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Overview of predicted results

Overview of the results

Contig_ID Contig_def CRISPR array number Contig Signature genes Self targeting spacer number Target MGE spacer number Prophage number Anti-CRISPR protein number
CP034061 Shigella flexneri strain FDAARGOS_535 plasmid unnamed2 0 crisprs NA 0 0 0 0
CP034063 Shigella flexneri strain FDAARGOS_535 plasmid unnamed4 0 crisprs NA 0 0 0 0
CP034059 Shigella flexneri strain FDAARGOS_535 plasmid unnamed1, complete sequence 0 crisprs RT 0 0 2 0
CP034062 Shigella flexneri strain FDAARGOS_535 plasmid unnamed3, complete sequence 0 crisprs NA 0 0 0 0
CP034065 Shigella flexneri strain FDAARGOS_535 plasmid unnamed6 0 crisprs NA 0 0 0 0
CP034060 Shigella flexneri strain FDAARGOS_535 chromosome, complete genome 6 crisprs csa3,cas3,DEDDh,c2c9_V-U4,DinG,RT,PrimPol 0 2 20 0
CP034064 Shigella flexneri strain FDAARGOS_535 plasmid unnamed5 0 crisprs NA 0 0 0 0

Results visualization

1. CP034060
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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP034060_1 972453-972554 Orphan NA
1 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP034060_2 1075920-1076085 Orphan NA
1 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP034060_3 1808830-1808947 Orphan NA
1 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP034060_4 2442642-2442765 Unclear NA
1 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP034060_5 3347625-3347773 Orphan I-F
2 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP034060_6 4141690-4141805 Orphan NA
1 spacers

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CRISPR_ID Spacer_Info Spacer_region Spacer_length Hit_ID Protospacer_location Mismatch Identity
CRISPR_ID Spacer_Info Spacer_region Spacer_length Hit_phage_ID Hit_phage_def Protospacer_location Mismatch Identity
CP034060_6 6.1|4141721|54|CP034060|CRISPRCasFinder 4141721-4141774 54 NZ_AP023206 Escherichia coli strain TUM18781 plasmid pMTY18781-1_lncX3, complete sequence 165411-165464 1 0.981
CP034060_4 4.1|2442685|38|CP034060|CRISPRCasFinder 2442685-2442722 38 NZ_CP043437 Enterobacter sp. LU1 plasmid unnamed 113727-113764 2 0.947
CP034060_6 6.1|4141721|54|CP034060|CRISPRCasFinder 4141721-4141774 54 NZ_CP048385 Citrobacter freundii strain 62 plasmid p6_C, complete sequence 72431-72484 12 0.778

1. spacer 6.1|4141721|54|CP034060|CRISPRCasFinder matches to NZ_AP023206 (Escherichia coli strain TUM18781 plasmid pMTY18781-1_lncX3, complete sequence) position: , mismatch: 1, identity: 0.981

tggcctacacgctgcgattttgtaggccggataagcaaagcgcatccggcattc	CRISPR spacer
tggcctacacgctgcgattttgtaggccggataagcaaagcgcatccggcattg	Protospacer
***************************************************** 

2. spacer 4.1|2442685|38|CP034060|CRISPRCasFinder matches to NZ_CP043437 (Enterobacter sp. LU1 plasmid unnamed) position: , mismatch: 2, identity: 0.947

cggacgcaggatggtgcgttcaattggactcgaaccaa	CRISPR spacer
cagacgcagaatggtgcgttcaattggactcgaaccaa	Protospacer
*.*******.****************************

3. spacer 6.1|4141721|54|CP034060|CRISPRCasFinder matches to NZ_CP048385 (Citrobacter freundii strain 62 plasmid p6_C, complete sequence) position: , mismatch: 12, identity: 0.778

tggcctacacgct-----gcgattttgtaggccggataagcaaagcgcatccggcattc	CRISPR spacer
-----tacaaattaattcgcggtattgtaggccggataagcaaagcgcatccggcagta	Protospacer
     **** ..*     ***.* ******************************** * 

