| 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 9 2 | 5 9 I | 6 9 3 | 7 9 I | 8 9 4 | 9 9 I | 10 9 5 | 11 9 I | 12 9 6 | 13 10 I | 14 11 | 15 10 I | 16 9 7 | 17 8 I | 18 7 8 | 19 6 I | 20 5 9 | 21 4 I | 22 3 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_18472.4_Instance_1 IL_18472.4,IL_5J7L_356,G23_C60 | G | G | U | C | C | C | G | A | A | A | C | |||||||||||||||||||
| IL_18472.4_Sequence_1 IL_18472.45J7L_G23_C60 | G | G | U | C | C | C | * | G | A | A | A | C | true | 93 | 0 | 0 | 1.16 | |||||||||||||
| IL_18472.4_Instance_2 IL_18472.4,IL_9DFE_111,G23_C60 | G | G | A | A | C | C | G | A | A | A | C | |||||||||||||||||||
| IL_18472.4_Sequence_2 IL_18472.49DFE_G23_C60 | G | G | A | A | C | C | * | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_18472.4_Instance_3 IL_18472.4,IL_7A0S_103,G25_C62 | G | G | A | A | C | C | G | A | A | A | C | |||||||||||||||||||
| IL_18472.4_Sequence_3 IL_18472.47A0S_G25_C62 | G | G | A | A | C | C | * | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 |
1 11 cWW 2 5 tSW 2 7 s33 3 4 s35 4 5 s35 5 6 s35 6 7 cWW 8 9 s35 9 10 s35 10 11 s35 4 2 7BRJAR3D SCFG/MRF model for IL_18472.4:
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 [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[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 G23 - C60 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [10] // Fixed node on right for 5J7L|1|DB|A|59 InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // Fixed node on right for 5J7L|1|DB|A|58 InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // Fixed node on right for 5J7L|1|DB|A|57 InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [7] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [5] | Num Right Bases [1] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Cluster node 5J7L|1|DB|G|24:5J7L|1|DB|C|28 and 5J7L|1|DB|G|56:5J7L|1|DB|G|56 Interaction | Interacting Bases [5,6] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DB|C|28 - 5J7L|1|DB|G|56 cWW Interaction | Interacting Bases [1,4] | Pair Probability [[0.006987385,0.006987385,0.006987385,0.006987385,0.000000000],[0.006987385,0.006987385,0.128079819,0.006987385,0.000000000],[0.006987385,0.774096792,0.006987385,0.006987385,0.000000000],[0.006987385,0.006987385,0.006987385,0.006987385,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DB|G|24 - 5J7L|1|DB|C|27 tSW 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],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DB|U|25 Interaction | Interacting Bases [3,3] | Pair Probability [[0.617647059,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.323529412,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DB|C|26 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 [7] | Right Index [6] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | 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_18472.4:
> IL_18472.4 5J7L G 23 C 60 GGUCCC*GAAAC > IL_18472.4 9DFE G 23 C 60 GGAACC*GAAAC > IL_18472.4 7A0S G 25 C 62 GGAACC*GAAAC