| 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 6 I | 8 7 4 | 9 7 I | 10 7 5 | 11 7 I | 12 7 6 | 13 7 I | 14 7 7 | 15 7 I | 16 7 8 | 17 7 I | 18 7 9 | 19 8 I | 20 9 | 21 8 I | 22 7 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_58960.1_Instance_1 IL_58960.1,IL_4M4O_003,U15_A45 | U | A | A | A | G | A | G | U | G | C | A | |||||||||||||||||||
| IL_58960.1_Sequence_1 IL_58960.14M4O_U15_A45 | U | A | A | A | G | A | G | U | G | * | C | A | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_58960.1_Instance_2 IL_58960.1,IL_4M6D_012,U15_A45 | U | A | A | A | G | A | G | U | G | C | A | |||||||||||||||||||
| IL_58960.1_Sequence_2 IL_58960.14M6D_U15_A45 | U | A | A | A | G | A | G | U | G | * | C | A | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_58960.1_Instance_3 IL_58960.1,IL_4FRN_003,A6_U76 | A | A | A | A | G | C | A | U | G | C | U | |||||||||||||||||||
| IL_58960.1_Sequence_3 IL_58960.14FRN_A6_U76 | A | A | A | A | G | C | A | U | G | * | C | U | true | 94 | 0 | 0 | 1.08 |
1 9 s35 1 11 cWW 2 3 s35 3 4 s35 4 5 s35 4 8 tWW 5 7 s33 6 7 s35 9 10 cWW 9 11 s55 10 11 s35 5 8 6BPhJAR3D SCFG/MRF model for IL_58960.1:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009028682,0.018848565,0.009815285,0.206696649,0.000000000],[0.020335986,0.009653230,0.194139783,0.010711201,0.000000000],[0.009821675,0.193306351,0.002023380,0.032781568,0.000000000],[0.219084491,0.010489590,0.042781149,0.010482415,0.000000000],[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 U15 - A45 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left for 4M4O|1|B|A|16 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 FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 4M4O|1|B|A|17 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 [4] | Right Index [10] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000078125000000000012233710187403301545271878291] | Num Left Bases [6] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [1.000000000000000] // Cluster node 4M4O|1|B|A|18:4M4O|1|B|G|23 and 4M4O|1|B|C|44:4M4O|1|B|C|44 Interaction | Interacting Bases [6,7] | 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]] // Cluster Interaction 4M4O|1|B|G|23 - 4M4O|1|B|C|44 cWW Interaction | Interacting Bases [1,5] | Pair Probability [[0.017039432,0.042106371,0.003564476,0.385573831,0.000000000],[0.016732762,0.038398828,0.014844312,0.041169008,0.000000000],[0.003564476,0.017668634,0.017060310,0.285531172,0.000000000],[0.040718855,0.034181906,0.017572000,0.024273627,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4M4O|1|B|A|18 - 4M4O|1|B|U|22 tWW Interaction | Interacting Bases [2,2] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4M4O|1|B|G|19 Interaction | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.300000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4M4O|1|B|A|20 Interaction | Interacting Bases [4,4] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4M4O|1|B|G|21 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 [10] | Right Index [9] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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_58960.1:
> IL_58960.1 4M4O U 15 A 45 UAAAGAGUG*CA > IL_58960.1 4M6D U 15 A 45 UAAAGAGUG*CA > IL_58960.1 4FRN A 6 U 76 AAAAGCAUG*CU