Alignment of IL_22551.4 sequences from 3D to the JAR3D model

Previous group | Next group | List of all groups | Motif atlas entry for IL_22551.4
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
2
I

4
3

2
5
4
I

6
5

3
7
6
I

8
7

4
9
7
I

10
8


11
7
I

12
7

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_22551.4_Instance_1 IL_22551.4,IL_8CRE_094,G2285_C2255GCAUGC
IL_22551.4_Sequence_1 IL_22551.48CRE_G_2285_C_2255GCAU*GCtrue98000.19
IL_22551.4_Instance_2 IL_22551.4,IL_8P9A_317,G2307_C2277GCAUGC
IL_22551.4_Sequence_2 IL_22551.48P9A_G_2307_C_2277GCAU*GCtrue98000.19
IL_22551.4_Instance_3 IL_22551.4,IL_4V9F_070,G2005_C1975GCAUGC
IL_22551.4_Sequence_3 IL_22551.44V9F_G_2005_C_1975GCAU*GCtrue98000.19
IL_22551.4_Instance_4 IL_22551.4,IL_9DFE_076,G1964_C1934GCACGC
IL_22551.4_Sequence_4 IL_22551.49DFE_G_1964_C_1934GCAC*GCtrue100000.00
IL_22551.4_Instance_5 IL_22551.4,IL_7A0S_071,G1947_C1917GCACGC
IL_22551.4_Sequence_5 IL_22551.47A0S_G_1947_C_1917GCAC*GCtrue100000.00
IL_22551.4_Instance_6 IL_22551.4,IL_5J7L_318,G1964_C1934GCACGC
IL_22551.4_Sequence_6 IL_22551.45J7L_G_1964_C_1934GCAC*GCtrue100000.00
IL_22551.4_Instance_7 IL_22551.4,IL_4WF9_076,G1991_C1961GCACGC
IL_22551.4_Sequence_7 IL_22551.44WF9_G_1991_C_1961GCAC*GCtrue100000.00
IL_22551.4_Instance_8 IL_22551.4,IL_8CRE_431,G803_C837GUUAUC
IL_22551.4_Sequence_8 IL_22551.48CRE_G803_C837GUUA*UCtrue69002.91
IL_22551.4_Instance_9 IL_22551.4,IL_397D_001,A22_U40AUCUGCU
IL_22551.4_Sequence_9 IL_22551.4397D_A22_U40AUCUG*CUtrue38005.93

Conserved interactions between motif group positions in IL_22551.4:
1 4 s35 
1 6 cWW 
2 3 s33 
4 5 cWW 
5 6 s35
JAR3D SCFG/MRF model for IL_22551.4:
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 [[0.009061724,0.019150725,0.010250635,0.197856760,0.000000000],[0.016043230,0.008935570,0.189066937,0.012126755,0.000000000],[0.010146237,0.267631953,0.001950102,0.027796317,0.000000000],[0.185697965,0.012615169,0.021907609,0.009762313,0.000000000],[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 G2285 - C2255 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.045454545,0.681818182,0.045454545,0.227272727,0.000000000] | Position [1] | Left Index [2] | Right Index [5] // Fixed node on left for 8CRE|1|1|C|2255
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.681818182,0.136363636,0.045454545,0.136363636,0.000000000] | Position [1] | Left Index [3] | Right Index [5] // Fixed node on left for 8CRE|1|1|G|2285
InitialNode  | Left Length Distribution [0.883805084,0.115305590,0.000858659,0.000030666] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009451519,0.015870800,0.011196618,0.145633584,0.000000000],[0.106401879,0.014746670,0.178120276,0.013195306,0.000000000],[0.011330518,0.147386698,0.002329873,0.022652090,0.000000000],[0.151680773,0.012685139,0.146616805,0.010701453,0.000000000],[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 U2288 - G2254 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_22551.4:
> IL_22551.4  8CRE G 2285 C 2255
GCAU*GC
> IL_22551.4  8P9A G 2307 C 2277
GCAU*GC
> IL_22551.4  4V9F G 2005 C 1975
GCAU*GC
> IL_22551.4  9DFE G 1964 C 1934
GCAC*GC
> IL_22551.4  7A0S G 1947 C 1917
GCAC*GC
> IL_22551.4  5J7L G 1964 C 1934
GCAC*GC
> IL_22551.4  4WF9 G 1991 C 1961
GCAC*GC
> IL_22551.4  8CRE G  803 C  837
GUUA*UC
> IL_22551.4  397D A   22 U   40
AUCUG*CU