| 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 | 11 5 I | 12 5 5 | 13 4 I | 14 3 6 | 15 2 I | 16 2 7 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_55938.4_Instance_1 IL_55938.4_IL_4A1B_038_G894_C915 | G | A | U | A | U | U | C | |||||||||||||||
| IL_55938.4_Sequence_1 IL_55938.4_IL_4A1B_038_G894_C915 | G | A | U | A | * | U | U | C | true | 74 | 0 | 0 | 2.49 | |||||||||
| IL_55938.4_Instance_2 IL_55938.4_IL_3V2F_022_G738_C758 | G | G | U | G | C | U | C | |||||||||||||||
| IL_55938.4_Sequence_2 IL_55938.4_IL_3V2F_022_G738_C758 | G | G | U | G | * | C | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_55938.4_Instance_3 IL_55938.4_IL_4IOA_018_G751_C771 | G | G | U | G | C | U | C | |||||||||||||||
| IL_55938.4_Sequence_3 IL_55938.4_IL_4IOA_018_G751_C771 | G | G | U | G | * | C | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_55938.4_Instance_4 IL_55938.4_IL_1S72_029_G830_C851 | G | U | U | G | C | U | C | |||||||||||||||
| IL_55938.4_Sequence_4 IL_55938.4_IL_1S72_029_G830_C851 | G | U | U | G | * | C | U | C | true | 98 | 0 | 0 | 0.18 | |||||||||
| IL_55938.4_Instance_5 IL_55938.4_IL_3U5H_033_G869_C890 | G | G | U | U | A | U | C | |||||||||||||||
| IL_55938.4_Sequence_5 IL_55938.4_IL_3U5H_033_G869_C890 | G | G | U | U | * | A | U | C | true | 97 | 0 | 0 | 0.26 | |||||||||
| IL_55938.4_Instance_6 IL_55938.4_IL_3U5F_014_U259_A206 | U | U | U | U | C | G | U | A | ||||||||||||||
| IL_55938.4_Sequence_6 IL_55938.4_IL_3U5F_014_U259_A206 | U | U | U | U | C | * | G | U | A | true | 81 | 0 | 0 | 1.84 | ||||||||
| IL_55938.4_Instance_7 IL_55938.4_IL_1S72_082_G2524_C2496 | G | G | C | U | U | G | U | C | ||||||||||||||
| IL_55938.4_Sequence_7 IL_55938.4_IL_1S72_082_G_2524_C_2496 | G | G | C | U | U | * | G | U | C | true | 69 | 0 | 0 | 2.94 | ||||||||
| IL_55938.4_Instance_8 IL_55938.4_IL_3V2F_091_G2489_C2461 | G | G | U | U | U | A | U | C | ||||||||||||||
| IL_55938.4_Sequence_8 IL_55938.4_IL_3V2F_091_G_2489_C_2461 | G | G | U | U | U | * | A | U | C | true | 84 | 0 | 0 | 1.54 | ||||||||
| IL_55938.4_Instance_9 IL_55938.4_IL_4BPP_014_U256_A201 | U | G | A | U | C | G | U | A | ||||||||||||||
| IL_55938.4_Sequence_9 IL_55938.4_IL_4BPP_014_U256_A201 | U | G | A | U | C | * | G | U | A | true | 83 | 0 | 0 | 1.66 | ||||||||
| IL_55938.4_Instance_10 IL_55938.4_IL_3U5H_061_G1262_C1277 | G | A | G | U | G | C | U | C | ||||||||||||||
| IL_55938.4_Sequence_10 IL_55938.4_IL_3U5H_061_G_1262_C_1277 | G | A | G | U | G | * | C | U | C | true | 68 | 0 | 0 | 3.04 | ||||||||
| IL_55938.4_Instance_11 IL_55938.4_IL_4A1B_109_U2846_G2818 | U | U | U | U | U | G | U | G | ||||||||||||||
| IL_55938.4_Sequence_11 IL_55938.4_IL_4A1B_109_U_2846_G_2818 | U | U | U | U | U | * | G | U | G | true | 63 | 0 | 0 | 3.47 | ||||||||
| IL_55938.4_Instance_12 IL_55938.4_IL_3U5H_111_U2858_G2830 | U | U | U | U | U | G | U | G | ||||||||||||||
| IL_55938.4_Sequence_12 IL_55938.4_IL_3U5H_111_U_2858_G_2830 | U | U | U | U | U | * | G | U | G | true | 63 | 0 | 0 | 3.47 | ||||||||
| IL_55938.4_Instance_13 IL_55938.4_IL_1S72_003_C440_G41 | C | A | A | C | G | C | G | |||||||||||||||
| IL_55938.4_Sequence_13 IL_55938.4_IL_1S72_003_C440_G41 | C | A | A | C | * | G | C | G | true | 81 | 0 | 0 | 1.80 | |||||||||
| IL_55938.4_Instance_14 IL_55938.4_IL_2QBZ_004_C33_G151 | C | U | C | C | G | U | G | |||||||||||||||
| IL_55938.4_Sequence_14 IL_55938.4_IL_2QBZ_004_C33_G151 | C | U | C | C | * | G | U | G | true | 64 | 0 | 0 | 3.40 | |||||||||
| IL_55938.4_Instance_15 IL_55938.4_IL_3V2F_003_C433_G44 | C | U | C | C | G | A | G | |||||||||||||||
| IL_55938.4_Sequence_15 IL_55938.4_IL_3V2F_003_C433_G44 | C | U | C | C | * | G | A | G | true | 65 | 0 | 0 | 3.32 | |||||||||
| IL_55938.4_Instance_16 IL_55938.4_IL_3P49_006_C34_G53 | C | G | A | A | G | C | A | G | ||||||||||||||
