Alignment of IL_87904.5 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_87904.5
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
5

4
9
5
I

10
6

5
11
6
I

12
7


13
6
I

14
6

6
15
5
I

16
5

7
17
4
I

18
4

8
19
3
I

20
3

9
21
2
I

22
2

10
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_87904.5_Instance_1 IL_87904.5_IL_3V2F_072_G1856_C1886GGGAGCGAAC
IL_87904.5_Sequence_1 IL_87904.5_IL_3V2F_072_G_1856_C_1886GGGAG*CGAACtrue100000.00
IL_87904.5_Instance_2 IL_87904.5_IL_4IOA_070_U1848_A1869UGGAGCGAAA
IL_87904.5_Sequence_2 IL_87904.5_IL_4IOA_070_U_1848_A_1869UGGAG*CGAAAtrue96000.36
IL_87904.5_Instance_3 IL_87904.5_IL_3U5H_075_A1806_U1649AGGAAUGAAU
IL_87904.5_Sequence_3 IL_87904.5_IL_3U5H_075_A_1806_U_1649AGGAA*UGAAUtrue90000.96
IL_87904.5_Instance_4 IL_87904.5_IL_2A64_006_C347_G382CGGAGCGAAG
IL_87904.5_Sequence_4 IL_87904.5_IL_2A64_006_C347_G382CGGAG*CGAAGtrue100000.03
IL_87904.5_Instance_5 IL_87904.5_IL_4BPP_090_U1649_A1676UGGACGAAAA
IL_87904.5_Sequence_5 IL_87904.5_IL_4BPP_090_U_1649_A_1676UGGAC*GAAAAtrue82001.72
IL_87904.5_Instance_6 IL_87904.5_IL_4FAW_002_G113_C74GGACGCUAAC
IL_87904.5_Sequence_6 IL_87904.5_IL_4FAW_002_G113_C74GGACG*CUAACtrue88001.10
IL_87904.5_Instance_7 IL_87904.5_IL_2A64_005_C297_G288CGGAGCGAAG
IL_87904.5_Sequence_7 IL_87904.5_IL_2A64_005_C297_G288CGGAG*CGAAGtrue100000.03
IL_87904.5_Instance_8 IL_87904.5_IL_3DHS_004_C297_G288CGGAGCGAAG
IL_87904.5_Sequence_8 IL_87904.5_IL_3DHS_004_C297_G288CGGAG*CGAAGtrue100000.03
IL_87904.5_Instance_9 IL_87904.5_IL_3IWN_002_G31_C16GGACGCAAAC
IL_87904.5_Sequence_9 IL_87904.5_IL_3IWN_002_G31_C16GGACG*CAAACtrue88001.13
IL_87904.5_Instance_10 IL_87904.5_IL_2QBG_068_U1736_G1724UGGAGUGAGG
IL_87904.5_Sequence_10 IL_87904.5_IL_2QBG_068_U_1736_G_1724UGGAG*UGAGGtrue62003.62
IL_87904.5_Instance_11 IL_87904.5_IL_4A1B_125_G3189_C3221GAGCGUUAAC
IL_87904.5_Sequence_11 IL_87904.5_IL_4A1B_125_G_3189_C_3221GAGCG*UUAACtrue76002.32
IL_87904.5_Instance_12 IL_87904.5_IL_1S72_083_G2501_C2519GCAAGCGACC
IL_87904.5_Sequence_12 IL_87904.5_IL_1S72_083_G_2501_C_2519GCAAG*CGACCtrue92000.79
IL_87904.5_Instance_13 IL_87904.5_IL_1S72_028_U815_G798UGGAAUGAAG
IL_87904.5_Sequence_13 IL_87904.5_IL_1S72_028_U815_G798UGGAA*UGAAGtrue86001.36
IL_87904.5_Instance_14 IL_87904.5_IL_2QBG_024_U724_G707UGGAGUGAAG
IL_87904.5_Sequence_14 IL_87904.5_IL_2QBG_024_U724_G707UGGAG*UGAAGtrue86001.36
IL_87904.5_Instance_15 IL_87904.5_IL_1U6B_002_G84_C60GCAACGAAAC
