Alignment of IL_42997.3 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

3
7
4
I

8
5


9
4
I

10
4

4
11
3
I

12
3

5
13
2
I

14
2

6
15
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_42997.3_Instance_1 IL_42997.3,IL_7VFT_002,C8_G16CAGCAG
IL_42997.3_Sequence_1 IL_42997.37VFT_C8_G16CAG*CAGtrue93000.66
IL_42997.3_Instance_2 IL_42997.3,IL_4V9F_077,G2237_C2138GACGAC
IL_42997.3_Sequence_2 IL_42997.34V9F_G_2237_C_2138GAC*GACtrue86001.30
IL_42997.3_Instance_3 IL_42997.3,IL_8CRE_412,A418_U411AAGCAU
IL_42997.3_Sequence_3 IL_42997.38CRE_A418_U411AAG*CAUtrue89001.08
IL_42997.3_Instance_4 IL_42997.3,IL_3NJ7_004,C3_G8CAGCAG
IL_42997.3_Sequence_4 IL_42997.33NJ7_C3_G8CAG*CAGtrue93000.66
IL_42997.3_Instance_5 IL_42997.3,IL_3NJ7_003,C3_G8CAGCAG
IL_42997.3_Sequence_5 IL_42997.33NJ7_C3_G8CAG*CAGtrue93000.66
IL_42997.3_Instance_6 IL_42997.3,IL_8P9A_395,A420_U413AAGCAU
IL_42997.3_Sequence_6 IL_42997.38P9A_A420_U413AAG*CAUtrue89001.08
IL_42997.3_Instance_7 IL_42997.3,IL_9DFE_029,U905_A872UGUAUA
IL_42997.3_Sequence_7 IL_42997.39DFE_U905_A872UGU*AUAtrue100000.00
IL_42997.3_Instance_8 IL_42997.3,IL_7VFT_001,C17_G7CAGCAG
IL_42997.3_Sequence_8 IL_42997.37VFT_C17_G7CAG*CAGtrue93000.66
IL_42997.3_Instance_9 IL_42997.3,IL_7A0S_030,U917_A885UAUACA
IL_42997.3_Sequence_9 IL_42997.37A0S_U917_A885UAU*ACAtrue78002.10
IL_42997.3_Instance_10 IL_42997.3,IL_2ZI0_001,U9_A11UUAUUA
IL_42997.3_Sequence_10 IL_42997.32ZI0_U9_A11UUA*UUAtrue78002.08
IL_42997.3_Instance_11 IL_42997.3,IL_5J7L_286,C1196_G1250CGUAGUG
IL_42997.3_Sequence_11 IL_42997.35J7L_C_1196_G_1250CGU*AGUGtrue94000.57
IL_42997.3_Instance_12 IL_42997.3,IL_7A0S_041,C1210_G1263CGUAGUG
IL_42997.3_Sequence_12 IL_42997.37A0S_C_1210_G_1263CGU*AGUGtrue94000.57
IL_42997.3_Instance_13 IL_42997.3,IL_4V9F_046,C1301_G1354CGCGACG
IL_42997.3_Sequence_13 IL_42997.34V9F_C_1301_G_1354CGC*GACGtrue66003.22
IL_42997.3_Instance_14 IL_42997.3,IL_8CRE_061,C1372_G1427CGUAGUG
IL_42997.3_Sequence_14 IL_42997.38CRE_C_1372_G_1427CGU*AGUGtrue94000.57
IL_42997.3_Instance_15 IL_42997.3,IL_8P9A_285,C1376_G1431CGUAGUG
IL_42997.3_Sequence_15 IL_42997.38P9A_C_1376_G_1431CGU*AGUGtrue94000.57
IL_42997.3_Instance_16 IL_42997.3,IL_4WF9_044,C1235_G1288CGUAGUG
IL_42997.3_Sequence_16 IL_42997.34WF9_C_1235_G_1288CGU*AGUGtrue94000.57
IL_42997.3_Instance_17 IL_42997.3,IL_9DFE_044,C1196_G1250CGUAGUG
IL_42997.3_Sequence_17 IL_42997.39DFE_C_1196_G_1250CGU*AGUGtrue94000.57
IL_42997.3_Instance_18 IL_42997.3,IL_5E81_401,C67_G6CGAUCG
IL_42997.3_Sequence_18 IL_42997.35E81_C67_G6CGA*UCGtrue91000.82
IL_42997.3_Instance_19 IL_42997.3,IL_7QR8_004,G11_C9GUGCUC
IL_42997.3_Sequence_19 IL_42997.37QR8_G11_C9GUG*CUCtrue80001.88
IL_42997.3_Instance_20 IL_42997.3,IL_4PCJ_002,C30_G6CUGCUG
IL_42997.3_Sequence_20 IL_42997.34PCJ_C30_G6CUG*CUGtrue85001.47

