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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
CP031020 Lactobacillus helveticus isolate NWC_2_4 plasmid pNWC_2_4, complete sequence 0 crisprs NA 0 0 0 0
CP031018 Lactobacillus helveticus isolate NWC_2_4 chromosome, complete genome 5 crisprs cas14j,cas3,csa3,cas2,cas14k,cas5,cas8c,cas7,cas4,cas1,DEDDh,DinG,Cas14u_CAS-V,c2c9_V-U4 1 5 19 4
CP031019 Lactobacillus helveticus isolate NWC_2_4 plasmid pNWC_2_3, complete sequence 0 crisprs NA 0 0 0 0

Results visualization

1. CP031018
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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP031018_1 608918-610494 TypeI I-C
23 spacers
cas1,cas4,cas7,cas8c,cas5,cas3

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP031018_2 738782-738872 Orphan I-B,III-A,III-B
1 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP031018_3 789148-789252 Orphan NA
1 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP031018_4 1656865-1657004 TypeV NA
1 spacers
cas14j

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP031018_5 1678476-1678655 TypeV NA
2 spacers
cas14j

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CRISPR_ID Spacer_Info Spacer_region Spacer_length Hit_ID Protospacer_location Mismatch Identity
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 CP031018.1 1876469-1876506 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 CP031018.1 1880855-1880892 0 1.0

1. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to position: 1876469-1876506, mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

2. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to position: 1880855-1880892, mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

CRISPR_ID Spacer_Info Spacer_region Spacer_length Hit_phage_ID Hit_phage_def Protospacer_location Mismatch Identity
CP031018_1 1.15|609894|35|CP031018|PILER-CR,CRISPRCasFinder,CRT 609894-609928 35 NC_019782 Lactobacillus phage AQ113, complete genome 32158-32192 0 1.0
CP031018_1 1.16|609961|34|CP031018|PILER-CR,CRISPRCasFinder,CRT 609961-609994 34 NC_019782 Lactobacillus phage AQ113, complete genome 32158-32191 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NC_015598 Lactobacillus kefiranofaciens ZW3 plasmid pWW1, complete sequence 33870-33907 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP021475 Pediococcus pentosaceus strain SRCM100892 plasmid pPC892-4, complete sequence 13494-13531 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP014631 Lactobacillus backii strain TMW 1.1988 plasmid L11988-7, complete sequence 17258-17295 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP035155 Pediococcus acidilactici strain SRCM103387 plasmid unnamed1 4250-4287 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP014892 Lactobacillus backii strain TMW 1.1992 plasmid pL11992-2, complete sequence 41970-42007 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP042372 Lactobacillus malefermentans strain CBA3618 plasmid unnamed1, complete sequence 14115-14152 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP012296 Pediococcus damnosus strain TMW 2.1536 plasmid pL21536-2, complete sequence 3640-3677 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP014882 Lactobacillus backii strain TMW 1.1991 plasmid pL11991-1, complete sequence 14790-14827 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP018765 Pediococcus acidilactici strain BCC1 plasmid pbcp2, complete sequence 36451-36488 0 1.0
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NC_015598 Lactobacillus kefiranofaciens ZW3 plasmid pWW1, complete sequence 26067-26104 2 0.947
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NC_015598 Lactobacillus kefiranofaciens ZW3 plasmid pWW1, complete sequence 81129-81166 2 0.947
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP015497 Lactobacillus helveticus strain FAM8105 plasmid pFAM8105, complete sequence 30012-30049 2 0.947
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP020458 Lactobacillus amylolyticus strain L6 plasmid pL6-1, complete sequence 36061-36098 2 0.947
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 CP031020 Lactobacillus helveticus isolate NWC_2_4 plasmid pNWC_2_4, complete sequence 14520-14557 2 0.947
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NC_017471 Lactobacillus amylovorus GRL1118 plasmid p1, complete sequence 4109-4146 3 0.921
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NC_017472 Lactobacillus amylovorus GRL1118 plasmid p2, complete sequence 72577-72614 3 0.921
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP015497 Lactobacillus helveticus strain FAM8105 plasmid pFAM8105, complete sequence 22904-22941 4 0.895
CP031018_4 4.1|1656916|38|CP031018|CRISPRCasFinder 1656916-1656953 38 NZ_CP040501 Lactobacillus paragasseri JV-V03 plasmid unnamed1, complete sequence 35732-35769 4 0.895
CP031018_1 1.12|609690|36|CP031018|PILER-CR,CRISPRCasFinder,CRT 609690-609725 36 MN856049 Siphoviridae sp. isolate 503, complete genome 4400-4435 7 0.806
CP031018_1 1.18|610095|35|CP031018|PILER-CR,CRISPRCasFinder,CRT 610095-610129 35 NZ_CP043762 Paenibacillus sp. 37 plasmid pART37, complete sequence 403572-403606 10 0.714