Region Region Position Protein_number Hit_taxonomy Key_proteins Att_site Prophage annotation
DBSCAN-SWA_1 266834 : 331120 46 Paramecium_bursaria_Chlorella_virus(20.0%) tRNA,transposase,protease NA
DBSCAN-SWA_2 801300 : 864312 53 Stx2-converting_phage(25.0%) protease,tRNA,transposase NA
DBSCAN-SWA_3 1335603 : 1345500 6 Pseudomonas_phage(50.0%) transposase NA
DBSCAN-SWA_4 1475805 : 1536367 50 Aeromonas_phage(10.53%) tail,tRNA,transposase NA
DBSCAN-SWA_5 1918399 : 1957202 32 Enterobacteria_phage(69.23%) integrase,tail,tRNA,lysis,transposase attL 1937298:1937317|attR 1949152:1949171
DBSCAN-SWA_6 2044257 : 2050564 6 Enterobacteria_phage(50.0%) NA NA
DBSCAN-SWA_7 2077587 : 2092441 13 Stx2-converting_phage(55.56%) transposase NA
DBSCAN-SWA_8 2103460 : 2142532 39 Enterobacteria_phage(29.63%) integrase,tail,holin,head,transposase attL 2105171:2105230|attR 2140239:2141488
DBSCAN-SWA_9 2213992 : 2311791 80 Enterobacteria_phage(27.59%) tail,tRNA,transposase NA
DBSCAN-SWA_10 2325306 : 2369807 36 Shigella_phage(33.33%) transposase NA
DBSCAN-SWA_11 2520712 : 2589941 64 Escherichia_phage(25.0%) integrase,holin,transposase,protease attL 2531921:2531935|attR 2540091:2540105
DBSCAN-SWA_12 2688903 : 2767522 79 Escherichia_phage(40.0%) integrase,tail,tRNA,protease,transposase attL 2737565:2737624|attR 2763267:2764520
DBSCAN-SWA_13 2900435 : 2973947 66 uncultured_Caudovirales_phage(43.75%) tail,tRNA,protease,terminase,head,portal,transposase NA
DBSCAN-SWA_14 3052368 : 3097097 48 Stx2-converting_phage(30.0%) tail,transposase NA
DBSCAN-SWA_15 3122799 : 3172554 31 Salmonella_phage(22.22%) integrase,transposase attL 3120505:3120564|attR 3130754:3131521
DBSCAN-SWA_16 3190201 : 3229467 41 Salmonella_phage(57.14%) tail,plate,protease,terminase,head,transposase NA
DBSCAN-SWA_17 3247788 : 3323428 56 Acinetobacter_phage(15.38%) transposase,tRNA,protease NA
DBSCAN-SWA_18 3437664 : 3602753 156 Enterobacteria_phage(23.17%) integrase,tail,holin,tRNA,terminase,head,capsid,transposase attL 3514568:3514627|attR 3548271:3549519
DBSCAN-SWA_19 3855244 : 3912316 51 Enterobacteria_phage(20.0%) integrase,tail,tRNA,coat,transposase attL 3897086:3897145|attR 3900093:3900244
DBSCAN-SWA_20 3926328 : 3973840 39 Shigella_phage(25.0%) integrase,tail,plate,transposase attL 3928394:3928425|attR 3969681:3969712
Acr ID Acr position Acr size Homology with known anti Neighbor HTH/AcRanker Neighbor Aca In prophage Protospacer in prophage
2. CP034059
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CRISPR_ID Spacer_Info Spacer_region Spacer_length Hit_ID Protospacer_location Mismatch Identity
CRISPR_ID Spacer_Info Spacer_region Spacer_length Hit_phage_ID Hit_phage_def Protospacer_location Mismatch Identity
Region Region Position Protein_number Hit_taxonomy Key_proteins Att_site Prophage annotation
DBSCAN-SWA_1 625 : 71627 56 Escherichia_phage(28.57%) transposase,tRNA,protease,integrase attL 2145:2167|attR 70347:70369
DBSCAN-SWA_2 82046 : 121378 26 Stx2-converting_phage(40.0%) transposase,protease NA
Acr ID Acr position Acr size Homology with known anti Neighbor HTH/AcRanker Neighbor Aca In prophage Protospacer in prophage