Alignment of IL_17136.7 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

4
9
5
I

10
6

5
11
6
I

12
7


13
6
I

14
6

6
15
5
I

16
5

7
17
4
I

18
4

8
19
3
I

20
3

9
21
2
I

22
2

10
23
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_17136.7_Instance_1 IL_17136.7,IL_8CRE_438,C975_G999CGAAGCGUAG
IL_17136.7_Sequence_1 IL_17136.78CRE_C975_G999CGAAG*CGUAGtrue94000.72
IL_17136.7_Instance_2 IL_17136.7,IL_8P9A_424,C990_G1014CGAAGCGUAG
IL_17136.7_Sequence_2 IL_17136.78P9A_C990_G_1014CGAAG*CGUAGtrue94000.72
IL_17136.7_Instance_3 IL_17136.7,IL_5J7L_037,C779_G803CAAACGGUAG
IL_17136.7_Sequence_3 IL_17136.75J7L_C779_G803CAAAC*GGUAGtrue84001.79
IL_17136.7_Instance_4 IL_17136.7,IL_4LFB_033,C779_G803CAAACGGUAG
IL_17136.7_Sequence_4 IL_17136.74LFB_C779_G803CAAAC*GGUAGtrue84001.79
IL_17136.7_Instance_5 IL_17136.7,IL_8CRE_426,U953_G629UCAAGCGUAG
IL_17136.7_Sequence_5 IL_17136.78CRE_U953_G629UCAAG*CGUAGtrue93000.75
IL_17136.7_Instance_6 IL_17136.7,IL_8P9A_407,U968_G631UCAAGCGUAG
IL_17136.7_Sequence_6 IL_17136.78P9A_U968_G631UCAAG*CGUAGtrue93000.75
IL_17136.7_Instance_7 IL_17136.7,IL_4LFB_023,U757_G584UGAGGUGUAG
IL_17136.7_Sequence_7 IL_17136.74LFB_U757_G584UGAGG*UGUAGtrue86001.64
IL_17136.7_Instance_8 IL_17136.7,IL_5J7L_027,U757_G584UCAGGCGCAG
IL_17136.7_Sequence_8 IL_17136.75J7L_U757_G584UCAGG*CGCAGtrue86001.63
IL_17136.7_Instance_9 IL_17136.7,IL_4WF9_052,U1394_G1411UGAGGCGUAG
IL_17136.7_Sequence_9 IL_17136.74WF9_U_1394_G_1411UGAGG*CGUAGtrue100000.00
IL_17136.7_Instance_10 IL_17136.7,IL_5J7L_293,C1357_G1374CGAGGCGUAG
IL_17136.7_Sequence_10 IL_17136.75J7L_C_1357_G_1374CGAGG*CGUAGtrue96000.48
IL_17136.7_Instance_11 IL_17136.7,IL_4V9F_055,U1639_G1546UCAACGGUCG
IL_17136.7_Sequence_11 IL_17136.74V9F_U_1639_G_1546UCAAC*GGUCGtrue88001.31
IL_17136.7_Instance_12 IL_17136.7,IL_4V9F_022,C719_G709CGAGGCGCAG
IL_17136.7_Sequence_12 IL_17136.74V9F_C719_G709CGAGG*CGCAGtrue86001.60
IL_17136.7_Instance_13 IL_17136.7,IL_9DFE_052,U1357_G1374UGAAGCGUAG
IL_17136.7_Sequence_13 IL_17136.79DFE_U_1357_G_1374UGAAG*CGUAGtrue98000.24
IL_17136.7_Instance_14 IL_17136.7,IL_7A0S_049,U1370_G1387UGAGGCGCAG
IL_17136.7_Sequence_14 IL_17136.77A0S_U_1370_G_1387UGAGG*CGCAGtrue90001.12

Conserved interactions between motif group positions in IL_17136.7:
1 2 s35 
1 10 cWW 
2 7 s33 
2 8 s33 
2 9 tSH 
3 4 s35 
3 8 tHW 
3 9 s55 
4 5 s35 
4 7 tHS 
4 8 s55 
5 6 cWW 
5 7 s55 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
7 3 6BPh
2 8 6BPh
9 2 6BR
4 7 6BR
JAR3D SCFG/MRF model for IL_17136.7:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009406793,0.013707370,0.011503862,0.095285184,0.000000000],[0.162456321,0.018015036,0.154419759,0.013486043,0.000000000],[0.011710885,0.096851345,0.002491696,0.016499798,0.000000000],[0.121284217,0.012600150,0.249477228,0.010804313,0.000000000],[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 [10] // Basepair C975 - G999 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.126200657,0.036042198,0.001157200,0.006488509,0.000000000],[0.165367853,0.125226296,0.001521107,0.001521107,0.000000000],[0.275366234,0.002027665,0.010549753,0.153411532,0.000000000],[0.047658537,0.046415582,0.000522886,0.000522886,0.000000000],[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 [2] | Right Index [9] // Basepair G976 - A998 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.019117863,0.128388417,0.003573270,0.394375693,0.000000000],[0.003573270,0.234040778,0.009369982,0.003573270,0.000000000],[0.034355291,0.003573270,0.028194796,0.019771442,0.000000000],[0.003573270,0.003573270,0.019400325,0.091545791,0.000000000],[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 [3] | Right Index [8] // Basepair A977 - U997 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.025882581,0.025336157,0.271863101,0.027458641,0.000000000],[0.025403813,0.025387036,0.004730615,0.025584918,0.000000000],[0.000675802,0.000675802,0.347131858,0.000675802,0.000000000],[0.038052600,0.000675802,0.179789670,0.000675802,0.000000000],[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 [4] | Right Index [7] // Basepair A978 - G996 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009061542,0.035208473,0.010100865,0.172183055,0.000000000],[0.015691569,0.008779683,0.198464727,0.012054463,0.000000000],[0.010026198,0.262836002,0.001943270,0.051111483,0.000000000],[0.167962559,0.012364674,0.021046798,0.011164641,0.000000000],[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 [5] | Right Index [6] // Basepair G979 - C995 cWW 
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_17136.7:
> IL_17136.7  8CRE C  975 G  999
CGAAG*CGUAG
> IL_17136.7  8P9A C  990 G 1014
CGAAG*CGUAG
> IL_17136.7  5J7L C  779 G  803
CAAAC*GGUAG
> IL_17136.7  4LFB C  779 G  803
CAAAC*GGUAG
> IL_17136.7  8CRE U  953 G  629
UCAAG*CGUAG
> IL_17136.7  8P9A U  968 G  631
UCAAG*CGUAG
> IL_17136.7  4LFB U  757 G  584
UGAGG*UGUAG
> IL_17136.7  5J7L U  757 G  584
UCAGG*CGCAG
> IL_17136.7  4WF9 U 1394 G 1411
UGAGG*CGUAG
> IL_17136.7  5J7L C 1357 G 1374
CGAGG*CGUAG
> IL_17136.7  4V9F U 1639 G 1546
UCAAC*GGUCG
> IL_17136.7  4V9F C  719 G  709
CGAGG*CGCAG
> IL_17136.7  9DFE U 1357 G 1374
UGAAG*CGUAG
> IL_17136.7  7A0S U 1370 G 1387
UGAGG*CGCAG