Alignment of IL_28947.2 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
3

2
5
3
I

6
4


7
3
I

8
3

3
9
2
I

10
2

4
11
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_28947.2_Instance_1 IL_28947.2_IL_2QBG_060_C1489_G1500CAGCG
IL_28947.2_Sequence_1 IL_28947.2_IL_2QBG_060_C_1489_G_1500CAG*CGtrue100000.00
IL_28947.2_Instance_2 IL_28947.2_IL_2AW7_005_C63_G104CGAAUG
IL_28947.2_Sequence_2 IL_28947.2_IL_2AW7_005_C63_G104CGAA*UGtrue78002.05
IL_28947.2_Instance_3 IL_28947.2_IL_1S72_022_C699_G727CAUGCG
IL_28947.2_Sequence_3 IL_28947.2_IL_1S72_022_C699_G727CAUG*CGtrue82001.69
IL_28947.2_Instance_4 IL_28947.2_IL_1FJG_005_C63_G104CGUGCG
IL_28947.2_Sequence_4 IL_28947.2_IL_1FJG_005_C63_G104CGUG*CGtrue75002.42
IL_28947.2_Instance_5 IL_28947.2_IL_2NZ4_007_C5_G53CAGCG
IL_28947.2_Sequence_5 IL_28947.2_IL_2NZ4_007_C5_G53CAG*CGtrue100000.00
IL_28947.2_Instance_6 IL_28947.2_IL_1S72_099_C64_G16CAGCG
IL_28947.2_Sequence_6 IL_28947.2_IL_1S72_099_C64_G16CAG*CGtrue100000.00
IL_28947.2_Instance_7 IL_28947.2_IL_1S72_042_U1136_G1226UGGCG
IL_28947.2_Sequence_7 IL_28947.2_IL_1S72_042_U_1136_G_1226UGG*CGtrue88001.14
IL_28947.2_Instance_8 IL_28947.2_IL_3U5H_137_U3381_G3325UUGCG
IL_28947.2_Sequence_8 IL_28947.2_IL_3U5H_137_U_3381_G_3325UUG*CGtrue88001.14
IL_28947.2_Instance_9 IL_28947.2_IL_3V2F_059_U1489_G1500UAGCG
IL_28947.2_Sequence_9 IL_28947.2_IL_3V2F_059_U_1489_G_1500UAG*CGtrue96000.41
IL_28947.2_Instance_10 IL_28947.2_IL_4A1B_063_U1424_A1438UUGUA
IL_28947.2_Sequence_10 IL_28947.2_IL_4A1B_063_U_1424_A_1438UUG*UAtrue81001.80
IL_28947.2_Instance_11 IL_28947.2_IL_2QBG_086_U2202_G2221UUGUG
IL_28947.2_Sequence_11 IL_28947.2_IL_2QBG_086_U_2202_G_2221UUG*UGtrue81001.80
IL_28947.2_Instance_12 IL_28947.2_IL_3V2F_069_U1898_G1842UGAAUG
IL_28947.2_Sequence_12 IL_28947.2_IL_3V2F_069_U_1898_G_1842UGAA*UGtrue74002.46
IL_28947.2_Instance_13 IL_28947.2_IL_4IOA_067_U1881_G1834UGAAUG
IL_28947.2_Sequence_13 IL_28947.2_IL_4IOA_067_U_1881_G_1834UGAA*UGtrue74002.46
IL_28947.2_Instance_14 IL_28947.2_IL_1XOK_001_A864_U847AAUGCU
IL_28947.2_Sequence_14 IL_28947.2_IL_1XOK_001_A864_U847AAUG*CUtrue77002.17
IL_28947.2_Instance_15 IL_28947.2_IL_1XOK_002_G877_C869GAUGCC
IL_28947.2_Sequence_15 IL_28947.2_IL_1XOK_002_G877_C869GAUG*CCtrue79002.02
IL_28947.2_Instance_16 IL_28947.2_IL_3U5H_019_C577_G513CAGUG
IL_28947.2_Sequence_16 IL_28947.2_IL_3U5H_019_C577_G513CAG*UGtrue93000.67
IL_28947.2_Instance_17 IL_28947.2_IL_387D_001_G15_C2GGAAUC
IL_28947.2_Sequence_17 IL_28947.2_IL_387D_001_G15_C2GGAA*UCtrue75002.37
IL_28947.2_Instance_18 IL_28947.2_IL_1U9S_008_G217_C196GGCGC
IL_28947.2_Sequence_18 IL_28947.2_IL_1U9S_008_G217_C196GGC*GCtrue84001.54
IL_28947.2_Instance_19 IL_28947.2_IL_4FAW_014_U375_A366UACGUA
IL_28947.2_Sequence_19 IL_28947.2_IL_4FAW_014_U375_A366UACG*UAtrue63003.53
IL_28947.2_Instance_20 IL_28947.2_IL_3U5H_063_C1385_G1421CAGCG
IL_28947.2_Sequence_20 IL_28947.2_IL_3U5H_063_C_1385_G_1421CAG*CGtrue100000.00
IL_28947.2_Instance_21 IL_28947.2_IL_1KXK_003_C42_G29CACGUG
IL_28947.2_Sequence_21 IL_28947.2_IL_1KXK_003_C42_G29CACG*UGtrue67003.12
IL_28947.2_Instance_22 IL_28947.2_IL_4C7O_003_C31_G13CCGCG
IL_28947.2_Sequence_22 IL_28947.2_IL_4C7O_003_C31_G13CCG*CGtrue84001.49

