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1 A·Program·to·find·Maximal·Matches1 A·Program·to·find·Maximal·Matches
2 in·Large·Sequences2 in·Large·Sequences
3 Manual∗3 Manual∗
4 Stefan·Kurtz†‡4 Stefan·Kurtz†‡
5 August·15,·20215 July·14,·2020
  
6 maxmat3·is·a·program·to·find·maximal·matches·of·some·minimum·length·between·a6 maxmat3·is·a·program·to·find·maximal·matches·of·some·minimum·length·between·a
7 reference-sequence·and·a·query-sequence.·It·also·allows·for·the·computation·of·MUMcandidates·as·well·as·MUMs.·This·document·describes·the·options·of·maxmat3·and7 reference-sequence·and·a·query-sequence.·It·also·allows·for·the·computation·of·MUMcandidates·as·well·as·MUMs.·This·document·describes·the·options·of·maxmat3·and
8 the·output·format.·In·Section·3,·we·formally·define·some·basic·notions·to·clarify8 the·output·format.·In·Section·3,·we·formally·define·some·basic·notions·to·clarify
9 the·semantics·of·maxmat3.·However,·the·reader·should·be·able·to·understand·the9 the·semantics·of·maxmat3.·However,·the·reader·should·be·able·to·understand·the
10 manual·without·reading·that·section.·In·the·following,·the·notion·match·always·refers10 manual·without·reading·that·section.·In·the·following,·the·notion·match·always·refers
11 to·maximal·matches·if·not·stated·otherwise.11 to·maximal·matches·if·not·stated·otherwise.
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