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### MinCED CRISPR Array Detection (`minced-crispr`) Detects CRISPR arrays in one or more nucleotide sequences. Returns, per input sequence, a list of `CrisprArray` objects; each carries an ordered list of `CrisprRepeatSpacer` units with the repeat's start position, the repeat sequence, and the following spacer (the last unit has no spacer). #### API Reference

Source Nucleotide sequence(s) to search for CRISPR arrays. Labeled positionally (`seq_0`, `seq_1`, ...); results are returned in input order.

Source Minimum repeats per array. Default 3. Minimum repeat length in nt. Default 23. Maximum repeat length in nt. Default 47. Must be ≥ `min_repeat_length`. Minimum spacer length in nt. Default 26. Maximum spacer length in nt. Default 50. Must be ≥ `min_spacer_length`. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source Per-sequence CRISPR detection results. ID of the input sequence CRISPR arrays detected in this sequence

#### Applications Use this to confirm and catalog CRISPR loci across newly sequenced bacterial and archaeal genomes, or to mine spacer libraries from metagenomic assemblies for phage-host interaction studies. As a pre-filter, run `minced-crispr` first to verify that a candidate contig actually carries a CRISPR array before spending compute on downstream Cas and tracrRNA analysis with [`pyhmmer-hmmsearch`](https://bio-pro.mintlify.app/tools/gene-annotation/pyhmmer) for Cas effector domains and [`crispr-tracr-rna`](https://bio-pro.mintlify.app/tools/gene-annotation/crispr-tracr-rna) for tracrRNA on the same locus. The spacer set returned for each array can then be aligned against phage or plasmid sequence databases to reconstruct the host's immune history. #### Usage Tips * **`min_num_repeats` controls the sensitivity-versus-specificity trade-off.** The default of 3 balances both for typical bacterial and archaeal genomes. Lower it to 2 to catch partial or degraded arrays at the cost of more false positives, and raise it to 4 or more when only high-confidence arrays should pass through. * **The 23 to 47 nt repeat and 26 to 50 nt spacer windows match canonical CRISPR loci.** Widen `max_repeat_length` and `max_spacer_length` to detect atypical families such as Type IV-A or CRISPR systems with unusually long spacers, and lower `min_repeat_length` only when chasing partial repeats since values below 23 nt start to pick up generic tandem repeats. * **MinCED only locates the array; it does not identify Cas genes or classify the CRISPR system.** Type assignment requires downstream Cas-effector annotation, typically `pyhmmer-hmmsearch` against curated Cas HMMs or a dedicated classifier such as CRISPRcasIdentifier. * **Inverted length ranges are caught at config time.** Setting `max_repeat_length < min_repeat_length` or `max_spacer_length < min_spacer_length` raises `ValueError` before the run starts, so the call fails fast instead of completing with an empty result set. * **Spacer count is not an immunity-breadth metric.** Multiple spacers in an array can target the same phage, and many spacers are degraded remnants of historical encounters, so the number of spacers overestimates how many distinct threats the host can recognize today.