Alignment of IL_39199.4 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_39199.4
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
3
I

4
4

2
5
4
I

6
5


7
4
I

8
4

3
9
3
I

10
2

4
11
2
I

12
2

5
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_39199.4_Instance_1 IL_39199.4_IL_4IOA_086_G2433_C2477GGCAC
IL_39199.4_Sequence_1 IL_39199.4_IL_4IOA_086_G_2433_C_2477GG*CACtrue96000.34
IL_39199.4_Instance_2 IL_39199.4_IL_3V2F_089_G2454_C2498GGCAC
IL_39199.4_Sequence_2 IL_39199.4_IL_3V2F_089_G_2454_C_2498GG*CACtrue96000.34
IL_39199.4_Instance_3 IL_39199.4_IL_1S72_080_G2489_C2533GAUAC
IL_39199.4_Sequence_3 IL_39199.4_IL_1S72_080_G_2489_C_2533GA*UACtrue93000.67
IL_39199.4_Instance_4 IL_39199.4_IL_2QBG_091_G2454_C2498GGCAC
IL_39199.4_Sequence_4 IL_39199.4_IL_2QBG_091_G_2454_C_2498GG*CACtrue96000.34
IL_39199.4_Instance_5 IL_39199.4_IL_1S03_008_U16_A36UGCAA
IL_39199.4_Sequence_5 IL_39199.4_IL_1S03_008_U16_A36UG*CAAtrue100000.04
IL_39199.4_Instance_6 IL_39199.4_IL_3D0U_004_G51_C38GGCAUC
IL_39199.4_Sequence_6 IL_39199.4_IL_3D0U_004_G51_C38GG*CAUCtrue69002.91
IL_39199.4_Instance_7 IL_39199.4_IL_3OWZ_007_G35_C70GGCUC
IL_39199.4_Sequence_7 IL_39199.4_IL_3OWZ_007_G35_C70GG*CUCtrue88001.09
IL_39199.4_Instance_8 IL_39199.4_IL_3OWZ_003_G35_C70GGCUC
IL_39199.4_Sequence_8 IL_39199.4_IL_3OWZ_003_G35_C70GG*CUCtrue88001.09
IL_39199.4_Instance_9 IL_39199.4_IL_4IOA_084_G2393_C2382GGUAC
IL_39199.4_Sequence_9 IL_39199.4_IL_4IOA_084_G_2393_C_2382GG*UACtrue97000.30
IL_39199.4_Instance_10 IL_39199.4_IL_3NKB_002_U47_A57UCGUA
IL_39199.4_Sequence_10 IL_39199.4_IL_3NKB_002_U47_A57UC*GUAtrue74002.49
IL_39199.4_Instance_11 IL_39199.4_IL_1XJR_002_G13_C39GGUAC
IL_39199.4_Sequence_11 IL_39199.4_IL_1XJR_002_G13_C39GG*UACtrue97000.30
IL_39199.4_Instance_12 IL_39199.4_IL_2QBG_078_U2617_A2052UGCAA
IL_39199.4_Sequence_12 IL_39199.4_IL_2QBG_078_U_2617_A_2052UG*CAAtrue100000.04
IL_39199.4_Instance_13 IL_39199.4_IL_1G1X_002_G657_C749GGCCC
IL_39199.4_Sequence_13 IL_39199.4_IL_1G1X_002_G657_C749GG*CCCtrue82001.69
IL_39199.4_Instance_14 IL_39199.4_IL_1FJG_024_G644_C596GCGGC
IL_39199.4_Sequence_14 IL_39199.4_IL_1FJG_024_G644_C596GC*GGCtrue95000.43
IL_39199.4_Instance_15 IL_39199.4_IL_3V2F_009_G272D_C364GGUAC
IL_39199.4_Sequence_15 IL_39199.4_IL_3V2F_009_G_272D_C364GG*UACtrue97000.30
IL_39199.4_Instance_16 IL_39199.4_IL_2AW7_031_U644_A596UGUAA
IL_39199.4_Sequence_16 IL_39199.4_IL_2AW7_031_U644_A596UG*UAAtrue100000.00
IL_39199.4_Instance_17 IL_39199.4_IL_4BPP_077_U1469_A1481UCGUA
