This dataset contains the input sequences and the complete bioinformatic output files supporting the analysis of the Cannabis sativa Monoecy1 sex-determination locus reported in the associated manuscript. All analyses were performed on the Cannabis sativa cv. 'Pink Pepper' genome assembly GCA_029168945.1 (ASM2916894v1), chromosome X (RefSeq accession NC_083610.1), using the Dardel high-performance computing system at the PDC Center for High Performance Computing, KTH Royal Institute of Technology, Stockholm. The files document four lines of evidence used to evaluate the mechanism by which the long non-coding RNA lncREM16 (LOC133032448; transcript XR_009685085.1) silences the B3-domain transcription factor gene CsREM16 (LOC115699937; transcripts XM_030627485.2 and XM_030627490.2) within the Monoecy1 locus. Contents: Input sequences (FASTA): the 80 kb Monoecy1 genomic locus (Monoecy1_locus.fa; NC_083610.1:81,080,000-81,160,000), the two CsREM16 mRNA isoforms (CsREM16_X1.fa, CsREM16_X2.fa, CsREM16_both.fa), the lncREM16 transcript (lncREM16.fa), and the extracted 73 bp shared region from both the lncREM16 transcript and the genomic locus (shared_73bp.fa, shared_genomic.fa, both_shared.fa). Transposable element annotation (RepeatMasker v4.1.5, RMBLAST v2.14.0+, Dfam 3.7, viridiplantae): annotation tables, summary statistics, masked sequences, category files, and GFF output for both the 80 kb locus (Monoecy1_locus.fa.out, .tbl, .cat, .masked, .out.gff) and the lncREM16 transcript (lncREM16.fa.out, .tbl, .cat, .masked, .out.gff, .out.html). These files report the 33% TE content of the locus and the 37% TE content of the lncREM16 transcript, and identify the unclassified element DR2330744 at the CsREM16 exon 3 / intron 2 boundary. Sequence complementarity tests (NCBI blastn): antisense BLAST of lncREM16 against the CsREM16 mRNAs (lnc_vs_REM16_antisense.txt), against the genomic locus (lnc_vs_genomic_antisense.txt), the corresponding sense-strand orientation check (lnc_vs_genomic_sense.txt), the lncREM16 self-BLAST for inverted-repeat / hairpin detection (lnc_selfblast.txt), the alignment of the 73 bp shared region (shared_vs_lnc.txt, shared_vs_rem16.txt), and the BLAST of the 73 bp query against the NCBI nt database (blast_results.xml, blast_rid.txt). All antisense complementarity tests returned zero hits. Small RNA mapping (Bowtie v1): size-filtered small RNA reads (18-30 nt) derived from NCBI SRA run SRR25938888 (gerola_18_30.fastq.gz), and the alignment outputs in antisense and sense orientation against the CsREM16 mRNAs and the genomic locus (antisense_CsREM16.sam, sense_CsREM16.sam, antisense_monoecy1.sam, sense_monoecy1.sam) with their mapping statistics (antisense_stats.txt, sense_stats.txt, antisense_monoecy1_stats.txt, sense_monoecy1_stats.txt, overall_mapping_stats.txt, and the relaxed three-mismatch run antisense_v3.sam, antisense_v3_stats.txt). Gene records: NCBI gene-information records documenting the assembly, coordinates, and exon structure of CsREM16 and lncREM16 (rem16_gene_info.txt, lnc_gene_info.txt). Software versions and parameters are documented in the associated manuscript. The preprint / published article DOI will be added to this record under related identifiers upon availability.