Alignment of IL_41766.6 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_41766.6
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


11
5
I

12
5

5
13
4
I

14
4

6
15
3
I

16
3

7
17
2
I

18
2

8
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_41766.6_Instance_1 IL_41766.6_IL_1S72_012_G362_C290GACGCAGC
IL_41766.6_Sequence_1 IL_41766.6_IL_1S72_012_G362_C290GACG*CAGCtrue87001.20
IL_41766.6_Instance_2 IL_41766.6_IL_4A1B_103_U2724_A2710UACAUUGA
IL_41766.6_Sequence_2 IL_41766.6_IL_4A1B_103_U_2724_A_2710UACA*UUGAtrue77002.23
IL_41766.6_Instance_3 IL_41766.6_IL_4BPP_089_A1676_U1649AAUAUUCU
IL_41766.6_Sequence_3 IL_41766.6_IL_4BPP_089_A_1676_U_1649AAUA*UUCUtrue87001.26
IL_41766.6_Instance_4 IL_41766.6_IL_2QBG_041_G1038_C1117GAAGCGGC
IL_41766.6_Sequence_4 IL_41766.6_IL_2QBG_041_G_1038_C_1117GAAG*CGGCtrue88001.18
IL_41766.6_Instance_5 IL_41766.6_IL_4BPP_086_U1635_A1690UCUGCCUA
IL_41766.6_Sequence_5 IL_41766.6_IL_4BPP_086_U_1635_A_1690UCUG*CCUAtrue73002.60
IL_41766.6_Instance_6 IL_41766.6_IL_1D4R_001_G22_C7GACCGACC
IL_41766.6_Sequence_6 IL_41766.6_IL_1D4R_001_G22_C7GACC*GACCtrue85001.43
IL_41766.6_Instance_7 IL_41766.6_IL_4EYA_008_C6_G9CUUGCUUG
IL_41766.6_Sequence_7 IL_41766.6_IL_4EYA_008_C6_G9CUUG*CUUGtrue100000.00
IL_41766.6_Instance_8 IL_41766.6_IL_3U5H_106_U2718_A2738UUGAUACA
IL_41766.6_Sequence_8 IL_41766.6_IL_3U5H_106_U_2718_A_2738UUGA*UACAtrue69002.94
IL_41766.6_Instance_9 IL_41766.6_IL_2PN4_004_G102_C65GUCGCUUC
IL_41766.6_Sequence_9 IL_41766.6_IL_2PN4_004_G102_C65GUCG*CUUCtrue93000.69
IL_41766.6_Instance_10 IL_41766.6_IL_1MFQ_004_G138_C159GACCGACC
IL_41766.6_Sequence_10 IL_41766.6_IL_1MFQ_004_G138_C159GACC*GACCtrue85001.43
IL_41766.6_Instance_11 IL_41766.6_IL_1GID_008_G103_C217GAAUUAGCC
IL_41766.6_Sequence_11 IL_41766.6_IL_1GID_008_G103_C217GAAUU*AGCCtrue47005.07
IL_41766.6_Instance_12 IL_41766.6_IL_1GID_001_G103_C217GAAUUAGCC
IL_41766.6_Sequence_12 IL_41766.6_IL_1GID_001_G103_C217GAAUU*AGCCtrue47005.07
IL_41766.6_Instance_13 IL_41766.6_IL_4BPP_043_G935_C848GUUUUGGAC
IL_41766.6_Sequence_13 IL_41766.6_IL_4BPP_043_G935_C848GUUUU*GGACtrue22007.37
IL_41766.6_Instance_14 IL_41766.6_IL_4K27_001_C49_G7CCUGCCUG
IL_41766.6_Sequence_14 IL_41766.6_IL_4K27_001_C49_G7CCUG*CCUGtrue77002.17
IL_41766.6_Instance_15 IL_41766.6_IL_3WBM_002_A10_U17ACCCGACU
IL_41766.6_Sequence_15 IL_41766.6_IL_3WBM_002_A10_U17ACCC*GACUtrue63003.56
IL_41766.6_Instance_16 IL_41766.6_IL_3WBM_003_A10_U17ACCCGACU
IL_41766.6_Sequence_16 IL_41766.6_IL_3WBM_003_A10_U17ACCC*GACUtrue63003.56
IL_41766.6_Instance_17 IL_41766.6_IL_3TZR_003_G102_C65GUCGCUUC
IL_41766.6_Sequence_17 IL_41766.6_IL_3TZR_003_G102_C65GUCG*CUUCtrue93000.69
