| 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 4 4 | 9 4 I | 10 4 5 | 11 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 3 I | 16 3 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_59710.7_Instance_1 HL_59710.7_HL_4TUE_034_G31_C39 | G | C | U | C | A | U | A | A | C | |||||||||||||||
| HL_59710.7_Sequence_1 HL_59710.7_HL_4TUE_034_G31_C39 | G | C | U | C | A | U | A | A | C | true | 95 | 0 | 0 | 0.74 | ||||||||||
| HL_59710.7_Instance_2 HL_59710.7_HL_4V9Q_214_G31_C39 | G | C | U | C | A | U | A | A | C | |||||||||||||||
| HL_59710.7_Sequence_2 HL_59710.7_HL_4V9Q_214_G31_C39 | G | C | U | C | A | U | A | A | C | true | 95 | 0 | 0 | 0.74 | ||||||||||
| HL_59710.7_Instance_3 HL_59710.7_HL_4V50_137_G31_C39 | G | C | U | C | A | U | A | A | C | |||||||||||||||
| HL_59710.7_Sequence_3 HL_59710.7_HL_4V50_137_G31_C39 | G | C | U | C | A | U | A | A | C | true | 95 | 0 | 0 | 0.74 | ||||||||||
| HL_59710.7_Instance_4 HL_59710.7_HL_2AZX_005_A531_U539 | A | C | U | C | C | A | G | A | U | |||||||||||||||
| HL_59710.7_Sequence_4 HL_59710.7_HL_2AZX_005_A531_U539 | A | C | U | C | C | A | G | A | U | true | 87 | 0 | 0 | 1.96 | ||||||||||
| HL_59710.7_Instance_5 HL_59710.7_HL_2AZX_008_A531_U539 | A | C | U | C | C | A | G | A | U | |||||||||||||||
| HL_59710.7_Sequence_5 HL_59710.7_HL_2AZX_008_A531_U539 | A | C | U | C | C | A | G | A | U | true | 87 | 0 | 0 | 1.96 | ||||||||||
| HL_59710.7_Instance_6 HL_59710.7_HL_4WT8_216_G32_C40 | G | C | U | C | A | U | A | A | C | |||||||||||||||
| HL_59710.7_Sequence_6 HL_59710.7_HL_4WT8_216_G32_C40 | G | C | U | C | A | U | A | A | C | true | 95 | 0 | 0 | 0.74 | ||||||||||
| HL_59710.7_Instance_7 HL_59710.7_HL_6UFG_007_G32_C40 | G | C | U | G | A | U | A | A | C | |||||||||||||||
| HL_59710.7_Sequence_7 HL_59710.7_HL_6UFG_007_G32_C40 | G | C | U | G | A | U | A | A | C | true | 95 | 0 | 0 | 0.74 | ||||||||||
| HL_59710.7_Instance_8 HL_59710.7_HL_5IBB_210_C31_G39 | C | C | U | U | A | C | A | A | G | |||||||||||||||
| HL_59710.7_Sequence_8 HL_59710.7_HL_5IBB_210_C31_G39 | C | C | U | U | A | C | A | A | G | true | 82 | 0 | 0 | 2.69 | ||||||||||
| HL_59710.7_Instance_9 HL_59710.7_HL_6ORD_036_C31_G39 | C | U | U | G | G | C | A | A | G | |||||||||||||||
| HL_59710.7_Sequence_9 HL_59710.7_HL_6ORD_036_C31_G39 | C | U | U | G | G | C | A | A | G | true | 66 | 0 | 0 | 5.06 | ||||||||||
| HL_59710.7_Instance_10 HL_59710.7_HL_4P95_002_G241_C249 | G | C | U | A | A | U | C | A | C | |||||||||||||||
| HL_59710.7_Sequence_10 HL_59710.7_HL_4P95_002_G241_C249 | G | C | U | A | A | U | C | A | C | true | 67 | 0 | 0 | 4.87 | ||||||||||
| HL_59710.7_Instance_11 HL_59710.7_HL_4V9I_039_U31_A39 | U | C | U | C | G | A | A | A | A | |||||||||||||||
| HL_59710.7_Sequence_11 HL_59710.7_HL_4V9I_039_U31_A39 | U | C | U | C | G | A | A | A | A | true | 88 | 0 | 0 | 1.86 | ||||||||||
| HL_59710.7_Instance_12 HL_59710.7_HL_4R4V_001_C626_G634 | C | G | U | C | G | U | C | G | G | |||||||||||||||
| HL_59710.7_Sequence_12 HL_59710.7_HL_4R4V_001_C626_G634 | C | G | U | C | G | U | C | G | G | true | 55 | 0 | 0 | 6.78 | ||||||||||