IL_39199.4_Sequence_17 IL_39199.4_IL_4BPP_077_U_1469_A_1481UC*GUAtrue74002.49
IL_39199.4_Instance_18 IL_39199.4_IL_3V2F_087_G2414_C2403GGUCC
IL_39199.4_Sequence_18 IL_39199.4_IL_3V2F_087_G_2414_C_2403GG*UCCtrue83001.66
IL_39199.4_Instance_19 IL_39199.4_IL_1FJG_028_G657_C749GGCCC
IL_39199.4_Sequence_19 IL_39199.4_IL_1FJG_028_G657_C749GG*CCCtrue82001.69
IL_39199.4_Instance_20 IL_39199.4_IL_3DIR_004_G54_C41GGCAUC
IL_39199.4_Sequence_20 IL_39199.4_IL_3DIR_004_G54_C41GG*CAUCtrue69002.91
IL_39199.4_Instance_21 IL_39199.4_IL_3V2F_075_C2617_G2052CGCAG
IL_39199.4_Sequence_21 IL_39199.4_IL_3V2F_075_C_2617_G_2052CG*CAGtrue82001.75
IL_39199.4_Instance_22 IL_39199.4_IL_1I6U_003_U28_A11UGUAA
IL_39199.4_Sequence_22 IL_39199.4_IL_1I6U_003_U28_A11UG*UAAtrue100000.00
IL_39199.4_Instance_23 IL_39199.4_IL_4IOA_073_C2596_G2035CGCAG
IL_39199.4_Sequence_23 IL_39199.4_IL_4IOA_073_C_2596_G_2035CG*CAGtrue82001.75
IL_39199.4_Instance_24 IL_39199.4_IL_4A1B_106_G2811_C2855GGUCC
IL_39199.4_Sequence_24 IL_39199.4_IL_4A1B_106_G_2811_C_2855GG*UCCtrue83001.66
IL_39199.4_Instance_25 IL_39199.4_IL_4IOA_087_U2472_A2438UGUGA
IL_39199.4_Sequence_25 IL_39199.4_IL_4IOA_087_U_2472_A_2438UG*UGAtrue95000.50
IL_39199.4_Instance_26 IL_39199.4_IL_3V2F_090_U2493_A2459UGUGA
IL_39199.4_Sequence_26 IL_39199.4_IL_3V2F_090_U_2493_A_2459UG*UGAtrue95000.50
IL_39199.4_Instance_27 IL_39199.4_IL_3U5H_108_G2823_C2867GGUUC
IL_39199.4_Sequence_27 IL_39199.4_IL_3U5H_108_G_2823_C_2867GG*UUCtrue89001.06
IL_39199.4_Instance_28 IL_39199.4_IL_2QBG_025_G757_C740GCGAC
IL_39199.4_Sequence_28 IL_39199.4_IL_2QBG_025_G757_C740GC*GACtrue96000.41
IL_39199.4_Instance_29 IL_39199.4_IL_2QBG_044_U1101_A1090UCGAAA
IL_39199.4_Sequence_29 IL_39199.4_IL_2QBG_044_U_1101_A_1090UC*GAAAtrue83001.59
IL_39199.4_Instance_30 IL_39199.4_IL_1QA6_002_U151_A140UCGAAA
IL_39199.4_Sequence_30 IL_39199.4_IL_1QA6_002_U151_A140UC*GAAAtrue83001.59
IL_39199.4_Instance_31 IL_39199.4_IL_3P49_010_G113_C142GGCUC
IL_39199.4_Sequence_31 IL_39199.4_IL_3P49_010_G113_C142GG*CUCtrue88001.09
IL_39199.4_Instance_32 IL_39199.4_IL_1FJG_027_G654_C754GAUGAC
IL_39199.4_Sequence_32 IL_39199.4_IL_1FJG_027_G654_C754GA*UGACtrue77002.17
IL_39199.4_Instance_33 IL_39199.4_IL_4A1B_021_U473_A505UGUAA
IL_39199.4_Sequence_33 IL_39199.4_IL_4A1B_021_U473_A505UG*UAAtrue100000.00
IL_39199.4_Instance_34 IL_39199.4_IL_2AW7_034_G654_C754GAUGAC
IL_39199.4_Sequence_34 IL_39199.4_IL_2AW7_034_G654_C754GA*UGACtrue77002.17
IL_39199.4_Instance_35 IL_39199.4_IL_1G1X_001_G654_C754GAUGAC
IL_39199.4_Sequence_35 IL_39199.4_IL_1G1X_001_G654_C754GA*UGACtrue77002.17