IL_41766.6_Instance_18 IL_41766.6_IL_3U5F_046_G957_C870GUUUUGGAC
IL_41766.6_Sequence_18 IL_41766.6_IL_3U5F_046_G957_C870GUUUU*GGACtrue22007.37
IL_41766.6_Instance_19 IL_41766.6_IL_4IOA_041_G1196_C1178GUCUAUUC
IL_41766.6_Sequence_19 IL_41766.6_IL_4IOA_041_G_1196_C_1178GUCU*AUUCtrue87001.26
IL_41766.6_Instance_20 IL_41766.6_IL_3U5H_135_C3311_G3303CUUAUUUG
IL_41766.6_Sequence_20 IL_41766.6_IL_3U5H_135_C_3311_G_3303CUUA*UUUGtrue97000.33
IL_41766.6_Instance_21 IL_41766.6_IL_1D4R_003_G22_C7GACCGACC
IL_41766.6_Sequence_21 IL_41766.6_IL_1D4R_003_G22_C7GACC*GACCtrue85001.43
IL_41766.6_Instance_22 IL_41766.6_IL_3U5H_043_A1006_U1044AUUAUUCU
IL_41766.6_Sequence_22 IL_41766.6_IL_3U5H_043_A_1006_U_1044AUUA*UUCUtrue81001.77
IL_41766.6_Instance_23 IL_41766.6_IL_3R2D_002_C6_G9CUUGCUUG
IL_41766.6_Sequence_23 IL_41766.6_IL_3R2D_002_C6_G9CUUG*CUUGtrue100000.00
IL_41766.6_Instance_24 IL_41766.6_IL_280D_001_C5_G20CUUGCUUG
IL_41766.6_Sequence_24 IL_41766.6_IL_280D_001_C5_G20CUUG*CUUGtrue100000.00
IL_41766.6_Instance_25 IL_41766.6_IL_1JID_002_G138_C159GACCGACC
IL_41766.6_Sequence_25 IL_41766.6_IL_1JID_002_G138_C159GACC*GACCtrue85001.43
IL_41766.6_Instance_26 IL_41766.6_IL_1S72_018_C558_G599CUCGCACG
IL_41766.6_Sequence_26 IL_41766.6_IL_1S72_018_C558_G599CUCG*CACGtrue82001.68
IL_41766.6_Instance_27 IL_41766.6_IL_4K27_003_C12_G44CCUGCCUG
IL_41766.6_Sequence_27 IL_41766.6_IL_4K27_003_C12_G44CCUG*CCUGtrue77002.17
IL_41766.6_Instance_28 IL_41766.6_IL_4A1B_127_C3271_G3263CUUAUUUG
IL_41766.6_Sequence_28 IL_41766.6_IL_4A1B_127_C_3271_G_3263CUUA*UUUGtrue97000.33
IL_41766.6_Instance_29 IL_41766.6_IL_3U5H_134_C3249_G3238CUUGCUUG
IL_41766.6_Sequence_29 IL_41766.6_IL_3U5H_134_C_3249_G_3238CUUG*CUUGtrue100000.00
IL_41766.6_Instance_30 IL_41766.6_IL_4EYA_012_C6_G9CUUGCUUG
IL_41766.6_Sequence_30 IL_41766.6_IL_4EYA_012_C6_G9CUUG*CUUGtrue100000.00
IL_41766.6_Instance_31 IL_41766.6_IL_2NOK_004_G102_C65GUCGCUUC
IL_41766.6_Sequence_31 IL_41766.6_IL_2NOK_004_G102_C65GUCG*CUUCtrue93000.69
IL_41766.6_Instance_32 IL_41766.6_IL_4K27_002_C8_G48CCUGCCUG
IL_41766.6_Sequence_32 IL_41766.6_IL_4K27_002_C8_G48CCUG*CCUGtrue77002.17
IL_41766.6_Instance_33 IL_41766.6_IL_4BPP_045_C928_G856CAAAUGGGG
IL_41766.6_Sequence_33 IL_41766.6_IL_4BPP_045_C928_G856CAAA*UGGGGtrue44005.30
IL_41766.6_Instance_34 IL_41766.6_IL_3U5F_047_G871_C956GGUCGGAC
IL_41766.6_Sequence_34 IL_41766.6_IL_3U5F_047_G871_C956GGUC*GGACtrue76002.26
IL_41766.6_Instance_35 IL_41766.6_IL_4BPP_044_A849_U934AGUUAGAU
IL_41766.6_Sequence_35 IL_41766.6_IL_4BPP_044_A849_U934AGUU*AGAUtrue69002.90
IL_41766.6_Instance_36 IL_41766.6_IL_3U5F_090_U1723_A1678UUUGCUCA