Conserved interactions between motif group positions in IL_28947.2:
1 2 s35 
1 4 cWW 
2 3 cWW 
2 4 s55 
3 4 s35 
JAR3D SCFG/MRF model for IL_28947.2:
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 [4] // Initial node C1489 - G1500 from junction 
BasepairNode | Deletion Probability [0.0000000111126777] | Pair Probability [[0.008987135,0.014737334,0.010442130,0.136123677,0.000000000],[0.084757914,0.008954844,0.219787357,0.011965985,0.000000000],[0.010562580,0.159202085,0.002111911,0.018568547,0.000000000],[0.146497848,0.011399971,0.145832717,0.010067968,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.001233920,0.543953276,0.453671428,0.001089963,0.000051413] | Left Letter Distribution [0.455882353,0.102941176,0.220588235,0.220588235,0.000000000] | 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 [4] // Basepair C1489 - G1500 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009572099,0.072799459,0.010276225,0.169471956,0.000000000],[0.014437509,0.007768090,0.147879255,0.011072350,0.000000000],[0.010146088,0.242115188,0.002044737,0.124309147,0.000000000],[0.133710503,0.011675351,0.018360351,0.014361691,0.000000000],[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 G1491 - C1499 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_28947.2:
> IL_28947.2 IL_2QBG_060 C 1489 G 1500
CAG*CG
> IL_28947.2 IL_2AW7_005 C   63 G  104
CGAA*UG
> IL_28947.2 IL_1S72_022 C  699 G  727
CAUG*CG
> IL_28947.2 IL_1FJG_005 C   63 G  104
CGUG*CG
> IL_28947.2 IL_2NZ4_007 C    5 G   53
CAG*CG
> IL_28947.2 IL_1S72_099 C   64 G   16
CAG*CG
> IL_28947.2 IL_1S72_042 U 1136 G 1226
UGG*CG
> IL_28947.2 IL_3U5H_137 U 3381 G 3325
UUG*CG
> IL_28947.2 IL_3V2F_059 U 1489 G 1500
UAG*CG
> IL_28947.2 IL_4A1B_063 U 1424 A 1438
UUG*UA
> IL_28947.2 IL_2QBG_086 U 2202 G 2221
UUG*UG
> IL_28947.2 IL_3V2F_069 U 1898 G 1842
UGAA*UG
> IL_28947.2 IL_4IOA_067 U 1881 G 1834
UGAA*UG
> IL_28947.2 IL_1XOK_001 A  864 U  847
AAUG*CU
> IL_28947.2 IL_1XOK_002 G  877 C  869
GAUG*CC
> IL_28947.2 IL_3U5H_019 C  577 G  513
CAG*UG
> IL_28947.2 IL_387D_001 G   15 C    2
GGAA*UC
> IL_28947.2 IL_1U9S_008 G  217 C  196
GGC*GC
> IL_28947.2 IL_4FAW_014 U  375 A  366
UACG*UA
> IL_28947.2 IL_3U5H_063 C 1385 G 1421
CAG*CG
> IL_28947.2 IL_1KXK_003 C   42 G   29
CACG*UG
> IL_28947.2 IL_4C7O_003 C   31 G   13
CCG*CG