1. spacer 1.15|609894|35|CP031018|PILER-CR,CRISPRCasFinder,CRT matches to NC_019782 (Lactobacillus phage AQ113, complete genome) position: , mismatch: 0, identity: 1.0

atttgatgactttaaagcagaaaaaggtactaaag	CRISPR spacer
atttgatgactttaaagcagaaaaaggtactaaag	Protospacer
***********************************

2. spacer 1.16|609961|34|CP031018|PILER-CR,CRISPRCasFinder,CRT matches to NC_019782 (Lactobacillus phage AQ113, complete genome) position: , mismatch: 0, identity: 1.0

atttgatgactttaaagcagaaaaaggtactaaa	CRISPR spacer
atttgatgactttaaagcagaaaaaggtactaaa	Protospacer
**********************************

3. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NC_015598 (Lactobacillus kefiranofaciens ZW3 plasmid pWW1, complete sequence) position: , mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

4. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP021475 (Pediococcus pentosaceus strain SRCM100892 plasmid pPC892-4, complete sequence) position: , mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

5. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP014631 (Lactobacillus backii strain TMW 1.1988 plasmid L11988-7, complete sequence) position: , mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

6. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP035155 (Pediococcus acidilactici strain SRCM103387 plasmid unnamed1) position: , mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

7. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP014892 (Lactobacillus backii strain TMW 1.1992 plasmid pL11992-2, complete sequence) position: , mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

8. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP042372 (Lactobacillus malefermentans strain CBA3618 plasmid unnamed1, complete sequence) position: , mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

9. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP012296 (Pediococcus damnosus strain TMW 2.1536 plasmid pL21536-2, complete sequence) position: , mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

10. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP014882 (Lactobacillus backii strain TMW 1.1991 plasmid pL11991-1, complete sequence) position: , mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

11. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP018765 (Pediococcus acidilactici strain BCC1 plasmid pbcp2, complete sequence) position: , mismatch: 0, identity: 1.0

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttttga	Protospacer
**************************************

12. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NC_015598 (Lactobacillus kefiranofaciens ZW3 plasmid pWW1, complete sequence) position: , mismatch: 2, identity: 0.947

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgttttagg	Protospacer
*********************************** *.

13. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NC_015598 (Lactobacillus kefiranofaciens ZW3 plasmid pWW1, complete sequence) position: , mismatch: 2, identity: 0.947

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgttttagg	Protospacer
*********************************** *.

14. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP015497 (Lactobacillus helveticus strain FAM8105 plasmid pFAM8105, complete sequence) position: , mismatch: 2, identity: 0.947

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgttttagg	Protospacer
*********************************** *.

15. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP020458 (Lactobacillus amylolyticus strain L6 plasmid pL6-1, complete sequence) position: , mismatch: 2, identity: 0.947

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgttttagg	Protospacer
*********************************** *.

16. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to CP031020 (Lactobacillus helveticus isolate NWC_2_4 plasmid pNWC_2_4, complete sequence) position: , mismatch: 2, identity: 0.947

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgttttagg	Protospacer
*********************************** *.

17. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NC_017471 (Lactobacillus amylovorus GRL1118 plasmid p1, complete sequence) position: , mismatch: 3, identity: 0.921

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgttttaag	Protospacer
*********************************** ..

18. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NC_017472 (Lactobacillus amylovorus GRL1118 plasmid p2, complete sequence) position: , mismatch: 3, identity: 0.921

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgttttaag	Protospacer
*********************************** ..

19. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP015497 (Lactobacillus helveticus strain FAM8105 plasmid pFAM8105, complete sequence) position: , mismatch: 4, identity: 0.895

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatattttaag	Protospacer
******************************.**** ..

20. spacer 4.1|1656916|38|CP031018|CRISPRCasFinder matches to NZ_CP040501 (Lactobacillus paragasseri JV-V03 plasmid unnamed1, complete sequence) position: , mismatch: 4, identity: 0.895

tcatacgagaaaggaactcctttttctaatgtttttga	CRISPR spacer
tcatacgagaaaggaactcctttttctaatgtttaaag	Protospacer
**********************************  ..