| HL_59710.7_Instance_13 HL_59710.7_HL_4R4V_005_C626_G634 | C | G | U | C | G | U | C | G | G | |||||||||||||||
| HL_59710.7_Sequence_13 HL_59710.7_HL_4R4V_005_C626_G634 | C | G | U | C | G | U | C | G | G | true | 55 | 0 | 0 | 6.78 | ||||||||||
| HL_59710.7_Instance_14 HL_59710.7_HL_4V9K_034_A31_U39 | A | C | U | C | A | U | A | A | U | |||||||||||||||
| HL_59710.7_Sequence_14 HL_59710.7_HL_4V9K_034_A31_U39 | A | C | U | C | A | U | A | A | U | true | 97 | 0 | 0 | 0.45 | ||||||||||
| HL_59710.7_Instance_15 HL_59710.7_HL_4YCO_002_A31_U39 | A | U | U | G | A | A | A | A | U | |||||||||||||||
| HL_59710.7_Sequence_15 HL_59710.7_HL_4YCO_002_A31_U39 | A | U | U | G | A | A | A | A | U | true | 84 | 0 | 0 | 2.44 | ||||||||||
| HL_59710.7_Instance_16 HL_59710.7_HL_1U0B_002_A31_U39 | A | U | U | G | C | A | A | A | U | |||||||||||||||
| HL_59710.7_Sequence_16 HL_59710.7_HL_1U0B_002_A31_U39 | A | U | U | G | C | A | A | A | U | true | 79 | 0 | 0 | 3.16 | ||||||||||
| HL_59710.7_Instance_17 HL_59710.7_HL_3TUP_002_A31_U39 | A | C | U | G | A | A | A | A | U | |||||||||||||||
| HL_59710.7_Sequence_17 HL_59710.7_HL_3TUP_002_A31_U39 | A | C | U | G | A | A | A | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_59710.7_Instance_18 HL_59710.7_HL_1N78_002_C531_G539 | C | C | U | C | U | C | A | A | G | |||||||||||||||
| HL_59710.7_Sequence_18 HL_59710.7_HL_1N78_002_C531_G539 | C | C | U | C | U | C | A | A | G | true | 81 | 0 | 0 | 2.88 | ||||||||||
| HL_59710.7_Instance_19 HL_59710.7_HL_6UFM_002_G32_C40 | G | C | U | G | A | U | A | A | C | |||||||||||||||
| HL_59710.7_Sequence_19 HL_59710.7_HL_6UFM_002_G32_C40 | G | C | U | G | A | U | A | A | C | true | 95 | 0 | 0 | 0.74 | ||||||||||
| HL_59710.7_Instance_20 HL_59710.7_HL_3WFS_002_A31_U39 | A | C | U | G | A | A | A | A | U | |||||||||||||||
| HL_59710.7_Sequence_20 HL_59710.7_HL_3WFS_002_A31_U39 | A | C | U | G | A | A | A | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_59710.7_Instance_21 HL_59710.7_HL_4V90_033_A31_U39 | A | U | U | G | A | A | A | A | U | |||||||||||||||
| HL_59710.7_Sequence_21 HL_59710.7_HL_4V90_033_A31_U39 | A | U | U | G | A | A | A | A | U | true | 84 | 0 | 0 | 2.44 | ||||||||||
| HL_59710.7_Instance_22 HL_59710.7_HL_5T83_002_U56_A64 | U | U | U | C | A | C | A | A | A | |||||||||||||||
| HL_59710.7_Sequence_22 HL_59710.7_HL_5T83_002_U56_A64 | U | U | U | C | A | C | A | A | A | true | 74 | 0 | 0 | 3.87 | ||||||||||
| HL_59710.7_Instance_23 HL_59710.7_HL_3W3S_002_A31_U39 | A | C | U | U | C | A | A | A | U | |||||||||||||||
| HL_59710.7_Sequence_23 HL_59710.7_HL_3W3S_002_A31_U39 | A | C | U | U | C | A | A | A | U | true | 86 | 0 | 0 | 2.14 | ||||||||||
| HL_59710.7_Instance_24 HL_59710.7_HL_3W3S_006_A31_U39 | A | C | U | U | C | A | A | A | U | |||||||||||||||
| HL_59710.7_Sequence_24 HL_59710.7_HL_3W3S_006_A31_U39 | A | C | U | U | C | A | A | A | U | true | 86 | 0 | 0 | 2.14 | ||||||||||
| HL_59710.7_Instance_25 HL_59710.7_HL_2AKE_002_A31_U39 | A | C | U | C | C | A | G | A | U | |||||||||||||||
