Alignment of IL_31555.5 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
5

2
5
5
I

6
6

3
7
6
I

8
7

4
9
7
I

10
8


11
7
I

12
7

5
13
6
I

14
6

6
15
5
I

16
5

7
17
4
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_31555.5_Instance_1 IL_31555.5_IL_4FAW_010_U172_G194UGAGCAAAG
IL_31555.5_Sequence_1 IL_31555.5_IL_4FAW_010_U172_G194UGAG*CAAAGtrue95000.52
IL_31555.5_Instance_2 IL_31555.5_IL_4A1B_026_U571_A598UGAGCAAAA
IL_31555.5_Sequence_2 IL_31555.5_IL_4A1B_026_U571_A598UGAG*CAAAAtrue90000.91
IL_31555.5_Instance_3 IL_31555.5_IL_4A1B_022_U499_G479UGAGCAGAG
IL_31555.5_Sequence_3 IL_31555.5_IL_4A1B_022_U499_G479UGAG*CAGAGtrue97000.33
IL_31555.5_Instance_4 IL_31555.5_IL_1X8W_002_U205_G116UAACGAAAG
IL_31555.5_Sequence_4 IL_31555.5_IL_1X8W_002_U205_G116UAAC*GAAAGtrue100000.00
IL_31555.5_Instance_5 IL_31555.5_IL_1GID_010_U205_G116UAACGAAAG
IL_31555.5_Sequence_5 IL_31555.5_IL_1GID_010_U205_G116UAAC*GAAAGtrue100000.00
IL_31555.5_Instance_6 IL_31555.5_IL_1GID_003_U205_G116UAACGAAAG
IL_31555.5_Sequence_6 IL_31555.5_IL_1GID_003_U205_G116UAAC*GAAAGtrue100000.00
IL_31555.5_Instance_7 IL_31555.5_IL_3FTM_001_U46_A4UGAGCGGAA
IL_31555.5_Sequence_7 IL_31555.5_IL_3FTM_001_U46_A4UGAG*CGGAAtrue90000.95
IL_31555.5_Instance_8 IL_31555.5_IL_4A1B_120_U3043_G3077UAAAUAUGAAG
IL_31555.5_Sequence_8 IL_31555.5_IL_4A1B_120_U_3043_G_3077UAAAUA*UGAAGtrue29006.77
IL_31555.5_Instance_9 IL_31555.5_IL_3FS0_001_U46_A4UGAGCGGAA
IL_31555.5_Sequence_9 IL_31555.5_IL_3FS0_001_U46_A4UGAG*CGGAAtrue90000.95
IL_31555.5_Instance_10 IL_31555.5_IL_3LOA_001_G1401_C1501GCCCGUAAC
IL_31555.5_Sequence_10 IL_31555.5_IL_3LOA_001_G_1401_C_1501GCCC*GUAACtrue87001.24
IL_31555.5_Instance_11 IL_31555.5_IL_3BNT_002_C6_G18CACCGCAAG
IL_31555.5_Sequence_11 IL_31555.5_IL_3BNT_002_C6_G18CACC*GCAAGtrue91000.89
IL_31555.5_Instance_12 IL_31555.5_IL_3BNT_005_C6_G18CACCGCAAG
IL_31555.5_Sequence_12 IL_31555.5_IL_3BNT_005_C6_G18CACC*GCAAGtrue91000.89
IL_31555.5_Instance_13 IL_31555.5_IL_3CUN_001_C22_G49CAGGUAUUGG
IL_31555.5_Sequence_13 IL_31555.5_IL_3CUN_001_C22_G49CAGG*UAUUGGtrue-3009.79

Conserved interactions between motif group positions in IL_31555.5:
1 2 s35 
1 9 cWW 
2 3 s35 
2 6 s33 
2 7 tSH 
3 4 s35 
3 6 tHS 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35 
8 9 s35 
3 6 6BR
JAR3D SCFG/MRF model for IL_31555.5:
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 [9] // Initial node U172 - G194 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010119758,0.015381041,0.011773713,0.112831708,0.000000000],[0.142681571,0.011045710,0.145037150,0.013259572,0.000000000],[0.011944510,0.123602112,0.002515582,0.018248559,0.000000000],[0.144091318,0.012444267,0.213280671,0.011742757,0.000000000],[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 [9] // Basepair U172 - G194 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.833333333,0.033333333,0.100000000,0.033333333,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000105840881771] | Pair Probability [[0.172671224,0.085919845,0.001808419,0.104872879,0.000000000],[0.114691441,0.055711829,0.001808419,0.001808419,0.000000000],[0.106569534,0.001808419,0.128790389,0.037772399,0.000000000],[0.093027893,0.089122053,0.001808419,0.001808419,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.919387860,0.080126081,0.000471330,0.000014729] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.919387860,0.080126081,0.000471330,0.000014729] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G173 - A192 tSH 
BasepairNode | Deletion Probability [0.0000160934329480] | Pair Probability [[0.177077827,0.121481100,0.141533733,0.119606275,0.000000000],[0.111119146,0.107057298,0.001305849,0.133418568,0.000000000],[0.019569829,0.001305849,0.009851328,0.001305849,0.000000000],[0.009110720,0.001305849,0.043644933,0.001305849,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.919387860,0.080126081,0.000471330,0.000014729] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | 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 [6] // Basepair A174 - A191 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009506456,0.037620190,0.010717425,0.174190618,0.000000000],[0.017026146,0.007935753,0.231011961,0.012191369,0.000000000],[0.010702666,0.222205897,0.002030899,0.054241435,0.000000000],[0.164390525,0.012266178,0.022436068,0.011526414,0.000000000],[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 G175 - C190 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_31555.5:
> IL_31555.5 IL_4FAW_010 U  172 G  194
UGAG*CAAAG
> IL_31555.5 IL_4A1B_026 U  571 A  598
UGAG*CAAAA
> IL_31555.5 IL_4A1B_022 U  499 G  479
UGAG*CAGAG
> IL_31555.5 IL_1X8W_002 U  205 G  116
UAAC*GAAAG
> IL_31555.5 IL_1GID_010 U  205 G  116
UAAC*GAAAG
> IL_31555.5 IL_1GID_003 U  205 G  116
UAAC*GAAAG
> IL_31555.5 IL_3FTM_001 U   46 A    4
UGAG*CGGAA
> IL_31555.5 IL_4A1B_120 U 3043 G 3077
UAAAUA*UGAAG
> IL_31555.5 IL_3FS0_001 U   46 A    4
UGAG*CGGAA
> IL_31555.5 IL_3LOA_001 G 1401 C 1501
GCCC*GUAAC
> IL_31555.5 IL_3BNT_002 C    6 G   18
CACC*GCAAG
> IL_31555.5 IL_3BNT_005 C    6 G   18
CACC*GCAAG
> IL_31555.5 IL_3CUN_001 C   22 G   49
CAGG*UAUUGG