Alignment of IL_24254.1 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 3 I	6 4 3	7 4 I	8 5 4	9 5 I	10 5 5	11 6 I	12 7 6	13 7 I	14 8 7	15 8 I	16 9	17 8 I	18 8 8	19 7 I	20 7 9	21 6 I	22 5 10	23 4 I	24 4 11	25 3 I	26 3 12	27 2 I	28 2 13	29 1 I	In acceptance region	Cutoff score	Full edit distance	Interior edit distance	Alignment score deficit
IL_24254.1_Instance_1 IL_24254.1,IL_1UN6_004,U72_A103		U		U		A		G		U		A		C				G		G		A		A		U		A
IL_24254.1_Sequence_1 IL_24254.11UN6_U72_A103		U		U		A		G		U		A		C		*		G		G		A		A		U		A		true	100	0	0	0.00

Conserved interactions between motif group positions in IL_24254.1:

1 2 s35 
1 13 cWW 
2 3 s33 
2 12 cWW 
3 5 s55 
3 11 tHH 
4 5 cSH 
4 9 s33 
5 6 s35 
5 9 s33 
5 10 tWH 
6 7 s35 
6 9 tHS 
6 10 s55 
7 8 cWW 
7 9 s55 
8 9 s35 
10 11 s35 
11 12 s35 
12 13 s35 
9 5 6BPh
7 6 7BPh
4 10 6BPh
3 11 6BPh
9 4 6BR
6 9 6BR

JAR3D SCFG/MRF model for IL_24254.1:

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 [13] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009123784,0.017718471,0.010008206,0.198264936,0.000000000],[0.022262210,0.009929018,0.198931998,0.011154256,0.000000000],[0.010027726,0.196386049,0.002064490,0.023275738,0.000000000],[0.216349992,0.010477281,0.053822220,0.010203624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair U72 - A103 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.015580470,0.285764820,0.013910732,0.024295965,0.000000000],[0.017220118,0.018567546,0.020767248,0.015270770,0.000000000],[0.013620185,0.021155527,0.004294262,0.054860011,0.000000000],[0.021224145,0.016538232,0.017602771,0.439327198,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [12] // Basepair U73 - U102 cWW 
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.426248873,0.334479782,0.019961529,0.020365520,0.000000000],[0.052326193,0.000594783,0.050705654,0.005651677,0.000000000],[0.002965422,0.050057641,0.001484577,0.000594783,0.000000000],[0.004039806,0.029334195,0.000594783,0.000594783,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [11] // Basepair A74 - A101 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.259025769291484] // Cluster node 1UN6|1|F|G|75:1UN6|1|F|U|76 and 1UN6|1|F|A|100:1UN6|1|F|A|100
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.018961504,0.004196211,0.019694625,0.004196211,0.000000000],[0.042198433,0.338134433,0.004196211,0.004196211,0.000000000],[0.004196211,0.010058595,0.031911832,0.018663303,0.000000000],[0.429522110,0.004196211,0.024345914,0.041331983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1UN6|1|F|U|76 - 1UN6|1|F|A|100 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.031413984,0.032009409,0.001759976,0.031282354,0.000000000],[0.023452592,0.035343467,0.000389689,0.031347933,0.000000000],[0.192125245,0.002727821,0.234360049,0.282683054,0.000000000],[0.031901402,0.031709893,0.000389689,0.037103443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 1UN6|1|F|G|75 - 1UN6|1|F|U|76 cSH 
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.044130649,0.044458508,0.380732303,0.049261589,0.000000000],[0.046718239,0.046610059,0.003708313,0.046358426,0.000000000],[0.000529759,0.000529759,0.018128765,0.000529759,0.000000000],[0.002496756,0.000529759,0.314747597,0.000529759,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A77 - G99 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003781516,0.006781167,0.004347319,0.078825460,0.000000000],[0.056281056,0.026959555,0.589952696,0.038278585,0.000000000],[0.004396140,0.080523937,0.000828645,0.009304998,0.000000000],[0.079847353,0.005268669,0.010615539,0.004007366,0.000000000],[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 [7] | Right Index [8] // Basepair C78 - G98 cWW 
HairpinNode  | Num Bases [1] | Left Index [8] | Right Index [8] | 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_24254.1:> IL_24254.1 1UN6 U 72 A 103 UUAGUAC*GGAAUA