Alignment of IL_73276.5 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


13
3
I

14
2

6
15
2
I

16
2

7
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_73276.5_Instance_1 IL_73276.5_IL_3V2F_100_C2680_G2727CCUCUAUG
IL_73276.5_Sequence_1 IL_73276.5_IL_3V2F_100_C_2680_G_2727CCUCU*AUGtrue75002.37
IL_73276.5_Instance_2 IL_73276.5_IL_4IOA_097_C2659_G2707CCGCUAUG
IL_73276.5_Sequence_2 IL_73276.5_IL_4IOA_097_C_2659_G_2707CCGCU*AUGtrue67003.22
IL_73276.5_Instance_3 IL_73276.5_IL_4JRC_003_C29_G75CCUCUACG
IL_73276.5_Sequence_3 IL_73276.5_IL_4JRC_003_C29_G75CCUCU*ACGtrue82001.76
IL_73276.5_Instance_4 IL_73276.5_IL_2QBG_102_U2680_A2727UCACUAAA
IL_73276.5_Sequence_4 IL_73276.5_IL_2QBG_102_U_2680_A_2727UCACU*AAAtrue100000.00
IL_73276.5_Instance_5 IL_73276.5_IL_1KOG_002_C96_G76CCACUAUG
IL_73276.5_Sequence_5 IL_73276.5_IL_1KOG_002_C96_G76CCACU*AUGtrue91000.82
IL_73276.5_Instance_6 IL_73276.5_IL_3U5F_060_U1617_A1160UCCCUACCA
IL_73276.5_Sequence_6 IL_73276.5_IL_3U5F_060_U_1617_A_1160UCCCU*ACCAtrue53004.53
IL_73276.5_Instance_7 IL_73276.5_IL_1S72_091_C2717_G2763CCACUACG
IL_73276.5_Sequence_7 IL_73276.5_IL_1S72_091_C_2717_G_2763CCACU*ACGtrue98000.20
IL_73276.5_Instance_8 IL_73276.5_IL_4BPP_057_U1589_A1132UCCCUACA
IL_73276.5_Sequence_8 IL_73276.5_IL_4BPP_057_U_1589_A_1132UCCCU*ACAtrue74002.46
IL_73276.5_Instance_9 IL_73276.5_IL_3V2F_048_G1319_C1333GCAAUAGC
IL_73276.5_Sequence_9 IL_73276.5_IL_3V2F_048_G_1319_C_1333GCAAU*AGCtrue87001.24
IL_73276.5_Instance_10 IL_73276.5_IL_1S72_051_G1425_C1439GCACUAGC
IL_73276.5_Sequence_10 IL_73276.5_IL_1S72_051_G_1425_C_1439GCACU*AGCtrue93000.65
IL_73276.5_Instance_11 IL_73276.5_IL_2QBG_033_G864_C912GCACUAAAC
IL_73276.5_Sequence_11 IL_73276.5_IL_2QBG_033_G864_C912GCACU*AAACtrue87001.22
IL_73276.5_Instance_12 IL_73276.5_IL_2QBG_050_C1319_G1333CCAACGGG
IL_73276.5_Sequence_12 IL_73276.5_IL_2QBG_050_C_1319_G_1333CCAAC*GGGtrue70002.89
IL_73276.5_Instance_13 IL_73276.5_IL_4MGN_003_C29_G75CCUCUACG
IL_73276.5_Sequence_13 IL_73276.5_IL_4MGN_003_C29_G75CCUCU*ACGtrue82001.76
IL_73276.5_Instance_14 IL_73276.5_IL_4IOA_028_G877_C924GCACUAAAC
IL_73276.5_Sequence_14 IL_73276.5_IL_4IOA_028_G877_C924GCACU*AAACtrue87001.22
IL_73276.5_Instance_15 IL_73276.5_IL_3V2F_029_G864_C912GCACUAAAC
IL_73276.5_Sequence_15 IL_73276.5_IL_3V2F_029_G864_C912GCACU*AAACtrue87001.22
IL_73276.5_Instance_16 IL_73276.5_IL_4IOA_049_G1332_C1346GGAAGCGC
IL_73276.5_Sequence_16 IL_73276.5_IL_4IOA_049_G_1332_C_1346GGAAG*CGCtrue35006.29
IL_73276.5_Instance_17 IL_73276.5_IL_1FJG_015_G371_C390GCAAUAC
IL_73276.5_Sequence_17 IL_73276.5_IL_1FJG_015_G371_C390GCAAU*ACtrue94000.58
IL_73276.5_Instance_18 IL_73276.5_IL_3U5H_042_G999_C1049GCGAAUAAAC
IL_73276.5_Sequence_18 IL_73276.5_IL_3U5H_042_G999_C_1049GCGAAU*AAACtrue53004.56
IL_73276.5_Instance_19 IL_73276.5_IL_4A1B_046_G1025_C1075GCGAAUAAAC
IL_73276.5_Sequence_19 IL_73276.5_IL_4A1B_046_G_1025_C_1075GCGAAU*AAACtrue53004.56
IL_73276.5_Instance_20 IL_73276.5_IL_2AW7_018_A371_U390ACAAUAU
IL_73276.5_Sequence_20 IL_73276.5_IL_2AW7_018_A371_U390ACAAU*AUtrue86001.31
IL_73276.5_Instance_21 IL_73276.5_IL_4A1C_005_U52_A27UUAAGCA
IL_73276.5_Sequence_21 IL_73276.5_IL_4A1C_005_U52_A27UUAAG*CAtrue27007.00
IL_73276.5_Instance_22 IL_73276.5_IL_1FJG_047_C1128_G1143CCAGCGG
IL_73276.5_Sequence_22 IL_73276.5_IL_1FJG_047_C_1128_G_1143CCAGC*GGtrue50004.78

