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| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | Adenine_Riboswitch_CMCT_adenine_1_to_CMCT_adenine_3_mean_cmct_mode | GGGGGCCUUCGGGCCAACGCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGUGUCGAUCCGGUUCGCCGGAUCCAAAUCGGGCUUCGGUCCGGUUC | G | G | G | G | G | C | C | U | U | C | G | G | G | C | C | A | A | C | G | C | U | U | C | A | U | A | U | A | A | U | C | C | U | A | A | U | G | A | U | A | U | G | G | U | U | U | G | G | G | A | G | U | U | U | C | U | A | C | C | A | A | G | A | G | C | C | U | U | A | A | A | C | U | C | U | U | G | A | U | U | A | U | G | A | A | G | U | G | U | C | G | A | U | C | C | G | G | U | U | C | G | C | C | G | G | A | U | C | C | A | A | A | U | C | G | G | G | C | U | U | C | G | G | U | C | C | G | G | U | U | C | |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | Adenine_Riboswitch_CMCT_adenine_1_to_CMCT_adenine_3_mean_cmct_mode | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | 0.23 | 0.09 | 0.05 | 0.10 | 0.12 | 0.03 | 0.06 | 0.06 | 0.04 | 0.10 | 0.05 | 0.05 | 0.09 | 0.50 | 0.05 | 0.05 | 0.01 | 0.01 | 0.04 | 0.06 | 0.07 | 0.09 | 0.10 | 0.11 | 0.02 | 0.11 | 0.26 | 1.00 | 0.22 | 0.04 | 0.05 | 0.02 | 0.03 | 0.01 | 0.02 | 0.02 | 0.09 | 0.13 | 0.64 | 1.00 | 0.84 | 0.09 | 1.00 | 0.03 | 0.00 | 0.00 | 0.02 | 0.05 | 0.04 | 0.01 | 0.01 | 0.02 | 0.13 | 1.00 | 1.00 | 0.26 | 0.06 | 0.00 | 0.00 | 0.01 | 0.02 | 0.01 | 0.01 | 0.03 | 0.04 | 0.31 | 0.27 | 0.04 | 0.04 | 0.04 | 0.01 | 0.00 | 0.00 | 0.02 | 0.01 | 0.04 | 0.02 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | -1.00 | ||
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | RNAstructure_Fold_CMCT | Adenine_Riboswitch_CMCT_adenine_1_to_CMCT_adenine_3_mean_cmct_mode | ...((((....)))).((((((((((...((((((.........))))))........((((((.......))))))..)))))))))).(((((((....)))))))..((((((((....)))))))). | . | . | . | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | User_provided_Secondary_Structure | ................((((((((((...((((((.........))))))........((((((.......))))))..)))))))))).......................................... | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | RNAfold | ...((((....)))).((((((((((...((((((.........))))))........((((((.......))))))..)))))))))).(((((((....)))))))..((((((((....)))))))). | . | . | . | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | RNAstructure_ProbKnot | ...((((....)))).((((((((((...(((((((......).))))))........((((((.......))))))..)))))))))).(((((((....)))))))..((((((((....)))))))). | . | . | . | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | ) | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | RNAstructure_Fold | ...((((....)))).((((((((((...((((((.........))))))........((((((.......))))))..)))))))))).(((((((....)))))))..((((((((....)))))))). | . | . | . | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | CentroidFold | ...((((....)))).((((((((((....(((((.........))))).........((((((.......))))))..)))))))))).(((((((....)))))))..((((((((....)))))))). | . | . | . | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | CONTRAfold | ...((((....)))).((((((((((..((((((((......).))))))((....))((((((.......)))))).))))))))))).(((((((....)))))))..((((((((....)))))))). | . | . | . | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | ) | . | ) | ) | ) | ) | ) | ) | ( | ( | . | . | . | . | ) | ) | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | IPknot | ...((((....)))).((((((((((....(((((.........))))).........((((((.......))))))..)))))))))).(((((((....)))))))..((((((((....)))))))). | . | . | . | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | Linearfold_C | ...((((....)))).((((((((((...((((((.........))))))........((((((.......))))))..)))))))))).(((((((....)))))))..((((((((....)))))))). | . | . | . | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | Linearfold_V | ...((((....)))).((((((((((...((((((.........))))))........((((((.......))))))..)))))))))).(((((((....)))))))..((((((((....)))))))). | . | . | . | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo9_Adenine_RIboswitch_no_ligand_CMCT_mode_uesr_provided_se_struct | Consensus_from_predictions | ...((((....)))).((((((((((...((((((.........))))))........((((((.......))))))..)))))))))).(((((((....)))))))..((((((((....)))))))). | . | . | . | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . |
CMCT reactivities mapped to the provided secondary structure
User-provided structure, mapping based on CMCT reactivities - radiate representation:
User-provided structure, mapping based on CMCT reactivities - circular representation:
User-provided structure, mapping based on CMCT reactivities - linear representation:
Secondary structure predictions
Fold predicted structure, based on CMCT reactivities:
Fold predicted structure, based on CMCT reactivities - radiate representation:
Fold predicted structure, based on CMCT reactivities - circular representation:
Fold predicted structure, based on CMCT reactivities - linear representation
Other secondary structure predictions methods and visualisations
Reactivity mapping to structures predicted by other methods are also ready to display or download. Secondary structure to display and copy to clipboard, links to external tools (SimRNAweb )
| method | radiate | circular | line | secondary structure | copy | SimRNAweb |
|---|---|---|---|---|---|---|
| RNAfold | display | | display | | display | | Predict 3D structure for this SS | ||
| ProbKnot | display | | display | | display | | Predict 3D structure for this SS | ||
| Fold | display | | display | | display | | Predict 3D structure for this SS | ||
| CentroidFold | display | | display | | display | | Predict 3D structure for this SS | ||
| CONTRAfold | display | | display | | display | | Predict 3D structure for this SS | ||
| IPknot | display | | display | | display | | Predict 3D structure for this SS | ||
| LinearFold_C | display | | display | | display | | Predict 3D structure for this SS | ||
| LinearFold_V | display | | display | | display | | Predict 3D structure for this SS | ||
| Consensus | display | | display | | display | | Predict 3D structure for this SS |
Tomasz K. Wirecki, Katarzyna Merdas, Agata Bernat, Michał J. Boniecki, Janusz M. Bujnicki, and Filip Stefaniak, RNAProbe - a web server for normalization and analysis of RNA structure probing data. Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W292–W299, https://doi.org/10.1093/nar/gkaa396
Analysis mode: cmct; outfilename core: Adenine_Riboswitch_CMCT_adenine_1_to_CMCT_adenine_3_mean_cmct_mode.