Alignment of IL_90729.1 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
4
I

6
5

3
7
5
I

8
6


9
5
I

10
5

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_90729.1_Instance_1 IL_90729.1,IL_4WF9_007,G215_C187GAGCC
IL_90729.1_Sequence_1 IL_90729.14WF9_G215_C187GAG*CCtrue100000.00
IL_90729.1_Instance_2 IL_90729.1,IL_5J7L_249,G212_C184GAGCC
IL_90729.1_Sequence_2 IL_90729.15J7L_G212_C184GAG*CCtrue100000.00
IL_90729.1_Instance_3 IL_90729.1,IL_9DFE_005,G212_C184GAGCC
IL_90729.1_Sequence_3 IL_90729.19DFE_G212_C184GAG*CCtrue100000.00
IL_90729.1_Instance_4 IL_90729.1,IL_7MLX_001,G48_C38GAUAC
IL_90729.1_Sequence_4 IL_90729.17MLX_G48_C38GAU*ACtrue95000.51
IL_90729.1_Instance_5 IL_90729.1,IL_7A0S_005,A189_U161AAGCU
IL_90729.1_Sequence_5 IL_90729.17A0S_A189_U161AAG*CUtrue96000.38
IL_90729.1_Instance_6 IL_90729.1,IL_8CRE_004,G55_C27GAGCC
IL_90729.1_Sequence_6 IL_90729.18CRE_G55_C27GAG*CCtrue100000.00
IL_90729.1_Instance_7 IL_90729.1,IL_8P9A_233,G56_C28GAGCC
IL_90729.1_Sequence_7 IL_90729.18P9A_G56_C28GAG*CCtrue100000.00
IL_90729.1_Instance_8 IL_90729.1,IL_4V9F_005,G182_C154GAGCC
IL_90729.1_Sequence_8 IL_90729.14V9F_G182_C154GAG*CCtrue100000.00
IL_90729.1_Instance_9 IL_90729.1,IL_8CRE_075,G1772_C1667GUGCC
IL_90729.1_Sequence_9 IL_90729.18CRE_G_1772_C_1667GUG*CCtrue96000.36
IL_90729.1_Instance_10 IL_90729.1,IL_7QR8_009,C14_G6CUAUG
IL_90729.1_Sequence_10 IL_90729.17QR8_C14_G6CUA*UGtrue90000.96
IL_90729.1_Instance_11 IL_90729.1,IL_8P9A_298,G1776_C1671GUGCC
IL_90729.1_Sequence_11 IL_90729.18P9A_G_1776_C_1671GUG*CCtrue96000.36
IL_90729.1_Instance_12 IL_90729.1,IL_5J7L_266,G940_C838GAGCC
IL_90729.1_Sequence_12 IL_90729.15J7L_G940_C838GAG*CCtrue100000.00
IL_90729.1_Instance_13 IL_90729.1,IL_9DFE_022,G940_C838GAGCC
IL_90729.1_Sequence_13 IL_90729.19DFE_G940_C838GAG*CCtrue100000.00
IL_90729.1_Instance_14 IL_90729.1,IL_8P9A_238,C163_G258CAAUG
IL_90729.1_Sequence_14 IL_90729.18P9A_C163_G258CAA*UGtrue94000.60
IL_90729.1_Instance_15 IL_90729.1,IL_7A0S_022,G951_C851GAGCC
IL_90729.1_Sequence_15 IL_90729.17A0S_G951_C851GAG*CCtrue100000.00
IL_90729.1_Instance_16 IL_90729.1,IL_8CRE_012,A236_U178AUGCU
IL_90729.1_Sequence_16 IL_90729.18CRE_A236_U178AUG*CUtrue92000.74
IL_90729.1_Instance_17 IL_90729.1,IL_7KGA_003,A37_U16ACUAU
IL_90729.1_Sequence_17 IL_90729.17KGA_A37_U16ACU*AUtrue71002.77
IL_90729.1_Instance_18 IL_90729.1,IL_8OI5_137,C47_G30CCGCG
IL_90729.1_Sequence_18 IL_90729.18OI5_C47_G30CCG*CGtrue77002.14
IL_90729.1_Instance_19 IL_90729.1,IL_8P9A_367,C47_G30CUGCG
IL_90729.1_Sequence_19 IL_90729.18P9A_C47_G30CUG*CGtrue94000.62
IL_90729.1_Instance_20 IL_90729.1,IL_4C7O_002,A36_U9AUGCU
IL_90729.1_Sequence_20 IL_90729.14C7O_A36_U9AUG*CUtrue92000.74
IL_90729.1_Instance_21 IL_90729.1,IL_5IBB_340,G63_C51GUCGC
IL_90729.1_Sequence_21 IL_90729.15IBB_G63_C51GUC*GCtrue90000.91
IL_90729.1_Instance_22 IL_90729.1,IL_4WF9_028,G984_C883GAGCC
IL_90729.1_Sequence_22 IL_90729.14WF9_G984_C883GAG*CCtrue100000.00
IL_90729.1_Instance_23 IL_90729.1,IL_4LFB_041,G1002_C1039GGGCC
IL_90729.1_Sequence_23 IL_90729.14LFB_G_1002_C_1039GGG*CCtrue75002.40
IL_90729.1_Instance_24 IL_90729.1,IL_8P9A_328,G2770_C2788GUCCGC
IL_90729.1_Sequence_24 IL_90729.18P9A_G_2770_C_2788GUCC*GCtrue53004.50
IL_90729.1_Instance_25 IL_90729.1,IL_6FZ0_001,C46_G21CUAUG
IL_90729.1_Sequence_25 IL_90729.16FZ0_C46_G21CUA*UGtrue90000.96
IL_90729.1_Instance_26 IL_90729.1,IL_2QWY_008,C43_G22CUAUG
IL_90729.1_Sequence_26 IL_90729.12QWY_C43_G22CUA*UGtrue90000.96
IL_90729.1_Instance_27 IL_90729.1,IL_4V83_236,C6155_G6173CAAUG
IL_90729.1_Sequence_27 IL_90729.14V83_C_6155_G_6173CAA*UGtrue94000.60
IL_90729.1_Instance_28 IL_90729.1,IL_3MOJ_004,C2540_G2523CAAUG
IL_90729.1_Sequence_28 IL_90729.13MOJ_C_2540_G_2523CAA*UGtrue94000.60
IL_90729.1_Instance_29 IL_90729.1,IL_7A0S_024,U942_G861UUAUG
IL_90729.1_Sequence_29 IL_90729.17A0S_U942_G861UUA*UGtrue71002.79
IL_90729.1_Instance_30 IL_90729.1,IL_5J7L_267,A844_U934AAUUAU
IL_90729.1_Sequence_30 IL_90729.15J7L_A844_U934AAUU*AUtrue53004.48