21. spacer 1.12|609690|36|CP031018|PILER-CR,CRISPRCasFinder,CRT matches to MN856049 (Siphoviridae sp. isolate 503, complete genome) position: , mismatch: 7, identity: 0.806

-aatagcatctttaccagtaaatcccattactagcaa	CRISPR spacer
caatgccggc-ttaccagtaaatcccataactagtaa	Protospacer
 ***. *. * ***************** *****.**

22. spacer 1.18|610095|35|CP031018|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP043762 (Paenibacillus sp. 37 plasmid pART37, complete sequence) position: , mismatch: 10, identity: 0.714

agcatatggagcgaaattatttagagactggagaa	CRISPR spacer
tggaagctaagctaaataatttagagactggagag	Protospacer
 * * .. .*** **** ****************.

Region Region Position Protein_number Hit_taxonomy Key_proteins Att_site Prophage annotation
DBSCAN-SWA_1 10464 : 81471 48 Streptococcus_phage(23.53%) transposase NA
DBSCAN-SWA_2 102551 : 147096 36 Bacillus_phage(30.0%) protease,transposase NA
DBSCAN-SWA_3 194860 : 313541 90 Bacillus_phage(11.54%) tRNA,protease,holin,transposase NA
DBSCAN-SWA_4 343050 : 381111 30 Bacillus_phage(27.27%) tRNA,transposase NA
DBSCAN-SWA_5 406251 : 457957 47 Burkholderia_virus(15.0%) holin,tRNA,transposase NA
DBSCAN-SWA_6 461597 : 540751 58 Staphylococcus_phage(28.57%) tRNA,transposase NA
DBSCAN-SWA_7 558726 : 702467 102 Bacillus_phage(34.62%) bacteriocin,protease,tRNA,transposase NA
DBSCAN-SWA_8 707721 : 778668 49 Bacillus_phage(20.0%) transposase NA
DBSCAN-SWA_9 787305 : 865662 60 Prochlorococcus_phage(11.76%) protease,tRNA,transposase NA
DBSCAN-SWA_10 875438 : 1075713 173 Lactobacillus_phage(41.89%) portal,capsid,integrase,head,transposase,tail,tRNA attL 901095:901154|attR 940487:941855
DBSCAN-SWA_11 1082492 : 1160276 49 Bacillus_phage(25.0%) protease,integrase,tRNA,transposase attL 1114704:1114720|attR 1150242:1150258
DBSCAN-SWA_12 1193434 : 1235203 32 Bacillus_phage(22.22%) tRNA,transposase NA
DBSCAN-SWA_13 1239476 : 1311568 55 Bacillus_virus(22.22%) transposase NA
DBSCAN-SWA_14 1393055 : 1528311 108 Streptococcus_phage(22.22%) protease,tRNA,transposase NA
DBSCAN-SWA_15 1537549 : 1590509 44 Bacillus_phage(23.08%) protease,tRNA,transposase NA
DBSCAN-SWA_16 1610909 : 1839992 170 Bacillus_phage(19.15%) holin,integrase,tRNA,transposase attL 1702000:1702059|attR 1776698:1778166
DBSCAN-SWA_17 1846724 : 1976092 117 Bacillus_phage(21.88%) bacteriocin,protease,transposase NA
DBSCAN-SWA_18 1986038 : 2052712 54 Bacillus_phage(16.67%) bacteriocin,transposase NA
DBSCAN-SWA_19 2056352 : 2135273 60 Heterosigma_akashiwo_virus(16.67%) protease,holin,transposase NA
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Acr ID Acr position Acr size Homology with known anti Neighbor HTH/AcRanker Neighbor Aca In prophage Protospacer in prophage
CP031018.1|AZA20499.1|1876346_1876550_-|hypothetical-protein 1876346_1876550_- 67 aa aa NA NA NA 1846724-1976092 yes
CP031018.1|AZA20823.1|1905963_1906233_-|ATPase 1905963_1906233_- 89 aa aa NA NA NA 1846724-1976092 yes
CP031018.1|AZA20826.1|1940938_1941130_-|hypothetical-protein 1940938_1941130_- 63 aa aa NA NA NA 1846724-1976092 yes
CP031018.1|AZA20575.1|1965850_1966093_-|hypothetical-protein 1965850_1966093_- 80 aa aa NA NA NA 1846724-1976092 yes