| 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 6 I | 10 7 5 | 11 8 I | 12 25 6 | 13 25 I | 14 25 7 | 15 25 I | 16 25 8 | 17 25 I | 18 25 9 | 19 25 I | 20 25 10 | 21 25 I | 22 25 11 | 23 25 I | 24 25 12 | 25 25 I | 26 25 13 | 27 26 I | 28 27 | 29 26 I | 30 25 14 | 31 24 I | 32 23 15 | 33 22 I | 34 21 16 | 35 20 I | 36 19 17 | 37 18 I | 38 17 18 | 39 16 I | 40 15 19 | 41 14 I | 42 13 20 | 43 12 I | 44 11 21 | 45 10 I | 46 9 22 | 47 4 I | 48 4 23 | 49 3 I | 50 3 24 | 51 2 I | 52 2 25 | 53 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_29826.1_Instance_1 IL_29826.1,IL_4V9F_109,C1228_G1134 | C | C | A | A | A | A | U | G | A | U | C | G | G | G | A | U | A | A | U | C | C | U | C | U | G | A | A | G | ||||||||||||||||||||||||||||||
| IL_29826.1_Sequence_1 IL_29826.14V9F_C_1228_G_1134 | C | C | A | A | A | A | U | G | A | U | C | G | G | G | A | * | U | A | A | U | C | C | U | C | U | G | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 25 cWW 2 3 s33 2 24 tSH 3 22 s53 3 23 tHH 4 5 s35 6 7 cSH 7 8 s35 9 12 tWH 9 13 s55 9 14 s53 10 11 s35 11 12 s35 12 13 s35 13 14 cWW 15 16 s35 16 17 s35 17 20 s35 18 19 s35 21 22 s35 23 24 s35 24 25 s35 23 3 6BPh 8 12 6BPh 9 12 7BPh 17 16 7BPh 19 18 7BPh 20 19 7BPh 3 23 6BPh 24 2 6BR 20 17 7BRJAR3D SCFG/MRF model for IL_29826.1:
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 [25] // Initial node BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[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 [25] // Basepair C1228 - G1134 cWW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.166739042,0.021588854,0.001719614,0.008552422,0.000000000],[0.181862370,0.120317856,0.001719614,0.001719614,0.000000000],[0.144313661,0.001719614,0.011932323,0.021770231,0.000000000],[0.155443097,0.157162461,0.001719614,0.001719614,0.000000000],[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 [24] // Basepair C1229 - A1133 tSH BasepairNode | Deletion Probability [0.0000001156129129] | Pair Probability [[0.760537866,0.086148033,0.005141257,0.005245308,0.000000000],[0.094339305,0.000153191,0.013059660,0.001455636,0.000000000],[0.005346383,0.012892759,0.000382365,0.000153191,0.000000000],[0.007283397,0.007555264,0.000153191,0.000153191,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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 [23] // Basepair A1230 - A1132 tHH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [4] | Right Index [22] // Fixed node on left for 4V9F|1|0|U|1125 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [22] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [5] | Right Index [22] // Fixed node on left for 4V9F|1|0|C|1126 InitialNode | Left Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [22] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Position [2] | Left Index [6] | Right Index [22] // Fixed node on right for 4V9F|1|0|A|1236 InitialNode | Left Length Distribution [1.000000000] | 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 [21] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [6] | Right Index [21] // Fixed node on right for 4V9F|1|0|G|1235 InitialNode | Left Length Distribution [1.000000000] | 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 [20] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.833333333,0.055555556,0.055555556,0.000000000] | Position [2] | Left Index [6] | Right Index [20] // Fixed node on right for 4V9F|1|0|U|1234 InitialNode | Left Length Distribution [1.000000000] | 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 [19] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.055555556,0.055555556,0.833333333,0.000000000] | Position [2] | Left Index [6] | Right Index [19] // Fixed node on right for 4V9F|1|0|A|1233 InitialNode | Left Length Distribution [1.000000000] | 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 [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [6] | Right Index [18] // Fixed node on right for 4V9F|1|0|A|1232 InitialNode | Left Length Distribution [1.000000000] | 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 [17] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.055555556,0.833333333,0.055555556,0.055555556,0.000000000] | Position [2] | Left Index [6] | Right Index [17] // Fixed node on right for 4V9F|1|0|A|1231 InitialNode | Left Length Distribution [1.000000000] | 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 [16] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [6] | Right Index [16] // Fixed node on right for 4V9F|1|0|A|1230 InitialNode | Left Length Distribution [1.000000000] | 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 [15] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [6] | Right Index [15] // Fixed node on right for 4V9F|1|0|C|1229 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [6] | Right Index [14] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000001953125000000000515889489244815448855715] | Num Left Bases [8] | Num Right Bases [1] | Left Index [6] | Right Index [14] | Norm Constant [1.000000000000000] // Cluster node 4V9F|1|0|G|1235:4V9F|1|0|A|1242 and 4V9F|1|0|U|1122:4V9F|1|0|U|1122 Interaction | Interacting Bases [8,9] | Pair Probability [[0.009374836,0.022228469,0.010012528,0.216037101,0.000000000],[0.017691617,0.009675113,0.196088410,0.010461402,0.000000000],[0.009993038,0.198630499,0.002061361,0.053740648,0.000000000],[0.197964449,0.011137350,0.023240462,0.011662716,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|A|1242 - 4V9F|1|0|U|1122 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.012230644,0.015054486,0.008372813,0.150869555,0.000000000],[0.015268224,0.127062259,0.001726179,0.162814127,0.000000000],[0.182518857,0.001726179,0.021556007,0.121577824,0.000000000],[0.014733840,0.021808946,0.001726179,0.140953883,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|G|1235 - 4V9F|1|0|A|1236 cSH Interaction | Interacting Bases [4,7] | Pair Probability [[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.173267327,0.173267327,0.183168317,0.173267327,0.000000000],[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.024752475,0.024752475,0.024752475,0.024752475,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4V9F|1|0|C|1238 - 4V9F|1|0|G|1241 tWH Interaction | Interacting Bases [3,3] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.833333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|0|U|1237 Interaction | Interacting Bases [5,5] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|0|G|1239 Interaction | Interacting Bases [6,6] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4V9F|1|0|G|1240 InitialNode | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [14] | Right Index [13] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [14] | Right Index [14] | 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_29826.1:
> IL_29826.1 4V9F C 1228 G 1134 CCAAAAUGAUCGGGA*UAAUCCUCUGAAG