| 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 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 2 I | 24 2 11 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_22829.2_Instance_1 IL_22829.2,IL_8CRE_079,A1879_U2327 | A | A | U | A | A | U | G | C | U | A | U | |||||||||||||||||||
| IL_22829.2_Sequence_1 IL_22829.28CRE_A_1879_U_2327 | A | A | U | A | A | U | G | * | C | U | A | U | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_22829.2_Instance_2 IL_22829.2,IL_8P9A_302,A1883_U2349 | A | A | U | A | A | U | G | C | U | A | U | |||||||||||||||||||
| IL_22829.2_Sequence_2 IL_22829.28P9A_A_1883_U_2349 | A | A | U | A | A | U | G | * | C | U | A | U | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_22829.2_Instance_3 IL_22829.2,IL_3NDB_002,G247_C131 | G | G | G | G | U | G | C | G | U | C | C | |||||||||||||||||||
| IL_22829.2_Sequence_3 IL_22829.23NDB_G247_C131 | G | G | G | G | U | G | C | * | G | U | C | C | true | 67 | 0 | 0 | 5.78 |
1 2 s35 1 11 cWW 2 3 s35 2 11 s55 3 10 tSH 4 5 s35 5 6 s35 5 10 tHS 6 7 s35 6 9 cWW 7 8 cWW 7 9 s55 8 9 s35 9 10 s35 10 11 s35 11 10 7BPhJAR3D SCFG/MRF model for IL_22829.2:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.005475412,0.012055866,0.006075059,0.434088272,0.000000000],[0.009913199,0.005485543,0.114338833,0.022056932,0.000000000],[0.006029723,0.126609062,0.001187116,0.099616489,0.000000000],[0.113377953,0.007238898,0.013352789,0.023098853,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair A1879 - U2327 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left for 8CRE|1|1|A|1880 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [10] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [3] | Right Index [10] | Norm Constant [0.253861993640454] // Cluster node 8CRE|1|1|U|1881:8CRE|1|1|A|1883 and 8CRE|1|1|A|2326:8CRE|1|1|A|2326 Interaction | Interacting Bases [1,4] | Pair Probability [[0.113545609,0.103712991,0.001260969,0.006202964,0.000000000],[0.113984241,0.107248177,0.001260969,0.001260969,0.000000000],[0.117255805,0.057201792,0.007793409,0.104683837,0.000000000],[0.145514342,0.116551990,0.001260969,0.001260969,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|1|U|1881 - 8CRE|1|1|A|2326 tSH Interaction | Interacting Bases [3,4] | Pair Probability [[0.186269350,0.161784709,0.138993036,0.150244001,0.000000000],[0.019472190,0.066272433,0.001668519,0.149927300,0.000000000],[0.001668519,0.001668519,0.014494009,0.001668519,0.000000000],[0.010174537,0.057609342,0.036416501,0.001668519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8CRE|1|1|A|1883 - 8CRE|1|1|A|2326 tHS Interaction | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8CRE|1|1|A|1882 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [0.0000234451146992] | Pair Probability [[0.014550416,0.266872370,0.012991067,0.022689713,0.000000000],[0.016081663,0.017340010,0.019394286,0.014261191,0.000000000],[0.012719729,0.019756895,0.004010360,0.107173936,0.000000000],[0.019820977,0.015444859,0.016439019,0.420453509,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair U1884 - U2325 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009574124,0.019028436,0.010936653,0.198530575,0.000000000],[0.017980846,0.009507606,0.212727929,0.013322270,0.000000000],[0.010896029,0.224384255,0.002069153,0.025416337,0.000000000],[0.197680266,0.013488440,0.024325847,0.010131233,0.000000000],[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 G1885 - C2324 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 truncationSequences of instances from IL_22829.2:
> IL_22829.2 8CRE A 1879 U 2327 AAUAAUG*CUAU > IL_22829.2 8P9A A 1883 U 2349 AAUAAUG*CUAU > IL_22829.2 3NDB G 247 C 131 GGGGUGC*GUCC