IL_87904.5_Sequence_15 IL_87904.5_IL_1U6B_002_G84_C60GCAAC*GAAACtrue72002.68
IL_87904.5_Instance_16 IL_87904.5_IL_3UCZ_001_G41_C26GGACGCAAAC
IL_87904.5_Sequence_16 IL_87904.5_IL_3UCZ_001_G41_C26GGACG*CAAACtrue88001.13
IL_87904.5_Instance_17 IL_87904.5_IL_3U5F_091_A1678_U1723AGGAUAGAAU
IL_87904.5_Sequence_17 IL_87904.5_IL_3U5F_091_A_1678_U_1723AGGAU*AGAAUtrue89001.03
IL_87904.5_Instance_18 IL_87904.5_IL_3V2F_021_U724_G707UGGAGUGAAG
IL_87904.5_Sequence_18 IL_87904.5_IL_3V2F_021_U724_G707UGGAG*UGAAGtrue86001.36
IL_87904.5_Instance_19 IL_87904.5_IL_4A1B_110_C2823_G2841CCAAGCGACG
IL_87904.5_Sequence_19 IL_87904.5_IL_4A1B_110_C_2823_G_2841CCAAG*CGACGtrue91000.82
IL_87904.5_Instance_20 IL_87904.5_IL_3U5H_032_U855_G838UGGAGUGAAG
IL_87904.5_Sequence_20 IL_87904.5_IL_3U5H_032_U855_G838UGGAG*UGAAGtrue86001.36
IL_87904.5_Instance_21 IL_87904.5_IL_2QBG_094_C2466_G2484CCAAGCGACG
IL_87904.5_Sequence_21 IL_87904.5_IL_2QBG_094_C_2466_G_2484CCAAG*CGACGtrue91000.82
IL_87904.5_Instance_22 IL_87904.5_IL_3V2F_092_C2466_G2484CCGAGCGGCG
IL_87904.5_Sequence_22 IL_87904.5_IL_3V2F_092_C_2466_G_2484CCGAG*CGGCGtrue77002.14
IL_87904.5_Instance_23 IL_87904.5_IL_4IOA_089_C2445_G2463CCGAGCGGCG
IL_87904.5_Sequence_23 IL_87904.5_IL_4IOA_089_C_2445_G_2463CCGAG*CGGCGtrue77002.14
IL_87904.5_Instance_24 IL_87904.5_IL_2AW7_058_G1272_C1263GCAAGCGACC
IL_87904.5_Sequence_24 IL_87904.5_IL_2AW7_058_G_1272_C_1263GCAAG*CGACCtrue92000.79
IL_87904.5_Instance_25 IL_87904.5_IL_3U5H_112_U2835_A2853UCAAGCGACA
IL_87904.5_Sequence_25 IL_87904.5_IL_3U5H_112_U_2835_A_2853UCAAG*CGACAtrue88001.15
IL_87904.5_Instance_26 IL_87904.5_IL_2QBG_019_G618_C610GGGAGUUAAC
IL_87904.5_Sequence_26 IL_87904.5_IL_2QBG_019_G618_C610GGGAG*UUAACtrue88001.14
IL_87904.5_Instance_27 IL_87904.5_IL_1S72_021_G679_C667GGGAGCUAAC
IL_87904.5_Sequence_27 IL_87904.5_IL_1S72_021_G679_C667GGGAG*CUAACtrue94000.59
IL_87904.5_Instance_28 IL_87904.5_IL_4BPP_028_G509_C529GAACAUUAGC
IL_87904.5_Sequence_28 IL_87904.5_IL_4BPP_028_G509_C529GAACA*UUAGCtrue51004.68
IL_87904.5_Instance_29 IL_87904.5_IL_3V2F_016_C618_G610CGGAGUUAAG
IL_87904.5_Sequence_29 IL_87904.5_IL_3V2F_016_C618_G610CGGAG*UUAAGtrue88001.17
IL_87904.5_Instance_30 IL_87904.5_IL_2QWY_001_C16_G50CGUAUAAAAG
IL_87904.5_Sequence_30 IL_87904.5_IL_2QWY_001_C16_G50CGUAU*AAAAGtrue76002.28
IL_87904.5_Instance_31 IL_87904.5_IL_4IOA_012_C629_G620CGGAGUUAAG
IL_87904.5_Sequence_31 IL_87904.5_IL_4IOA_012_C629_G620CGGAG*UUAAGtrue88001.17

