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align 230-ribonucleotide fragment 100 times

Dear all, I have to align 230-ribonucleotide fragment many times (100) to a single reference. Unfortunately there are 80 symbols in any single line. What tool may I use to do it? Is it possible to make it nice somehow? There was a post about that a long time ago, but I lost its number. Thank you very much! Natalia

alignment tool a long nucleotide fragment

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