IL_39199.4_Instance_36 IL_39199.4_IL_1F7Y_001_G18_C53GAUGAC
IL_39199.4_Sequence_36 IL_39199.4_IL_1F7Y_001_G18_C53GA*UGACtrue77002.17
IL_39199.4_Instance_37 IL_39199.4_IL_1S72_061_U2034_A1747UCGGAA
IL_39199.4_Sequence_37 IL_39199.4_IL_1S72_061_U_2034_A_1747UC*GGAAtrue78002.09
IL_39199.4_Instance_38 IL_39199.4_IL_3P49_007_G38_C51GAUUC
IL_39199.4_Sequence_38 IL_39199.4_IL_3P49_007_G38_C51GA*UUCtrue85001.43
IL_39199.4_Instance_39 IL_39199.4_IL_3U5H_084_U2336_A1901UCGGAA
IL_39199.4_Sequence_39 IL_39199.4_IL_3U5H_084_U_2336_A_1901UC*GGAAtrue78002.09
IL_39199.4_Instance_40 IL_39199.4_IL_3V2F_063_U1993_A1669UCGGAA
IL_39199.4_Sequence_40 IL_39199.4_IL_3V2F_063_U_1993_A_1669UC*GGAAtrue78002.09
IL_39199.4_Instance_41 IL_39199.4_IL_2QBG_064_U1993_A1669UCGGAA
IL_39199.4_Sequence_41 IL_39199.4_IL_2QBG_064_U_1993_A_1669UC*GGAAtrue78002.09
IL_39199.4_Instance_42 IL_39199.4_IL_3Q1Q_001_G328_C53GCGUC
IL_39199.4_Sequence_42 IL_39199.4_IL_3Q1Q_001_G328_C53GC*GUCtrue88001.17
IL_39199.4_Instance_43 IL_39199.4_IL_4A1B_080_U2331_A1925UCGGAA
IL_39199.4_Sequence_43 IL_39199.4_IL_4A1B_080_U_2331_A_1925UC*GGAAtrue78002.09
IL_39199.4_Instance_44 IL_39199.4_IL_2QBG_049_A1603_U1313ACGGUU
IL_39199.4_Sequence_44 IL_39199.4_IL_2QBG_049_A_1603_U_1313AC*GGUUtrue49004.83
IL_39199.4_Instance_45 IL_39199.4_IL_4A1B_108_U2850_G2816UGUUG
IL_39199.4_Sequence_45 IL_39199.4_IL_4A1B_108_U_2850_G_2816UG*UUGtrue32006.43
IL_39199.4_Instance_46 IL_39199.4_IL_3SUX_002_G37_U49GAUGU
IL_39199.4_Sequence_46 IL_39199.4_IL_3SUX_002_G37_U49GA*UGUtrue67003.13
IL_39199.4_Instance_47 IL_39199.4_IL_2QBG_001_C17_G67CGUAG
IL_39199.4_Sequence_47 IL_39199.4_IL_2QBG_001_C17_G67CG*UAGtrue82001.71
IL_39199.4_Instance_48 IL_39199.4_IL_4A1B_087_U2195_A2239UGUAAA
IL_39199.4_Sequence_48 IL_39199.4_IL_4A1B_087_U_2195_A_2239UG*UAAAtrue84001.48
IL_39199.4_Instance_49 IL_39199.4_IL_3V2F_097_C2591_G2603CGCAG
IL_39199.4_Sequence_49 IL_39199.4_IL_3V2F_097_C_2591_G_2603CG*CAGtrue82001.75
IL_39199.4_Instance_50 IL_39199.4_IL_4IOA_090_C2486_G2561CGUGG
IL_39199.4_Sequence_50 IL_39199.4_IL_4IOA_090_C_2486_G_2561CG*UGGtrue70002.85
IL_39199.4_Instance_51 IL_39199.4_IL_2QBG_092_U2493_A2459UGUGA
IL_39199.4_Sequence_51 IL_39199.4_IL_2QBG_092_U_2493_A_2459UG*UGAtrue95000.50
IL_39199.4_Instance_52 IL_39199.4_IL_4A1B_111_C2864_G2939CGUGG
IL_39199.4_Sequence_52 IL_39199.4_IL_4A1B_111_C_2864_G_2939CG*UGGtrue70002.85
IL_39199.4_Instance_53 IL_39199.4_IL_2QBG_095_C2507_G2582CGUGG
IL_39199.4_Sequence_53 IL_39199.4_IL_2QBG_095_C_2507_G_2582CG*UGGtrue70002.85