Conserved interactions between motif group positions in IL_42997.3:
1 2 s35 
1 6 cWW 
2 3 s35 
2 5 cWS 
2 6 s55 
3 4 cWW 
3 5 s55 
4 5 s35
JAR3D SCFG/MRF model for IL_42997.3:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008037250,0.015279466,0.009105722,0.185990786,0.000000000],[0.016955645,0.008245457,0.282668808,0.011037195,0.000000000],[0.009164108,0.188135037,0.001766318,0.022701851,0.000000000],[0.195874422,0.010773166,0.025536418,0.008728351,0.000000000],[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 [6] // Basepair C8 - G16 cWW 
BasepairNode | Deletion Probability [0.0000038223279522] | Pair Probability [[0.137412152,0.047100721,0.032983169,0.033122936,0.000000000],[0.016244876,0.015224507,0.015868271,0.015489890,0.000000000],[0.036866039,0.149296629,0.019009083,0.382912081,0.000000000],[0.013474369,0.013157189,0.010776463,0.061061624,0.000000000],[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 [0.648604883,0.350398605,0.000952915,0.000043597] | Right Letter Distribution [0.166666667,0.055555556,0.722222222,0.055555556,0.000000000] | Left Index [2] | Right Index [5] // Basepair A9 - A15 cWS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.007980787,0.016182142,0.008912632,0.186111802,0.000000000],[0.016520630,0.008227927,0.186936517,0.010324532,0.000000000],[0.008886176,0.237798079,0.001756527,0.023454123,0.000000000],[0.237522360,0.010281895,0.030328475,0.008775394,0.000000000],[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 [3] | Right Index [4] // Basepair G10 - C14 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_42997.3:
> IL_42997.3  7VFT C    8 G   16
CAG*CAG
> IL_42997.3  4V9F G 2237 C 2138
GAC*GAC
> IL_42997.3  8CRE A  418 U  411
AAG*CAU
> IL_42997.3  3NJ7 C    3 G    8
CAG*CAG
> IL_42997.3  3NJ7 C    3 G    8
CAG*CAG
> IL_42997.3  8P9A A  420 U  413
AAG*CAU
> IL_42997.3  9DFE U  905 A  872
UGU*AUA
> IL_42997.3  7VFT C   17 G    7
CAG*CAG
> IL_42997.3  7A0S U  917 A  885
UAU*ACA
> IL_42997.3  2ZI0 U    9 A   11
UUA*UUA
> IL_42997.3  5J7L C 1196 G 1250
CGU*AGUG
> IL_42997.3  7A0S C 1210 G 1263
CGU*AGUG
> IL_42997.3  4V9F C 1301 G 1354
CGC*GACG
> IL_42997.3  8CRE C 1372 G 1427
CGU*AGUG
> IL_42997.3  8P9A C 1376 G 1431
CGU*AGUG
> IL_42997.3  4WF9 C 1235 G 1288
CGU*AGUG
> IL_42997.3  9DFE C 1196 G 1250
CGU*AGUG
> IL_42997.3  5E81 C   67 G    6
CGA*UCG
> IL_42997.3  7QR8 G   11 C    9
GUG*CUC
> IL_42997.3  4PCJ C   30 G    6
CUG*CUG