Trimming an alignment around a given sequence

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Hello, I have a simple question but actually I have troubles finding how to solve it. I have many alignment files. And I want for each of them get rid in the alignment of overhang bases. The twist is that I want this done relatively to a specific sequence, which is always the first of the alignment and is always named "Scaffoldxxxx" (where x are numbers and others). Here is a pic

what needs to be cropped is in the red squares

As you see, I want to trim everything that is upstream and downstream of the start and end of the first sequence. That's easy in a sequence editor such as Jalview. But as I have thousands of alignments, I need to automate it. Surprisingly I don't even know where to start.

Many thanks for any help or insight.


pairwise


script


crop


alignment

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