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This release consists of two modular Python scripts designed to identify and quantify clonotype-specific sequences based on motif matching: 1. Clonotype_analysis_code1.py This script filters sequences from a FASTQ file, retaining only those that contain both user-defined motifs—typically representing 5 bp reference sequences in the IGLJ and IGLV regions of interest. Filtered sequences are exported in FASTA format. 2. Clonotype_analysis_code2.py This script processes the filtered FASTA file, extracting sequences between the specified motifs and counting their frequencies. It outputs a tabulated summary in .csv format.