| 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 3 3 | 7 4 I | 8 5 4 | 9 5 I | 10 6 5 | 11 6 I | 12 7 | 13 6 I | 14 6 6 | 15 5 I | 16 5 7 | 17 4 I | 18 3 8 | 19 3 I | 20 3 9 | 21 2 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_39585.1_Instance_1 IL_39585.1_IL_3V2F_098_U2636_G2782 | U | U | G | A | G | C | A | A | G | A | UGA | G | ||||||||||||||||
| IL_39585.1_Sequence_1 IL_39585.1_IL_3V2F_098_U_2636_G_2782 | U | U | G | A | G | * | C | A | A | G | A | UGA | G | true | 73 | 0 | 0 | 3.40 | ||||||||||
| IL_39585.1_Instance_2 IL_39585.1_IL_4IOA_095_U2615_G2762 | U | U | G | A | G | C | A | A | G | A | UGA | G | ||||||||||||||||
| IL_39585.1_Sequence_2 IL_39585.1_IL_4IOA_095_U_2615_G_2762 | U | U | G | A | G | * | C | A | A | G | A | UGA | G | true | 73 | 0 | 0 | 3.40 | ||||||||||
| IL_39585.1_Instance_3 IL_39585.1_IL_1S72_089_C2672_G2817 | C | U | G | A | C | G | G | A | A | A | AGA | G | ||||||||||||||||
| IL_39585.1_Sequence_3 IL_39585.1_IL_1S72_089_C_2672_G_2817 | C | U | G | A | C | * | G | G | A | A | A | AGA | G | true | 67 | 0 | 0 | 4.14 | ||||||||||
| IL_39585.1_Instance_4 IL_39585.1_IL_3V2F_071_U1851_G1891 | U | C | A | A | G | C | G | A | A | G | ||||||||||||||||||
| IL_39585.1_Sequence_4 IL_39585.1_IL_3V2F_071_U_1851_G_1891 | U | C | A | A | G | * | C | G | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_39585.1_Instance_5 IL_39585.1_IL_4IOA_069_U1843_G1874 | U | C | A | A | G | U | G | A | A | G | ||||||||||||||||||
| IL_39585.1_Sequence_5 IL_39585.1_IL_4IOA_069_U_1843_G_1874 | U | C | A | A | G | * | U | G | A | A | G | true | 93 | 0 | 0 | 0.92 | ||||||||||||
| IL_39585.1_Instance_6 IL_39585.1_IL_4IOA_050_C1389_G1368 | C | G | A | U | G | C | U | A | A | G | ||||||||||||||||||
| IL_39585.1_Sequence_6 IL_39585.1_IL_4IOA_050_C_1389_G_1368 | C | G | A | U | G | * | C | U | A | A | G | true | 67 | 0 | 0 | 4.14 |
1 2 s35 1 10 cWW 2 3 s35 2 8 tWH 2 9 tSH 2 10 s55 3 4 s35 3 7 s33 3 8 s55 3 9 tSH 4 5 s35 4 7 tHS 4 9 s55 5 6 cWW 5 7 s55 6 7 s35 8 9 s53 8 10 s35 9 10 s35 4 7 6BRJAR3D SCFG/MRF model for IL_39585.1:
Character Definition | A,C,G,U,* // Define characters here InitialNode | 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 [1] | Right Index [10] // Initial node U2636 - G2782 from junction BasepairNode | Deletion Probability [0.0000000082449969] | Pair Probability [[0.011568670,0.015004905,0.013717942,0.086563999,0.000000000],[0.210007908,0.013051939,0.116859137,0.015670913,0.000000000],[0.013991452,0.091895298,0.002952919,0.017566300,0.000000000],[0.091345969,0.014368361,0.272912695,0.012521592,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493624023,0.004113534,0.004319210,0.493624023,0.004113534,0.000205677] | Right Letter Distribution [0.409090909,0.045454545,0.318181818,0.227272727,0.000000000] | Left Index [1] | Right Index [10] // Basepair U2636 - G2782 cWW ClusterNode | Deletion Probability [0.0000000000425867] | Num Left Bases [2] | Num Right Bases [2] | Left Index [2] | Right Index [9] | Norm Constant [0.135108635236567] // Cluster node U2637:G2638 and A2776:A2778 Interaction | Interacting Bases [1,3] | Pair Probability [[0.022193440,0.004032174,0.068294143,0.004032174,0.000000000],[0.144395317,0.030088333,0.108454026,0.004032174,0.000000000],[0.031964102,0.004032174,0.042564995,0.024183430,0.000000000],[0.346043401,0.004032174,0.042578165,0.119079776,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2637 - A2776 tWH Interaction | Interacting Bases [1,4] | Pair Probability [[0.118423907,0.109714818,0.001277960,0.007504879,0.000000000],[0.140269246,0.096413576,0.001277960,0.001277960,0.000000000],[0.122838246,0.001277960,0.008044388,0.043009991,0.000000000],[0.232162706,0.113950484,0.001277960,0.001277960,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2637 - A2778 tSH Interaction | Interacting Bases [2,4] | Pair Probability [[0.211954656,0.114102715,0.001179443,0.005616359,0.000000000],[0.098760399,0.103515300,0.001179443,0.001179443,0.000000000],[0.146246221,0.001179443,0.005714155,0.098106004,0.000000000],[0.106402395,0.102505136,0.001179443,0.001179443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2638 - A2778 tSH Insertion | Location [3] | Length Distribution [0.497737557,0.497737557,0.004319210,0.000205677] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000]// Insertion after nucleotide 8, position 3 in cluster node InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.143107073,0.122479494,0.173101272,0.122989924,0.000000000],[0.118256878,0.083202990,0.001347441,0.118428795,0.000000000],[0.001347441,0.001347441,0.009331305,0.001347441,0.000000000],[0.008716688,0.001347441,0.060405157,0.033243218,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair A2639 - A2775 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010795257,0.065846457,0.011939594,0.162136419,0.000000000],[0.016688363,0.008619217,0.183721697,0.013216907,0.000000000],[0.011812838,0.216159781,0.002277618,0.086324791,0.000000000],[0.160516374,0.013801104,0.022111314,0.014032271,0.000000000],[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 [5] | Right Index [6] // Basepair G2640 - C2774 cWW HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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_39585.1:
> IL_39585.1 IL_3V2F_098 U 2636 G 2782 UUGAG*CAAGAUGAG > IL_39585.1 IL_4IOA_095 U 2615 G 2762 UUGAG*CAAGAUGAG > IL_39585.1 IL_1S72_089 C 2672 G 2817 CUGAC*GGAAAAGAG > IL_39585.1 IL_3V2F_071 U 1851 G 1891 UCAAG*CGAAG > IL_39585.1 IL_4IOA_069 U 1843 G 1874 UCAAG*UGAAG > IL_39585.1 IL_4IOA_050 C 1389 G 1368 CGAUG*CUAAG