IL_65553.8_IL_3V7E_006_C231_G221CGAUGAAA*UGGAGtrue97000.46
IL_65553.8_Instance_3 IL_65553.8_IL_3V2F_044_C1208_G1238CGAUGAAGUGGAG
IL_65553.8_Sequence_3 IL_65553.8_IL_3V2F_044_C_1208_G_1238CGAUGAAG*UGGAGtrue100000.00
IL_65553.8_Instance_4 IL_65553.8_IL_3U5H_064_U1388_A1419UGACGAAGUCGAA
IL_65553.8_Sequence_4 IL_65553.8_IL_3U5H_064_U_1388_A_1419UGACGAAG*UCGAAtrue78003.69
IL_65553.8_Instance_5 IL_65553.8_IL_4KQY_002_C31_G21CGACGAAGCAGAG
IL_65553.8_Sequence_5 IL_65553.8_IL_4KQY_002_C31_G21CGACGAAG*CAGAGtrue84002.69
IL_65553.8_Instance_6 IL_65553.8_IL_4C4W_001_U26_G7UGAUGACCGCAAG
IL_65553.8_Sequence_6 IL_65553.8_IL_4C4W_001_U26_G7UGAUGACC*GCAAGtrue73004.61
IL_65553.8_Instance_7 IL_65553.8_IL_1S72_048_G1312_C1342GAUGGAAGUGGAC
IL_65553.8_Sequence_7 IL_65553.8_IL_1S72_048_G_1312_C_1342GAUGGAAG*UGGACtrue78003.70
IL_65553.8_Instance_8 IL_65553.8_IL_4IOA_045_C1221_G1251CGGAGAAGUGGAG
IL_65553.8_Sequence_8 IL_65553.8_IL_4IOA_045_C_1221_G_1251CGGAGAAG*UGGAGtrue89001.87
IL_65553.8_Instance_9 IL_65553.8_IL_2QBG_047_C1208_G1238CUGCGAAGUGGAG
IL_65553.8_Sequence_9 IL_65553.8_IL_2QBG_047_C_1208_G_1238CUGCGAAG*UGGAGtrue79003.50
IL_65553.8_Instance_10 IL_65553.8_IL_4A1B_062_C1414_G1445CCUAGAAGUGGAG
IL_65553.8_Sequence_10 IL_65553.8_IL_4A1B_062_C_1414_G_1445CCUAGAAG*UGGAGtrue77003.97
IL_65553.8_Instance_11 IL_65553.8_IL_4AOB_002_U31_G21UGAUGACCGCAAG
IL_65553.8_Sequence_11 IL_65553.8_IL_4AOB_002_U31_G21UGAUGACC*GCAAGtrue73004.61
IL_65553.8_Instance_12 IL_65553.8_IL_1T0K_001_C54_G13CAGAGAUGCGGAG
IL_65553.8_Sequence_12 IL_65553.8_IL_1T0K_001_C54_G13CAGAGAUG*CGGAGtrue79003.53
IL_65553.8_Instance_13 IL_65553.8_IL_1S72_004_C93_G81CGAAGAACGGGAG
IL_65553.8_Sequence_13 IL_65553.8_IL_1S72_004_C93_G81CGAAGAAC*GGGAGtrue94001.06
IL_65553.8_Instance_14 IL_65553.8_IL_4GXY_005_C139_G86CGAGGAUCGGGAG
IL_65553.8_Sequence_14 IL_65553.8_IL_4GXY_005_C139_G86CGAGGAUC*GGGAGtrue92001.33
IL_65553.8_Instance_15 IL_65553.8_IL_3V2F_004_C97_G85CGUGGAUCGGGAG
IL_65553.8_Sequence_15 IL_65553.8_IL_3V2F_004_C97_G85CGUGGAUC*GGGAGtrue89001.85
IL_65553.8_Instance_16 IL_65553.8_IL_4IOA_004_C96_G84CUUUGACUACGAG
IL_65553.8_Sequence_16 IL_65553.8_IL_4IOA_004_C96_G84CUUUGACU*ACGAGtrue75004.23
IL_65553.8_Instance_17 IL_65553.8_IL_4GMA_003_G143_C97GGAUGAGUAGGAC
IL_65553.8_Sequence_17 IL_65553.8_IL_4GMA_003_G143_C97GGAUGAGU*AGGACtrue80003.39
IL_65553.8_Instance_18 IL_65553.8_IL_3U5F_051_C910_G899CUUGGAUUGUCAG
IL_65553.8_Sequence_18 IL_65553.8_IL_3U5F_051_C910_G899CUUGGAUU*GUCAGtrue45009.46
IL_65553.8_Instance_19 IL_65553.8_IL_1S72_032_C1026_G940CGUUUGACGCCGAG
IL_65553.8_Sequence_19 IL_65553.8_IL_1S72_032_C_1026_G940CGUUUGACG*CCGAGtrue64006.08
IL_65553.8_Instance_20 IL_65553.8_IL_3RW6_002_C43_G18CAAUGACGUAAGACAG
IL_65553.8_Sequence_20 IL_65553.8_IL_3RW6_002_C43_G18CAAUGACG*UAAGACAGtrue380010.53