IL_41766.6_Sequence_36 IL_41766.6_IL_3U5F_090_U_1723_A_1678UUUG*CUCAtrue84001.53
IL_41766.6_Instance_37 IL_41766.6_IL_4EYA_010_C6_G9CUUGCUUG
IL_41766.6_Sequence_37 IL_41766.6_IL_4EYA_010_C6_G9CUUG*CUUGtrue100000.00
IL_41766.6_Instance_38 IL_41766.6_IL_4BPP_051_G1046_U1022GCACGGAU
IL_41766.6_Sequence_38 IL_41766.6_IL_4BPP_051_G_1046_U_1022GCAC*GGAUtrue61003.70
IL_41766.6_Instance_39 IL_41766.6_IL_3U5F_048_C950_G878CAAGCGGGG
IL_41766.6_Sequence_39 IL_41766.6_IL_3U5F_048_C950_G878CAAG*CGGGGtrue48004.97
IL_41766.6_Instance_40 IL_41766.6_IL_3U5F_008_G109_C305GUUAUUUC
IL_41766.6_Sequence_40 IL_41766.6_IL_3U5F_008_G109_C305GUUA*UUUCtrue97000.25
IL_41766.6_Instance_41 IL_41766.6_IL_3U5F_049_G885_C927GUAUAGAC
IL_41766.6_Sequence_41 IL_41766.6_IL_3U5F_049_G885_C927GUAU*AGACtrue72002.69
IL_41766.6_Instance_42 IL_41766.6_IL_2AW7_036_U662_A743UAGAGUGGA
IL_41766.6_Sequence_42 IL_41766.6_IL_2AW7_036_U662_A743UAGAG*UGGAtrue27006.93
IL_41766.6_Instance_43 IL_41766.6_IL_4BPP_008_G105_C296GUUAUUUC
IL_41766.6_Sequence_43 IL_41766.6_IL_4BPP_008_G105_C296GUUA*UUUCtrue97000.25
IL_41766.6_Instance_44 IL_41766.6_IL_1G1X_003_G662_U743GAGAGUGGU
IL_41766.6_Sequence_44 IL_41766.6_IL_1G1X_003_G662_U743GAGAG*UGGUtrue19007.72
IL_41766.6_Instance_45 IL_41766.6_IL_402D_001_C111_G106CCAGCCAG
IL_41766.6_Sequence_45 IL_41766.6_IL_402D_001_C111_G106CCAG*CCAGtrue69002.91
IL_41766.6_Instance_46 IL_41766.6_IL_3U5F_055_G1074_U1044GCACGGAU
IL_41766.6_Sequence_46 IL_41766.6_IL_3U5F_055_G_1074_U_1044GCAC*GGAUtrue61003.70
IL_41766.6_Instance_47 IL_41766.6_IL_1FJG_029_G662_U743GAGAGUGGU
IL_41766.6_Sequence_47 IL_41766.6_IL_1FJG_029_G662_U743GAGAG*UGGUtrue19007.72
IL_41766.6_Instance_48 IL_41766.6_IL_4A1B_047_A1032_U1070AUUAUUCU
IL_41766.6_Sequence_48 IL_41766.6_IL_4A1B_047_A_1032_U_1070AUUA*UUCUtrue81001.77
IL_41766.6_Instance_49 IL_41766.6_IL_2NOK_007_G102_C65GUCGCUUC
IL_41766.6_Sequence_49 IL_41766.6_IL_2NOK_007_G102_C65GUCG*CUUCtrue93000.69
IL_41766.6_Instance_50 IL_41766.6_IL_3U5F_083_A1753_U1647AAAAGCGCU
IL_41766.6_Sequence_50 IL_41766.6_IL_3U5F_083_A_1753_U_1647AAAAG*CGCUtrue58003.98
IL_41766.6_Instance_51 IL_41766.6_IL_2A64_004_G236_C194GGUAAAUGCC
IL_41766.6_Sequence_51 IL_41766.6_IL_2A64_004_G236_C194GGUAAA*UGCCtrue18007.81
IL_41766.6_Instance_52 IL_41766.6_IL_3U5F_078_C1509_G1498CUUGCUUG
IL_41766.6_Sequence_52 IL_41766.6_IL_3U5F_078_C_1509_G_1498CUUG*CUUGtrue100000.00
IL_41766.6_Instance_53 IL_41766.6_IL_1F7Y_003_G26_U42GAGAGUGGU
IL_41766.6_Sequence_53 IL_41766.6_IL_1F7Y_003_G26_U42GAGAG*UGGUtrue19007.72
IL_41766.6_Instance_54 IL_41766.6_IL_2QBG_055_C1557_G1435CCUGCGAAG
IL_41766.6_Sequence_54 IL_41766.6_IL_2QBG_055_C_1557_G_1435CCUGC*GAAGtrue37006.03