Conserved interactions between motif group positions in IL_39199.4:
1 2 s35 
1 4 tHS 
1 5 cWW 
2 3 cWW 
2 5 s55 
3 4 s35 
3 5 s35 
4 5 cSH 
JAR3D SCFG/MRF model for IL_39199.4:
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 G2433 - C2477 from junction 
ClusterNode  | Deletion Probability [0.0000000339040770] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [5] | Norm Constant [0.022570743379188] // Cluster node G2433:G2433 and A2476:C2477
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.023174854,0.020802096,0.063364650,0.037691947,0.000000000],[0.091213019,0.018093295,0.029881461,0.019334421,0.000000000],[0.095268990,0.039222537,0.167381916,0.057904688,0.000000000],[0.183689544,0.001858235,0.121236887,0.029881461,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2433 - A2476 tHS 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.006640898,0.017001667,0.007476669,0.135004367,0.000000000],[0.017207632,0.006020718,0.177571505,0.008289648,0.000000000],[0.007446706,0.296464579,0.001467737,0.027543671,0.000000000],[0.247592329,0.008422878,0.027675888,0.008173106,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2433 - C2477 cWW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.106562097,0.127283530,0.054124748,0.013905486,0.000000000],[0.053122930,0.079513339,0.001438079,0.053688995,0.000000000],[0.098173903,0.071086581,0.053071691,0.066815342,0.000000000],[0.061147678,0.098077305,0.009490488,0.052497807,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A2476 - C2477 cSH 
Insertion    | Location [2] | Length Distribution [0.754026986,0.245694786,0.000266673,0.000011556] | Letter Distribution [0.700000000,0.033333333,0.033333333,0.233333333,0.000000000]// Insertion after nucleotide 4, position 2 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 [0.961313284,0.038604031,0.000080907,0.000001778] | Right Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Left Index [2] | Right Index [3] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008114349,0.079137857,0.008522903,0.142745883,0.000000000],[0.011688303,0.006421270,0.185018901,0.009178599,0.000000000],[0.008439672,0.199732170,0.001728229,0.207381295,0.000000000],[0.094728355,0.009578507,0.014506460,0.013077248,0.000000000],[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 [2] | Right Index [3] // Basepair G2434 - C2475 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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_39199.4:
