When an automatically transcribed file returns with misaligned text (i.e. your transcript is not lining up correctly with the corresponding audio), you can run realignment. This initiates a word alignment re-evaluation for parts of your script where the words are not lined up correctly to the underlying media. Here's how to do that:
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Select a range of script — by highlighting the text in the Script editor, or by using the Range tool in the Timeline.
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From the Timeline, right-click on the selected range.
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Select Realign words in range.
Manually correcting alignment
If you need to make any further corrections to the transcript alignment, you can manually adjust word boundaries with the wordbar.