Conserved interactions between motif group positions in IL_41766.6:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 cWW 
2 8 s55 
3 4 s35 
3 6 cWW 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35 
7 8 s35 
JAR3D SCFG/MRF model for IL_41766.6:
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 [8] // Initial node G362 - C290 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.006957785,0.031044682,0.007726000,0.166929207,0.000000000],[0.012665965,0.005940363,0.237074222,0.008622507,0.000000000],[0.007698997,0.257196629,0.001503910,0.069207395,0.000000000],[0.153290803,0.008750611,0.016247783,0.009143139,0.000000000],[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 [8] // Basepair G362 - C290 cWW 
BasepairNode | Deletion Probability [0.0000137278371017] | Pair Probability [[0.034754732,0.130982684,0.116844038,0.026075053,0.000000000],[0.049738314,0.024189615,0.022507864,0.068746157,0.000000000],[0.070256634,0.029528564,0.002488241,0.046827864,0.000000000],[0.045332517,0.078248470,0.020461623,0.233017631,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.925031731,0.074853505,0.000111338,0.000003426] | Left Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000] | Right Length Distribution [0.962028959,0.037890532,0.000078796,0.000001713] | Right Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair A363 - G289 cWW 
BasepairNode | Deletion Probability [0.0000112217093753] | Pair Probability [[0.034499020,0.052942702,0.116617256,0.018280503,0.000000000],[0.114946246,0.008964170,0.016808599,0.095584687,0.000000000],[0.070111370,0.016038497,0.033987346,0.021253993,0.000000000],[0.018036964,0.080552333,0.094262581,0.207113735,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.869523514,0.111812030,0.018641333,0.000022266,0.000000856] | Left Letter Distribution [0.650000000,0.050000000,0.050000000,0.250000000,0.000000000] | 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 [6] // Basepair C364 - A288 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.006917479,0.027832696,0.007686497,0.192071859,0.000000000],[0.019887914,0.006119788,0.188345103,0.008495618,0.000000000],[0.007655131,0.267461875,0.001521626,0.058854920,0.000000000],[0.152192675,0.008637940,0.037076584,0.009242294,0.000000000],[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 G365 - C287 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_41766.6:
> IL_41766.6 IL_1S72_012 G  362 C  290
GACG*CAGC
> IL_41766.6 IL_4A1B_103 U 2724 A 2710
UACA*UUGA
> IL_41766.6 IL_4BPP_089 A 1676 U 1649
