Muscle MSA program
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It is normal. No regular alignment program is meant for sequences that are 30000 long. They usually deal better with large number of relatively short sequences, and the only way to accommodate long sequences is usually if they are >95% identical.
If your sequences are highly identical, you may have luck with this option. Also see these tips. Searching Biostars may uncover other clues as well.
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Mensur Dlakic
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Thank you for these info.