IL_65553.8_Instance_21 IL_65553.8_IL_2AW7_014_C277_G247CGACGAUCGAUUAG
IL_65553.8_Sequence_21 IL_65553.8_IL_2AW7_014_C277_G247CGACGAUC*GAUUAGtrue53007.96
IL_65553.8_Instance_22 IL_65553.8_IL_3U5F_019_U348_A316UUUCAACGUAUCAA
IL_65553.8_Sequence_22 IL_65553.8_IL_3U5F_019_U348_A316UUUCAACG*UAUCAAtrue390010.40
IL_65553.8_Instance_23 IL_65553.8_IL_4BPP_017_C339_G307CAGUCACGUAUCAG
IL_65553.8_Sequence_23 IL_65553.8_IL_4BPP_017_C339_G307CAGUCACG*UAUCAGtrue53008.02

Conserved interactions between motif group positions in IL_65553.8:
1 2 s35 
1 12 cWW 
2 11 tSS 
2 12 s55 
3 4 s35 
3 11 s33 
4 10 s33 
4 11 tSH 
5 6 s35 
5 10 tHS 
5 11 s55 
5 12 tSS 
6 7 s35 
6 9 tHS 
7 8 cWW 
8 9 s35 
9 10 s35 
10 11 s35 
9 5 6BPh
10 5 6BPh
11 2 6BR
10 4 6BR
11 4 6BR
JAR3D SCFG/MRF model for IL_65553.8:
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 [12] // Initial node C31 - G21 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000001549484556559301900000000000000000000000] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [12] | Norm Constant [0.094806833173160] // Cluster node C31:A36 and G19:G21
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.081378496,0.098546092,0.388749317,0.053999063,0.000000000],[0.063189619,0.045680214,0.002558985,0.039956944,0.000000000],[0.000713427,0.000588948,0.012712851,0.000457180,0.000000000],[0.004459938,0.000588948,0.205962796,0.000457180,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A36 - G19 tHS 
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.165813762,0.027446076,0.026469528,0.026092728,0.000000000],[0.033494723,0.007176489,0.007176489,0.007176489,0.000000000],[0.456888233,0.071193943,0.071937937,0.015714203,0.000000000],[0.061889933,0.007176489,0.007176489,0.007176489,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G32 - A20 tSS 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.167477241,0.036008291,0.000377768,0.001878311,0.000000000],[0.168744503,0.032054522,0.000377768,0.000377768,0.000000000],[0.356845819,0.000377768,0.001929297,0.029052875,0.000000000],[0.170826576,0.032915957,0.000377768,0.000377768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G35 - A20 tSH 
Interaction  | Interacting Bases [1,8] | Pair Probability [[0.008479529,0.014561897,0.009826657,0.149620471,0.000000000],[0.038597518,0.007703173,0.302258354,0.011499664,0.000000000],[0.009933633,0.176224842,0.001882503,0.019390841,0.000000000],[0.167564853,0.011015113,0.062328090,0.009112862,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C31 - G21 cWW 