AAUA*UUCU
> IL_41766.6 IL_2QBG_041 G 1038 C 1117
GAAG*CGGC
> IL_41766.6 IL_4BPP_086 U 1635 A 1690
UCUG*CCUA
> IL_41766.6 IL_1D4R_001 G   22 C    7
GACC*GACC
> IL_41766.6 IL_4EYA_008 C    6 G    9
CUUG*CUUG
> IL_41766.6 IL_3U5H_106 U 2718 A 2738
UUGA*UACA
> IL_41766.6 IL_2PN4_004 G  102 C   65
GUCG*CUUC
> IL_41766.6 IL_1MFQ_004 G  138 C  159
GACC*GACC
> IL_41766.6 IL_1GID_008 G  103 C  217
GAAUU*AGCC
> IL_41766.6 IL_1GID_001 G  103 C  217
GAAUU*AGCC
> IL_41766.6 IL_4BPP_043 G  935 C  848
GUUUU*GGAC
> IL_41766.6 IL_4K27_001 C   49 G    7
CCUG*CCUG
> IL_41766.6 IL_3WBM_002 A   10 U   17
ACCC*GACU
> IL_41766.6 IL_3WBM_003 A   10 U   17
ACCC*GACU
> IL_41766.6 IL_3TZR_003 G  102 C   65
GUCG*CUUC
> IL_41766.6 IL_3U5F_046 G  957 C  870
GUUUU*GGAC
> IL_41766.6 IL_4IOA_041 G 1196 C 1178
GUCU*AUUC
> IL_41766.6 IL_3U5H_135 C 3311 G 3303
CUUA*UUUG
> IL_41766.6 IL_1D4R_003 G   22 C    7
GACC*GACC
> IL_41766.6 IL_3U5H_043 A 1006 U 1044
AUUA*UUCU
> IL_41766.6 IL_3R2D_002 C    6 G    9
CUUG*CUUG
> IL_41766.6 IL_280D_001 C    5 G   20
CUUG*CUUG
> IL_41766.6 IL_1JID_002 G  138 C  159
GACC*GACC
> IL_41766.6 IL_1S72_018 C  558 G  599
CUCG*CACG
> IL_41766.6 IL_4K27_003 C   12 G   44
CCUG*CCUG
> IL_41766.6 IL_4A1B_127 C 3271 G 3263
CUUA*UUUG
> IL_41766.6 IL_3U5H_134 C 3249 G 3238
CUUG*CUUG
> IL_41766.6 IL_4EYA_012 C    6 G    9
CUUG*CUUG
> IL_41766.6 IL_2NOK_004 G  102 C   65
GUCG*CUUC
> IL_41766.6 IL_4K27_002 C    8 G   48
CCUG*CCUG
> IL_41766.6 IL_4BPP_045 C  928 G  856
CAAA*UGGGG
> IL_41766.6 IL_3U5F_047 G  871 C  956
GGUC*GGAC
> IL_41766.6 IL_4BPP_044 A  849 U  934
AGUU*AGAU
> IL_41766.6 IL_3U5F_090 U 1723 A 1678
UUUG*CUCA
> IL_41766.6 IL_4EYA_010 C    6 G    9
CUUG*CUUG
> IL_41766.6 IL_4BPP_051 G 1046 U 1022
GCAC*GGAU
> IL_41766.6 IL_3U5F_048 C  950 G  878
CAAG*CGGGG
> IL_41766.6 IL_3U5F_008 G  109 C  305
GUUA*UUUC
> IL_41766.6 IL_3U5F_049 G  885 C  927
GUAU*AGAC
> IL_41766.6 IL_2AW7_036 U  662 A  743
UAGAG*UGGA
> IL_41766.6 IL_4BPP_008 G  105 C  296
GUUA*UUUC
> IL_41766.6 IL_1G1X_003 G  662 U  743
GAGAG*UGGU
> IL_41766.6 IL_402D_001 C  111 G  106
CCAG*CCAG
> IL_41766.6 IL_3U5F_055 G 1074 U 1044
GCAC*GGAU
> IL_41766.6 IL_1FJG_029 G  662 U  743
GAGAG*UGGU
> IL_41766.6 IL_4A1B_047 A 1032 U 1070
AUUA*UUCU
> IL_41766.6 IL_2NOK_007 G  102 C   65
GUCG*CUUC
> IL_41766.6 IL_3U5F_083 A 1753 U 1647
AAAAG*CGCU
> IL_41766.6 IL_2A64_004 G  236 C  194
GGUAAA*UGCC
> IL_41766.6 IL_3U5F_078 C 1509 G 1498
CUUG*CUUG
> IL_41766.6 IL_1F7Y_003 G   26 U   42
GAGAG*UGGU
> IL_41766.6 IL_2QBG_055 C 1557 G 1435
CCUGC*GAAG