> IL_39199.4 IL_4IOA_086 G 2433 C 2477
GG*CAC
> IL_39199.4 IL_3V2F_089 G 2454 C 2498
GG*CAC
> IL_39199.4 IL_1S72_080 G 2489 C 2533
GA*UAC
> IL_39199.4 IL_2QBG_091 G 2454 C 2498
GG*CAC
> IL_39199.4 IL_1S03_008 U   16 A   36
UG*CAA
> IL_39199.4 IL_3D0U_004 G   51 C   38
GG*CAUC
> IL_39199.4 IL_3OWZ_007 G   35 C   70
GG*CUC
> IL_39199.4 IL_3OWZ_003 G   35 C   70
GG*CUC
> IL_39199.4 IL_4IOA_084 G 2393 C 2382
GG*UAC
> IL_39199.4 IL_3NKB_002 U   47 A   57
UC*GUA
> IL_39199.4 IL_1XJR_002 G   13 C   39
GG*UAC
> IL_39199.4 IL_2QBG_078 U 2617 A 2052
UG*CAA
> IL_39199.4 IL_1G1X_002 G  657 C  749
GG*CCC
> IL_39199.4 IL_1FJG_024 G  644 C  596
GC*GGC
> IL_39199.4 IL_3V2F_009 G 272D C  364
GG*UAC
> IL_39199.4 IL_2AW7_031 U  644 A  596
UG*UAA
> IL_39199.4 IL_4BPP_077 U 1469 A 1481
UC*GUA
> IL_39199.4 IL_3V2F_087 G 2414 C 2403
GG*UCC
> IL_39199.4 IL_1FJG_028 G  657 C  749
GG*CCC
> IL_39199.4 IL_3DIR_004 G   54 C   41
GG*CAUC
> IL_39199.4 IL_3V2F_075 C 2617 G 2052
CG*CAG
> IL_39199.4 IL_1I6U_003 U   28 A   11
UG*UAA
> IL_39199.4 IL_4IOA_073 C 2596 G 2035
CG*CAG
> IL_39199.4 IL_4A1B_106 G 2811 C 2855
GG*UCC
> IL_39199.4 IL_4IOA_087 U 2472 A 2438
UG*UGA
> IL_39199.4 IL_3V2F_090 U 2493 A 2459
UG*UGA
> IL_39199.4 IL_3U5H_108 G 2823 C 2867
GG*UUC
> IL_39199.4 IL_2QBG_025 G  757 C  740
GC*GAC
> IL_39199.4 IL_2QBG_044 U 1101 A 1090
UC*GAAA
> IL_39199.4 IL_1QA6_002 U  151 A  140
UC*GAAA
> IL_39199.4 IL_3P49_010 G  113 C  142
GG*CUC
> IL_39199.4 IL_1FJG_027 G  654 C  754
GA*UGAC
> IL_39199.4 IL_4A1B_021 U  473 A  505
UG*UAA
> IL_39199.4 IL_2AW7_034 G  654 C  754
GA*UGAC
> IL_39199.4 IL_1G1X_001 G  654 C  754
GA*UGAC
> IL_39199.4 IL_1F7Y_001 G   18 C   53
GA*UGAC
> IL_39199.4 IL_1S72_061 U 2034 A 1747
UC*GGAA
> IL_39199.4 IL_3P49_007 G   38 C   51
GA*UUC
> IL_39199.4 IL_3U5H_084 U 2336 A 1901
UC*GGAA
> IL_39199.4 IL_3V2F_063 U 1993 A 1669
UC*GGAA
> IL_39199.4 IL_2QBG_064 U 1993 A 1669
UC*GGAA
> IL_39199.4 IL_3Q1Q_001 G  328 C   53
GC*GUC
> IL_39199.4 IL_4A1B_080 U 2331 A 1925
UC*GGAA
> IL_39199.4 IL_2QBG_049 A 1603 U 1313
AC*GGUU
> IL_39199.4 IL_4A1B_108 U 2850 G 2816
UG*UUG
> IL_39199.4 IL_3SUX_002 G   37 U   49
GA*UGU
> IL_39199.4 IL_2QBG_001 C   17 G   67
CG*UAG
> IL_39199.4 IL_4A1B_087 U 2195 A 2239
UG*UAAA
> IL_39199.4 IL_3V2F_097 C 2591 G 2603
CG*CAG
> IL_39199.4 IL_4IOA_090 C 2486 G 2561
CG*UGG
> IL_39199.4 IL_2QBG_092 U 2493 A 2459
UG*UGA
> IL_39199.4 IL_4A1B_111 C 2864 G 2939
CG*UGG
> IL_39199.4 IL_2QBG_095 C 2507 G 2582
CG*UGG