├── COPYING ├── COPYRIGHT ├── CRISPRCasFinder.patch ├── CRISPRCasFinder.pl ├── CRISPRCasFinder_Viewer_manual.pdf ├── CasFinder-2.0.3 ├── CASprofiles-2.0.3 │ ├── Cas10_0_III.hmm │ ├── Cas10_0_IIIA.hmm │ ├── Cas10_0_IIIB.hmm │ ├── Cas10_0_IIIC.hmm │ ├── Cas10_1_IIIB.hmm │ ├── Cas10d_0_ID.hmm │ ├── Cas12a_0_VA.hmm │ ├── Cas12a_1_VA.hmm │ ├── Cas12b_0_VB.hmm │ ├── Cas12c_0_VC.hmm │ ├── Cas13a_0_VIA.hmm │ ├── Cas13b_0_VIB1.hmm │ ├── Cas13b_1_VIB2.hmm │ ├── Cas13c_0_VIC.hmm │ ├── Cas1_0_I-II-III-V.hmm │ ├── Cas1_0_I-II-III.hmm │ ├── Cas1_0_IA.hmm │ ├── Cas1_0_IC.hmm │ ├── Cas1_0_IE.hmm │ ├── Cas1_0_IF.hmm │ ├── Cas1_0_II.hmm │ ├── Cas1_0_V.hmm │ ├── Cas2_0_I-II-III-V.hmm │ ├── Cas2_0_I-II-III.hmm │ ├── Cas2_0_IE.hmm │ ├── Cas3-Cas2_0_IF.hmm │ ├── Cas3_0_I.hmm │ ├── Cas3_0_ID.hmm │ ├── Cas3_0_IU.hmm │ ├── Cas3_1_I.hmm │ ├── Cas4_0_I-II-V.hmm │ ├── Cas4_0_I-II.hmm │ ├── Cas4_0_IA.hmm │ ├── Cas4_0_V.hmm │ ├── Cas5_0_I.hmm │ ├── Cas5_0_IA.hmm │ ├── Cas5_0_IB.hmm │ ├── Cas5_0_IC.hmm │ ├── Cas5_0_IE.hmm │ ├── Cas5_1_IB.hmm │ ├── Cas5_1_IC.hmm │ ├── Cas6_0_I-III.hmm │ ├── Cas6_0_IA.hmm │ ├── Cas6_0_IE.hmm │ ├── Cas6_0_IF.hmm │ ├── Cas7_0_I.hmm │ ├── Cas7_0_IA.hmm │ ├── Cas7_0_IC.hmm │ ├── Cas7_0_IE.hmm │ ├── Cas7_1_IB.hmm │ ├── Cas7_1_IC.hmm │ ├── Cas7_2_IB.hmm │ ├── Cas7_3_IB.hmm │ ├── Cas8a1_0_IA.hmm │ ├── Cas8a1_0_IB.hmm │ ├── Cas8a1_1_IA.hmm │ ├── Cas8a1_1_IB.hmm │ ├── Cas8a1_2_IB.hmm │ ├── Cas8b_0_IB.hmm │ ├── Cas8c_0_IC.hmm │ ├── Cas8c_1_IC.hmm │ ├── Cas9_0_II.hmm │ ├── Cas9_0_IIB.hmm │ ├── Cas9_1_II.hmm │ ├── Cas9_1_IIB.hmm │ ├── Cas9_2_II.hmm │ ├── Cmr1_0_IIIB.hmm │ ├── Cmr1_0_IIIC.hmm │ ├── Cmr3_0_IIIB.hmm │ ├── Cmr3_0_IIIC.hmm │ ├── Cmr3_1_IIIB.hmm │ ├── Cmr4_0_IIIB.hmm │ ├── Cmr4_1_IIIB.hmm │ ├── Cmr5_0_IIIB.hmm │ ├── Cmr5_0_IIIC.hmm │ ├── Cmr5_1_IIIB.hmm │ ├── Cmr5_1_IIIC.hmm │ ├── Cmr6_0_IIIB.hmm │ ├── Cmr6_0_IIIC.hmm │ ├── Cmr6_1_IIIB.hmm │ ├── Cmr7_0_IIIB.hmm │ ├── Cmr8_0_IIIB.hmm │ ├── Csa5_0_IA.hmm │ ├── CsaX_0_IA.hmm │ ├── Csb1_0_IU.hmm │ ├── Csb2_0_IU.hmm │ ├── Csb3_0_IU.hmm │ ├── Csc1_0_ID.hmm │ ├── Csc2_0_ID.hmm │ ├── Cse1_0_IE.hmm │ ├── Cse2_0_IE.hmm │ ├── Csf1_0_IV.hmm │ ├── Csf1_1_IV.hmm │ ├── Csf2_0_IV.hmm │ ├── Csf2_1_IV.hmm │ ├── Csf3_0_IV.hmm │ ├── Csf3_1_IV.hmm │ ├── Csf4_0_IV.hmm │ ├── Csf4_1_IV.hmm │ ├── Csf5_0_IV.hmm │ ├── Csm2_0_IIIA.hmm │ ├── Csm2_0_IIID.hmm │ ├── Csm2_1_IIIA.hmm │ ├── Csm3_0_IIIA.hmm │ ├── Csm3_0_IIIAD.hmm │ ├── Csm3_0_IIID.hmm │ ├── Csm3_1_IIIAD.hmm │ ├── Csm3_1_IIID.hmm │ ├── Csm4_0_IIIA.hmm │ ├── Csm4_1_IIIA.hmm │ ├── Csm5_0_IIIA.hmm │ ├── Csm5_1_IIIA.hmm │ ├── Csm6_0_IIIA.hmm │ ├── Csn2_0_IIA.hmm │ ├── Csx10_0_IIID.hmm │ ├── Csx10_1_IIID.hmm │ ├── Csx17_0_IU.hmm │ ├── Csx19_0_IIID.hmm │ ├── Csy1_0_IF.hmm │ ├── Csy2_0_IF.hmm │ └── Csy3_0_IF.hmm ├── DEF-Class-2.0.3 │ ├── General-Class1.xml │ └── General-Class2.xml ├── DEF-SubTyping-2.0.3 │ ├── CAS-TypeIA.xml │ ├── CAS-TypeIB.xml │ ├── CAS-TypeIC.xml │ ├── CAS-TypeID.xml │ ├── CAS-TypeIE.xml │ ├── CAS-TypeIF.xml │ ├── CAS-TypeIIA.xml │ ├── CAS-TypeIIB.xml │ ├── CAS-TypeIIC.xml │ ├── CAS-TypeIIIA.xml │ ├── CAS-TypeIIIB.xml │ ├── CAS-TypeIIIC.xml │ ├── CAS-TypeIIID.xml │ ├── CAS-TypeIU.xml │ ├── CAS-TypeIV.xml │ ├── CAS-TypeVA.xml │ ├── CAS-TypeVB.xml │ ├── CAS-TypeVC.xml │ ├── CAS-TypeVIA.xml │ ├── CAS-TypeVIB1.xml │ ├── CAS-TypeVIB2.xml │ ├── CAS-TypeVIC.xml │ └── CAS.xml └── DEF-Typing-2.0.3 │ ├── CAS-TypeI.xml │ ├── CAS-TypeII.xml │ ├── CAS-TypeIII.xml │ ├── CAS-TypeIV.xml │ ├── CAS-TypeV.xml │ ├── CAS-TypeVI.xml │ └── CAS.xml ├── NEWS.txt ├── README.md ├── ccf.environment.yml ├── crispr-cas_logo.png ├── install_test ├── Cas_REPORT.tsv ├── Crisprs_REPORT.tsv └── sequence.fasta ├── installer_CENTOS.sh ├── installer_FEDORA.sh ├── installer_MAC.sh ├── installer_README.txt ├── installer_UBUNTU.sh ├── sel392v2.so ├── singularity ├── CRISPRCasFinder.singularity.patch ├── Singularity └── Singularity.4.2.18 ├── supplementary_files ├── CRISPR_crisprdb.csv ├── Repeat_List.csv ├── crispr.css └── repeatDirection.tsv └── 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