| HL_59710.7_Sequence_25 HL_59710.7_HL_2AKE_002_A31_U39 | A | C | U | C | C | A | G | A | U | true | 87 | 0 | 0 | 1.96 | ||||||||||
| HL_59710.7_Instance_26 HL_59710.7_HL_2AKE_005_A31_U39 | A | C | U | C | C | A | G | A | U | |||||||||||||||
| HL_59710.7_Sequence_26 HL_59710.7_HL_2AKE_005_A31_U39 | A | C | U | C | C | A | G | A | U | true | 87 | 0 | 0 | 1.96 | ||||||||||
| HL_59710.7_Instance_27 HL_59710.7_HL_2IY5_002_A31_U39 | A | C | U | G | A | A | A | A | U | |||||||||||||||
| HL_59710.7_Sequence_27 HL_59710.7_HL_2IY5_002_A31_U39 | A | C | U | G | A | A | A | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_59710.7_Instance_28 HL_59710.7_HL_2IY5_005_A31_U39 | A | C | U | G | A | A | A | A | U | |||||||||||||||
| HL_59710.7_Sequence_28 HL_59710.7_HL_2IY5_005_A31_U39 | A | C | U | G | A | A | A | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_59710.7_Instance_29 HL_59710.7_HL_4P5J_002_C25_G33 | C | U | C | G | A | C | A | C | G | |||||||||||||||
| HL_59710.7_Sequence_29 HL_59710.7_HL_4P5J_002_C25_G33 | C | U | C | G | A | C | A | C | G | true | 44 | 0 | 0 | 8.36 | ||||||||||
| HL_59710.7_Instance_30 HL_59710.7_HL_7KGA_001_U22_G31 | U | C | A | A | G | C | C | U | A | G | ||||||||||||||
| HL_59710.7_Sequence_30 HL_59710.7_HL_7KGA_001_U22_G31 | U | C | A | A | G | C | C | U | A | G | true | 7 | 0 | 0 | 13.84 | |||||||||
| HL_59710.7_Instance_31 HL_59710.7_HL_1J1U_002_A532_U540 | A | C | U | G | U | A | G | A | U | |||||||||||||||
| HL_59710.7_Sequence_31 HL_59710.7_HL_1J1U_002_A532_U540 | A | C | U | G | U | A | G | A | U | true | 81 | 0 | 0 | 2.85 | ||||||||||
| HL_59710.7_Instance_32 HL_59710.7_HL_1J1U_005_A532_U540 | A | C | U | G | U | A | G | A | U | |||||||||||||||
| HL_59710.7_Sequence_32 HL_59710.7_HL_1J1U_005_A532_U540 | A | C | U | G | U | A | G | A | U | true | 81 | 0 | 0 | 2.85 |
1 2 s35 1 9 cWW 2 3 s35 2 8 bif 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 3 6 6BPhJAR3D SCFG/MRF model for HL_59710.7:
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 [9] // Initial node G31 - C39 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.007321517,0.015593468,0.008115979,0.273288254,0.000000000],[0.020966448,0.007871885,0.195605409,0.009166410,0.000000000],[0.008114035,0.204048003,0.001623127,0.029951416,0.000000000],[0.165611877,0.009372059,0.034868952,0.008481159,0.000000000],[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 [1] | Right Index [9] // Basepair G31 - C39 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.020608131,0.023150601,0.005028382,0.005028382,0.000000000],[0.703315889,0.058889179,0.005028382,0.005028382,0.000000000],[0.005028382,0.005028382,0.043715289,0.032191143,0.000000000],[0.061566671,0.016336040,0.005028382,0.005028382,0.000000000],[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 [2] | Right Index [8] // Basepair C32 - A38 bif HairpinNode | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [0.999999999999999] // Hairpin node U33:A37 Interaction | Interacting Bases [1,1] | Pair Probability [[0.033185841,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.033185841,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.002212389,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.931415929,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U33 Interaction | Interacting Bases [2,2] | Pair Probability [[0.044117647,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.426470588,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.426470588,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.102941176,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C34 Interaction | Interacting Bases [3,3] | Pair Probability [[0.514705882,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.132352941,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.102941176,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35 Interaction | Interacting Bases [4,4] | Pair Probability [[0.485294118,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.191176471,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.014705882,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.308823529,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U36 Interaction | Interacting Bases [5,5] | Pair Probability [[0.661764706,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.102941176,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.191176471,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.044117647,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A37 Insertion | Location [1] | Length Distribution [0.967164848,0.032708413,0.000124302,0.000002437] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1Sequences of instances from HL_59710.7:
> HL_59710.7 HL_4TUE_034 G 31 C 39 GCUCAUAAC > HL_59710.7 HL_4V9Q_214 G 31 C 39 GCUCAUAAC > HL_59710.7 HL_4V50_137 G 31 C 39 GCUCAUAAC > HL_59710.7 HL_2AZX_005 A 531 U 539 ACUCCAGAU > HL_59710.7 HL_2AZX_008 A 531 U 539 ACUCCAGAU > HL_59710.7 HL_4WT8_216 G 32 C 40 GCUCAUAAC > HL_59710.7 HL_6UFG_007 G 32 C 40 GCUGAUAAC > HL_59710.7 HL_5IBB_210 C 31 G 39 CCUUACAAG > HL_59710.7 HL_6ORD_036 C 31 G 39 CUUGGCAAG > HL_59710.7 HL_4P95_002 G 241 C 249 GCUAAUCAC > HL_59710.7 HL_4V9I_039 U 31 A 39 UCUCGAAAA > HL_59710.7 HL_4R4V_001 C 626 G 634 CGUCGUCGG > HL_59710.7 HL_4R4V_005 C 626 G 634 CGUCGUCGG > HL_59710.7 HL_4V9K_034 A 31 U 39 ACUCAUAAU > HL_59710.7 HL_4YCO_002 A 31 U 39 AUUGAAAAU > HL_59710.7 HL_1U0B_002 A 31 U 39 AUUGCAAAU > HL_59710.7 HL_3TUP_002 A 31 U 39 ACUGAAAAU > HL_59710.7 HL_1N78_002 C 531 G 539 CCUCUCAAG > HL_59710.7 HL_6UFM_002 G 32 C 40 GCUGAUAAC > HL_59710.7 HL_3WFS_002 A 31 U 39 ACUGAAAAU > HL_59710.7 HL_4V90_033 A 31 U 39 AUUGAAAAU > HL_59710.7 HL_5T83_002 U 56 A 64 UUUCACAAA > HL_59710.7 HL_3W3S_002 A 31 U 39 ACUUCAAAU > HL_59710.7 HL_3W3S_006 A 31 U 39 ACUUCAAAU > HL_59710.7 HL_2AKE_002 A 31 U 39 ACUCCAGAU > HL_59710.7 HL_2AKE_005 A 31 U 39 ACUCCAGAU > HL_59710.7 HL_2IY5_002 A 31 U 39 ACUGAAAAU > HL_59710.7 HL_2IY5_005 A 31 U 39 ACUGAAAAU > HL_59710.7 HL_4P5J_002 C 25 G 33 CUCGACACG > HL_59710.7 HL_7KGA_001 U 22 G 31 UCAAGCCUAG > HL_59710.7 HL_1J1U_002 A 532 U 540 ACUGUAGAU > HL_59710.7 HL_1J1U_005 A 532 U 540 ACUGUAGAU