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The intent of this work is to better understand influenza from an RNA-centric perspective to provide local, structural motifs with likely significance to the influenza infectious cycle for therapeutic targeting. To accomplish this, we analyzed over four hundred thousand RNA sequences spanning three major clades: influenza A, B and C. We scanned influenza segments for local secondary structure, identified\/modeled motifs of likely functionality, and coupled the results to an analysis of evolutionary conservation. We discovered 185 significant regions of predicted ordered stability, yet evidence of sequence covariation was limited to 7 motifs, where 3\u2014found in influenza C\u2014had higher than expected amounts of sequence covariation.<\/jats:p>","DOI":"10.1038\/s41598-021-03767-x","type":"journal-article","created":{"date-parts":[[2022,1,10]],"date-time":"2022-01-10T11:02:59Z","timestamp":1641812579000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["In silico analysis of local RNA secondary structure in influenza virus A, B and C finds evidence of widespread ordered stability but little evidence of significant covariation"],"prefix":"10.1038","volume":"12","author":[{"given":"Jake M.","family":"Peterson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Collin A.","family":"O\u2019Leary","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walter N.","family":"Moss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,1,10]]},"reference":[{"key":"3767_CR1","doi-asserted-by":"publisher","first-page":"531","DOI":"10.3389\/fimmu.2019.00531","volume":"10","author":"A Pizzorno","year":"2019","unstructured":"Pizzorno, A. et al. 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