Conserved interactions between motif group positions in IL_73276.5:
1 2 s35 
1 7 cWW 
2 4 cSH 
2 6 tWH 
2 7 s55 
3 4 s35 
4 5 s35 
4 7 cWS 
5 6 cWW 
6 7 s35 
JAR3D SCFG/MRF model for IL_73276.5:
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 [7] // Initial node C2680 - G2727 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000146283685379421310000000000000000000000000] | Num Left Bases [5] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.008888954407175] // Cluster node C2680:U2684 and A2725:G2727
Interaction  | Interacting Bases [2,6] | Pair Probability [[0.016212895,0.002088714,0.111481584,0.002088714,0.000000000],[0.355482037,0.009855145,0.215225219,0.002088714,0.000000000],[0.002088714,0.014532442,0.014015048,0.021263925,0.000000000],[0.020326329,0.014532442,0.009960906,0.188757171,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2681 - A2725 tWH 
Interaction  | Interacting Bases [5,6] | Pair Probability [[0.007773162,0.016660361,0.008500029,0.171131704,0.000000000],[0.019645867,0.007811276,0.181182794,0.009165013,0.000000000],[0.008511496,0.180416929,0.001800083,0.020080857,0.000000000],[0.324199513,0.009115154,0.022960409,0.011045352,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2684 - A2725 cWW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.008273910,0.016324110,0.009447193,0.172538687,0.000000000],[0.016686769,0.007282678,0.238983699,0.010738157,0.000000000],[0.009443468,0.247301898,0.001797856,0.021312961,0.000000000],[0.198008406,0.010754857,0.021649574,0.009455779,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2680 - G2727 cWW 
Interaction  | Interacting Bases [4,7] | Pair Probability [[0.069820510,0.113337012,0.066293327,0.077837807,0.000000000],[0.136330573,0.145599904,0.162841133,0.111769004,0.000000000],[0.010416831,0.009184966,0.054902910,0.007662833,0.000000000],[0.009188309,0.009573906,0.007480149,0.007760825,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2683 - G2727 cWS 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.088151994,0.087434743,0.005896706,0.004967894,0.000000000],[0.146654711,0.205693479,0.013917998,0.094278770,0.000000000],[0.041390756,0.005358183,0.009542222,0.094186828,0.000000000],[0.021244251,0.084343406,0.001266537,0.095671523,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C2681 - C2683 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.104166667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.145833333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U2682
Insertion    | Location [2] | Length Distribution [0.906945833,0.092734748,0.000309116,0.000010304] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [6] | Length Distribution [0.182283898,0.544177099,0.272829207,0.000678936,0.000030861] | Letter Distribution [0.442307692,0.250000000,0.173076923,0.134615385,0.000000000]// Insertion after nucleotide 6, position 6 in cluster node
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 [6] | Right Index [5] // New Initial node after Cluster
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_73276.5:
> IL_73276.5 IL_3V2F_100 C 2680 G 2727
CCUCU*AUG
> IL_73276.5 IL_4IOA_097 C 2659 G 2707
CCGCU*AUG
> IL_73276.5 IL_4JRC_003 C   29 G   75
CCUCU*ACG
> IL_73276.5 IL_2QBG_102 U 2680 A 2727
UCACU*AAA
> IL_73276.5 IL_1KOG_002 C   96 G   76
CCACU*AUG
> IL_73276.5 IL_3U5F_060 U 1617 A 1160
UCCCU*ACCA
> IL_73276.5 IL_1S72_091 C 2717 G 2763
CCACU*ACG
> IL_73276.5 IL_4BPP_057 U 1589 A 1132
UCCCU*ACA
> IL_73276.5 IL_3V2F_048 G 1319 C 1333
GCAAU*AGC
> IL_73276.5 IL_1S72_051 G 1425 C 1439
GCACU*AGC
> IL_73276.5 IL_2QBG_033 G  864 C  912
GCACU*AAAC
> IL_73276.5 IL_2QBG_050 C 1319 G 1333
CCAAC*GGG
> IL_73276.5 IL_4MGN_003 C   29 G   75
CCUCU*ACG
> IL_73276.5 IL_4IOA_028 G  877 C  924
GCACU*AAAC
> IL_73276.5 IL_3V2F_029 G  864 C  912
GCACU*AAAC
> IL_73276.5 IL_4IOA_049 G 1332 C 1346
GGAAG*CGC
> IL_73276.5 IL_1FJG_015 G  371 C  390
GCAAU*AC
> IL_73276.5 IL_3U5H_042 G  999 C 1049
GCGAAU*AAAC
> IL_73276.5 IL_4A1B_046 G 1025 C 1075
GCGAAU*AAAC
> IL_73276.5 IL_2AW7_018 A  371 U  390
ACAAU*AU
> IL_73276.5 IL_4A1C_005 U   52 A   27
UUAAG*CA
> IL_73276.5 IL_1FJG_047 C 1128 G 1143
CCAGC*GG