Conserved interactions between motif group positions in IL_90729.1:
1 2 s35 
1 5 cWW 
2 3 s35 
2 5 s55 
3 4 cWW 
4 5 s35
JAR3D SCFG/MRF model for IL_90729.1:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.007576572,0.015305137,0.008602064,0.191966237,0.000000000],[0.021600464,0.008010182,0.216720053,0.010218242,0.000000000],[0.008581966,0.279685400,0.001664913,0.023452502,0.000000000],[0.153187008,0.010375656,0.034767342,0.008286261,0.000000000],[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 [5] // Basepair G215 - C187 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.515625000,0.078125000,0.046875000,0.359375000,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left for 4WF9|1|X|C|187
InitialNode  | Left Length Distribution [0.931710428,0.068095489,0.000188538,0.000005545] | Left Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.007489496,0.015844083,0.008384169,0.211792420,0.000000000],[0.014046361,0.007526811,0.172897128,0.009738120,0.000000000],[0.008330643,0.298706518,0.001626962,0.025378244,0.000000000],[0.179099508,0.010018755,0.020839653,0.008281130,0.000000000],[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 G217 - C186 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_90729.1:
> IL_90729.1  4WF9 G  215 C  187
GAG*CC
> IL_90729.1  5J7L G  212 C  184
GAG*CC
> IL_90729.1  9DFE G  212 C  184
GAG*CC
> IL_90729.1  7MLX G   48 C   38
GAU*AC
> IL_90729.1  7A0S A  189 U  161
AAG*CU
> IL_90729.1  8CRE G   55 C   27
GAG*CC
> IL_90729.1  8P9A G   56 C   28
GAG*CC
> IL_90729.1  4V9F G  182 C  154
GAG*CC
> IL_90729.1  8CRE G 1772 C 1667
GUG*CC
> IL_90729.1  7QR8 C   14 G    6
CUA*UG
> IL_90729.1  8P9A G 1776 C 1671
GUG*CC
> IL_90729.1  5J7L G  940 C  838
GAG*CC
> IL_90729.1  9DFE G  940 C  838
GAG*CC
> IL_90729.1  8P9A C  163 G  258
CAA*UG
> IL_90729.1  7A0S G  951 C  851
GAG*CC
> IL_90729.1  8CRE A  236 U  178
AUG*CU
> IL_90729.1  7KGA A   37 U   16
ACU*AU
> IL_90729.1  8OI5 C   47 G   30
CCG*CG
> IL_90729.1  8P9A C   47 G   30
CUG*CG
> IL_90729.1  4C7O A   36 U    9
AUG*CU
> IL_90729.1  5IBB G   63 C   51
GUC*GC
> IL_90729.1  4WF9 G  984 C  883
GAG*CC
> IL_90729.1  4LFB G 1002 C 1039
GGG*CC
> IL_90729.1  8P9A G 2770 C 2788
GUCC*GC
> IL_90729.1  6FZ0 C   46 G   21
CUA*UG
> IL_90729.1  2QWY C   43 G   22
CUA*UG
> IL_90729.1  4V83 C 6155 G 6173
CAA*UG
> IL_90729.1  3MOJ C 2540 G 2523
CAA*UG
> IL_90729.1  7A0S U  942 G  861
UUA*UG
> IL_90729.1  5J7L A  844 U  934
AAUU*AU