import { ISeqSplitted } from './types';
export type AlignmentOptions = {
    gapPenalty: number;
    matchScore: number;
    gapSymbol: string;
    localAlignment: boolean;
};
export declare const defaultAlignmentOptions: AlignmentOptions;
export declare function alignSequencePair(template: ISeqSplitted, seq: ISeqSplitted, alignmentOptions?: Partial<AlignmentOptions>): {
    seq1: string;
    seq2: string;
    seq1Splitted: ISeqSplitted;
    seq2Splitted: ISeqSplitted;
};
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