| IL_55938.4_Sequence_16 IL_55938.4_IL_3P49_006_C34_G53 | C | G | A | A | G | * | C | A | G | true | 47 | 0 | 0 | 4.99 | ||||||||
| IL_55938.4_Instance_17 IL_55938.4_IL_3P49_009_C109_G144 | C | G | A | A | G | C | A | G | ||||||||||||||
| IL_55938.4_Sequence_17 IL_55938.4_IL_3P49_009_C109_G144 | C | G | A | A | G | * | C | A | G | true | 47 | 0 | 0 | 4.99 | ||||||||
| IL_55938.4_Instance_18 IL_55938.4_IL_1XJR_001_C9_G41 | C | C | G | A | G | C | A | G | ||||||||||||||
| IL_55938.4_Sequence_18 IL_55938.4_IL_1XJR_001_C9_G41 | C | C | G | A | G | * | C | A | G | true | 50 | 0 | 0 | 4.80 |
1 2 s35 1 7 cWW 2 3 cSH 3 4 s35 3 6 cWW 3 7 s55 4 5 cWW 4 6 s55 5 6 s35 6 7 s35JAR3D SCFG/MRF model for IL_55938.4:
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 [7] // Initial node G894 - C915 from junction BasepairNode | Deletion Probability [0.0000135111498549] | Pair Probability [[0.008932872,0.016290939,0.010331188,0.153396411,0.000000000],[0.045391698,0.008156512,0.215817026,0.011782149,0.000000000],[0.010352346,0.232691981,0.001990992,0.021205394,0.000000000],[0.171676602,0.011675089,0.070593401,0.009715400,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.886338815,0.113215093,0.000430710,0.000015382] | Left Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G894 - C915 cWW ClusterNode | Deletion Probability [0.0000000117080752] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [6] | Norm Constant [0.334293237869045] // Cluster node A895:U896 and U914:U914 Interaction | Interacting Bases [2,3] | Pair Probability [[0.058992769,0.156320290,0.012890526,0.031035873,0.000000000],[0.031742405,0.016837534,0.019466934,0.029412503,0.000000000],[0.012640957,0.019827790,0.004057590,0.041315015,0.000000000],[0.026061957,0.015427032,0.016516928,0.507453895,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U896 - U914 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.101544766,0.094028770,0.005043888,0.018571486,0.000000000],[0.103752614,0.100300448,0.001088231,0.101311333,0.000000000],[0.036651732,0.005055117,0.008908682,0.162632283,0.000000000],[0.014736849,0.109801903,0.001088231,0.135483665,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A895 - U896 cSH Insertion | Location [1] | Length Distribution [0.554488312,0.444143909,0.001306306,0.000061473] | Letter Distribution [0.350000000,0.150000000,0.150000000,0.350000000,0.000000000]// Insertion after nucleotide 2, position 1 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 [5] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009030986,0.016350867,0.010422527,0.155516523,0.000000000],[0.059754563,0.008559478,0.198415479,0.011808726,0.000000000],[0.010459788,0.215045531,0.002057107,0.020817135,0.000000000],[0.165266294,0.011623489,0.094677147,0.010194359,0.000000000],[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 [4] | Right Index [5] // Basepair A897 - U913 cWW HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | 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_55938.4:
> IL_55938.4 IL_4A1B_038 G 894 C 915 GAUA*UUC > IL_55938.4 IL_3V2F_022 G 738 C 758 GGUG*CUC > IL_55938.4 IL_4IOA_018 G 751 C 771 GGUG*CUC > IL_55938.4 IL_1S72_029 G 830 C 851 GUUG*CUC > IL_55938.4 IL_3U5H_033 G 869 C 890 GGUU*AUC > IL_55938.4 IL_3U5F_014 U 259 A 206 UUUUC*GUA > IL_55938.4 IL_1S72_082 G 2524 C 2496 GGCUU*GUC > IL_55938.4 IL_3V2F_091 G 2489 C 2461 GGUUU*AUC > IL_55938.4 IL_4BPP_014 U 256 A 201 UGAUC*GUA > IL_55938.4 IL_3U5H_061 G 1262 C 1277 GAGUG*CUC > IL_55938.4 IL_4A1B_109 U 2846 G 2818 UUUUU*GUG > IL_55938.4 IL_3U5H_111 U 2858 G 2830 UUUUU*GUG > IL_55938.4 IL_1S72_003 C 440 G 41 CAAC*GCG > IL_55938.4 IL_2QBZ_004 C 33 G 151 CUCC*GUG > IL_55938.4 IL_3V2F_003 C 433 G 44 CUCC*GAG > IL_55938.4 IL_3P49_006 C 34 G 53 CGAAG*CAG > IL_55938.4 IL_3P49_009 C 109 G 144 CGAAG*CAG > IL_55938.4 IL_1XJR_001 C 9 G 41 CCGAG*CAG