Conserved interactions between motif group positions in IL_87904.5:
1 2 s35 
1 10 cWW 
2 3 s35 
2 8 s33 
2 9 tSH 
2 10 s55 
3 7 s33 
3 8 tSH 
4 5 s35 
4 7 tHS 
4 8 s55 
5 6 cWW 
5 7 s55 
6 7 s35 
8 9 s35 
9 10 s35 
9 2 6BR
JAR3D SCFG/MRF model for IL_87904.5:
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 [10] // Initial node G1856 - C1886 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008122691,0.014661627,0.009375677,0.148321841,0.000000000],[0.052633032,0.007677310,0.217856305,0.010653760,0.000000000],[0.009416586,0.224845442,0.001847153,0.018715187,0.000000000],[0.156997400,0.010454861,0.099256991,0.009164136,0.000000000],[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 [1] | Right Index [10] // Basepair G1856 - C1886 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.090319003,0.093678642,0.012073407,0.017424652,0.000000000],[0.093928424,0.159982766,0.001106375,0.001106375,0.000000000],[0.249506271,0.001106375,0.026084151,0.077828330,0.000000000],[0.088479441,0.085163037,0.001106375,0.001106375,0.000000000],[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 [2] | Right Index [9] // Basepair G1857 - A1885 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.172658120,0.091625881,0.001252191,0.028779862,0.000000000],[0.092017248,0.068763516,0.001252191,0.001252191,0.000000000],[0.244092294,0.001252191,0.046055822,0.054742799,0.000000000],[0.103973853,0.089777455,0.001252191,0.001252191,0.000000000],[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 [3] | Right Index [8] // Basepair G1858 - A1884 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.114226799,0.091684732,0.250077615,0.138459354,0.000000000],[0.114669271,0.086616634,0.001065282,0.117277227,0.000000000],[0.001065282,0.001065282,0.005710459,0.001065282,0.000000000],[0.005519222,0.001065282,0.069366997,0.001065282,0.000000000],[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 [4] | Right Index [7] // Basepair A1859 - G1883 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009071527,0.074411793,0.009690705,0.145893352,0.000000000],[0.013609116,0.007309360,0.141711403,0.010426233,0.000000000],[0.009568793,0.252142141,0.001935840,0.146021452,0.000000000],[0.136309275,0.010994406,0.017166296,0.013738307,0.000000000],[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 [5] | Right Index [6] // Basepair G1860 - C1882 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_87904.5:
> IL_87904.5 IL_3V2F_072 G 1856 C 1886
GGGAG*CGAAC
> IL_87904.5 IL_4IOA_070 U 1848 A 1869
UGGAG*CGAAA
> IL_87904.5 IL_3U5H_075 A 1806 U 1649
AGGAA*UGAAU
> IL_87904.5 IL_2A64_006 C  347 G  382
CGGAG*CGAAG
> IL_87904.5 IL_4BPP_090 U 1649 A 1676
UGGAC*GAAAA
> IL_87904.5 IL_4FAW_002 G  113 C   74
GGACG*CUAAC
> IL_87904.5 IL_2A64_005 C  297 G  288
CGGAG*CGAAG
> IL_87904.5 IL_3DHS_004 C  297 G  288
CGGAG*CGAAG
> IL_87904.5 IL_3IWN_002 G   31 C   16
GGACG*CAAAC
> IL_87904.5 IL_2QBG_068 U 1736 G 1724
UGGAG*UGAGG
> IL_87904.5 IL_4A1B_125 G 3189 C 3221
GAGCG*UUAAC
> IL_87904.5 IL_1S72_083 G 2501 C 2519
GCAAG*CGACC
> IL_87904.5 IL_1S72_028 U  815 G  798
UGGAA*UGAAG
> IL_87904.5 IL_2QBG_024 U  724 G  707
UGGAG*UGAAG
> IL_87904.5 IL_1U6B_002 G   84 C   60
GCAAC*GAAAC
> IL_87904.5 IL_3UCZ_001 G   41 C   26
GGACG*CAAAC
> IL_87904.5 IL_3U5F_091 A 1678 U 1723
AGGAU*AGAAU
> IL_87904.5 IL_3V2F_021 U  724 G  707
UGGAG*UGAAG
> IL_87904.5 IL_4A1B_110 C 2823 G 2841
CCAAG*CGACG
> IL_87904.5 IL_3U5H_032 U  855 G  838
UGGAG*UGAAG
> IL_87904.5 IL_2QBG_094 C 2466 G 2484
CCAAG*CGACG
> IL_87904.5 IL_3V2F_092 C 2466 G 2484
CCGAG*CGGCG
> IL_87904.5 IL_4IOA_089 C 2445 G 2463
CCGAG*CGGCG
> IL_87904.5 IL_2AW7_058 G 1272 C 1263
GCAAG*CGACC
> IL_87904.5 IL_3U5H_112 U 2835 A 2853
UCAAG*CGACA
> IL_87904.5 IL_2QBG_019 G  618 C  610
GGGAG*UUAAC
> IL_87904.5 IL_1S72_021 G  679 C  667
GGGAG*CUAAC
> IL_87904.5 IL_4BPP_028 G  509 C  529
GAACA*UUAGC
> IL_87904.5 IL_3V2F_016 C  618 G  610
CGGAG*UUAAG
> IL_87904.5 IL_2QWY_001 C   16 G   50
CGUAU*AAAAG
> IL_87904.5 IL_4IOA_012 C  629 G  620
CGGAG*UUAAG