Interaction  | Interacting Bases [5,8] | Pair Probability [[0.161548555,0.169966367,0.372406758,0.139858546,0.000000000],[0.001593759,0.001593759,0.001593759,0.001593759,0.000000000],[0.008609318,0.009842421,0.014904474,0.110113490,0.000000000],[0.001593759,0.001593759,0.001593759,0.001593759,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A36 - G21 tSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.020000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.180000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A33
Insertion    | Location [3] | Length Distribution [0.002070169,0.952371991,0.045355528,0.000197607,0.000004705] | Letter Distribution [0.173076923,0.250000000,0.173076923,0.403846154,0.000000000]// Insertion after nucleotide 3, position 3 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 [0.824177637,0.131879734,0.000466622,0.043377026,0.000094267,0.000004713] | Right Letter Distribution [0.312500000,0.062500000,0.187500000,0.437500000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.047811319,0.050466058,0.302105938,0.047561334,0.000000000],[0.090847252,0.086472653,0.002900073,0.043001204,0.000000000],[0.000629921,0.000629921,0.061099075,0.000629921,0.000000000],[0.021682211,0.000629921,0.229627575,0.013905624,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A37 - G18 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010420873,0.110403380,0.010827885,0.125139785,0.000000000],[0.025695383,0.008447915,0.159702672,0.011573885,0.000000000],[0.010744835,0.136352265,0.002255713,0.197636037,0.000000000],[0.123320488,0.011981439,0.038018641,0.017478805,0.000000000],[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 [7] | Right Index [8] // Basepair A38 - U17 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_65553.8:
> IL_65553.8 IL_3GX5_002 C   31 G   21
CGACGAAA*UGGAG
> IL_65553.8 IL_3V7E_006 C  231 G  221
CGAUGAAA*UGGAG
> IL_65553.8 IL_3V2F_044 C 1208 G 1238
CGAUGAAG*UGGAG
> IL_65553.8 IL_3U5H_064 U 1388 A 1419
UGACGAAG*UCGAA
> IL_65553.8 IL_4KQY_002 C   31 G   21
CGACGAAG*CAGAG
> IL_65553.8 IL_4C4W_001 U   26 G    7
UGAUGACC*GCAAG
> IL_65553.8 IL_1S72_048 G 1312 C 1342
GAUGGAAG*UGGAC
> IL_65553.8 IL_4IOA_045 C 1221 G 1251
CGGAGAAG*UGGAG
> IL_65553.8 IL_2QBG_047 C 1208 G 1238
CUGCGAAG*UGGAG
> IL_65553.8 IL_4A1B_062 C 1414 G 1445
CCUAGAAG*UGGAG
> IL_65553.8 IL_4AOB_002 U   31 G   21
UGAUGACC*GCAAG
> IL_65553.8 IL_1T0K_001 C   54 G   13
CAGAGAUG*CGGAG
> IL_65553.8 IL_1S72_004 C   93 G   81
CGAAGAAC*GGGAG
> IL_65553.8 IL_4GXY_005 C  139 G   86
CGAGGAUC*GGGAG
> IL_65553.8 IL_3V2F_004 C   97 G   85
CGUGGAUC*GGGAG
> IL_65553.8 IL_4IOA_004 C   96 G   84
CUUUGACU*ACGAG
> IL_65553.8 IL_4GMA_003 G  143 C   97
GGAUGAGU*AGGAC
> IL_65553.8 IL_3U5F_051 C  910 G  899
CUUGGAUU*GUCAG
> IL_65553.8 IL_1S72_032 C 1026 G  940
CGUUUGACG*CCGAG
> IL_65553.8 IL_3RW6_002 C   43 G   18
CAAUGACG*UAAGACAG
> IL_65553.8 IL_2AW7_014 C  277 G  247
CGACGAUC*GAUUAG
> IL_65553.8 IL_3U5F_019 U  348 A  316
UUUCAACG*UAUCAA
> IL_65553.8 IL_4BPP_017 C  339 G  307
CAGUCACG*UAUCAG