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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
NZ_CP013255 Kocuria flava strain HO-9041 plasmid 1, complete sequence 0 crisprs NA 0 0 0 0
NZ_CP013258 Kocuria flava strain HO-9041 plasmid 4, complete sequence 0 crisprs NA 0 0 0 0
NZ_CP013254 Kocuria flava strain HO-9041 chromosome, complete genome 6 crisprs csa3,cas3,DinG,WYL,DEDDh 2 4 5 0
NZ_CP013257 Kocuria flava strain HO-9041 plasmid 3, complete sequence 0 crisprs NA 0 0 0 0
NZ_CP013256 Kocuria flava strain HO-9041 plasmid 2, complete sequence 0 crisprs NA 0 0 0 0

Results visualization

1. NZ_CP013254
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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
NZ_CP013254_1 1169301-1169395 Orphan NA
1 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
NZ_CP013254_2 1742269-1742418 Unclear NA
2 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
NZ_CP013254_3 1745440-1745507 Unclear NA
1 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
NZ_CP013254_4 1953613-1953719 Orphan NA
1 spacers

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
NZ_CP013254_5 2660449-2660528 Orphan NA
1 spacers
csa3

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
NZ_CP013254_6 3184204-3184329 Orphan NA
1 spacers

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CRISPR_ID Spacer_Info Spacer_region Spacer_length Hit_ID Protospacer_location Mismatch Identity
NZ_CP013254_2 2.1|1742301|42|NZ_CP013254|PILER-CR 1742301-1742342 42 NZ_CP013254.1 1742857-1742898 0 1.0
NZ_CP013254_2 2.2|1742375|31|NZ_CP013254|PILER-CR 1742375-1742405 31 NZ_CP013254.1 1742795-1742825 0 1.0

1. spacer 2.1|1742301|42|NZ_CP013254|PILER-CR matches to position: 1742857-1742898, mismatch: 0, identity: 1.0

gcccccggcccgcgcccgcgccgagtgcccacagcactgacc	CRISPR spacer
gcccccggcccgcgcccgcgccgagtgcccacagcactgacc	Protospacer
******************************************

2. spacer 2.2|1742375|31|NZ_CP013254|PILER-CR matches to position: 1742795-1742825, mismatch: 0, identity: 1.0

tcccgcaccgccaggactccagcacatcggg	CRISPR spacer
tcccgcaccgccaggactccagcacatcggg	Protospacer
*******************************

CRISPR_ID Spacer_Info Spacer_region Spacer_length Hit_phage_ID Hit_phage_def Protospacer_location Mismatch Identity
NZ_CP013254_4 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder 1953654-1953678 25 NZ_CP040820 Paraoceanicella profunda strain D4M1 plasmid pD4M1B, complete sequence 271150-271174 3 0.88
NZ_CP013254_4 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder 1953654-1953678 25 NC_016113 Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCAT, complete sequence 1018520-1018544 4 0.84
NZ_CP013254_4 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder 1953654-1953678 25 NC_014310 Ralstonia solanacearum PSI07 plasmid mpPSI07, complete sequence 124016-124040 4 0.84
NZ_CP013254_4 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder 1953654-1953678 25 NC_017585 Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCATT, complete sequence 794613-794637 4 0.84
NZ_CP013254_4 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder 1953654-1953678 25 NZ_CP022760 Ralstonia solanacearum strain T98 plasmid unnamed, complete sequence 121988-122012 4 0.84
NZ_CP013254_4 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder 1953654-1953678 25 NZ_CP022789 Ralstonia solanacearum strain SL3175 plasmid unnamed, complete sequence 121989-122013 4 0.84
NZ_CP013254_4 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder 1953654-1953678 25 NC_015169 Deinococcus proteolyticus MRP plasmid pDEIPR01, complete sequence 276899-276923 5 0.8
NZ_CP013254_6 6.1|3184252|30|NZ_CP013254|CRISPRCasFinder 3184252-3184281 30 NZ_CP016083 Streptomyces sp. SAT1 plasmid unnamed3, complete sequence 289505-289534 6 0.8
NZ_CP013254_2 2.2|1742375|31|NZ_CP013254|PILER-CR 1742375-1742405 31 MT498053 Streptomyces phage PHTowN, complete genome 19425-19455 8 0.742
NZ_CP013254_2 2.2|1742375|31|NZ_CP013254|PILER-CR 1742375-1742405 31 MK305891 Streptomyces phage Gibson, complete genome 19618-19648 8 0.742
NZ_CP013254_2 2.2|1742375|31|NZ_CP013254|PILER-CR 1742375-1742405 31 MT897908 Streptomyces phage ShakeNBake, complete genome 19443-19473 8 0.742
NZ_CP013254_5 5.1|2660472|34|NZ_CP013254|CRISPRCasFinder 2660472-2660505 34 GQ919031 Streptomyces phage ZL12, complete genome 17123-17156 8 0.765
NZ_CP013254_6 6.1|3184252|30|NZ_CP013254|CRISPRCasFinder 3184252-3184281 30 NZ_CP017756 Cupriavidus malaysiensis strain USMAA1020 isolate pure plasmid unnamed1, complete sequence 54099-54128 8 0.733
NZ_CP013254_2 2.2|1742375|31|NZ_CP013254|PILER-CR 1742375-1742405 31 NC_020056 Anabaena cylindrica PCC 7122 plasmid pANACY.05, complete sequence 10417-10447 9 0.71
NZ_CP013254_5 5.1|2660472|34|NZ_CP013254|CRISPRCasFinder 2660472-2660505 34 NZ_CP007794 Azospirillum brasilense strain Az39 plasmid AbAZ39_p1, complete sequence 1390560-1390593 10 0.706
NZ_CP013254_5 5.1|2660472|34|NZ_CP013254|CRISPRCasFinder 2660472-2660505 34 NZ_CP045721 Pantoea eucalypti strain LMG 24197 plasmid unnamed1, complete sequence 163957-163990 10 0.706
NZ_CP013254_5 5.1|2660472|34|NZ_CP013254|CRISPRCasFinder 2660472-2660505 34 NZ_CP022517 Pantoea vagans strain FBS135 plasmid pPant1, complete sequence 222839-222872 10 0.706

1. spacer 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder matches to NZ_CP040820 (Paraoceanicella profunda strain D4M1 plasmid pD4M1B, complete sequence) position: , mismatch: 3, identity: 0.88

tcggcgcgggggttacggtgagcgc	CRISPR spacer
tgggcgcgggggtttcggtgagggc	Protospacer
* ************ ******* **

2. spacer 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder matches to NC_016113 (Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCAT, complete sequence) position: , mismatch: 4, identity: 0.84

tcggcgcgggggttacggtgagcgc	CRISPR spacer
gaggcgcgggggcgacggtgagcgc	Protospacer
  **********. ***********

3. spacer 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder matches to NC_014310 (Ralstonia solanacearum PSI07 plasmid mpPSI07, complete sequence) position: , mismatch: 4, identity: 0.84

tcggcgcgggggttacggtgagcgc	CRISPR spacer
acggcgcggcgtttacggtgagcgg	Protospacer
 ******** * ************ 

4. spacer 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder matches to NC_017585 (Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCATT, complete sequence) position: , mismatch: 4, identity: 0.84

tcggcgcgggggttacggtgagcgc	CRISPR spacer
gaggcgcgggggcgacggtgagcgc	Protospacer
  **********. ***********

5. spacer 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder matches to NZ_CP022760 (Ralstonia solanacearum strain T98 plasmid unnamed, complete sequence) position: , mismatch: 4, identity: 0.84

tcggcgcgggggttacggtgagcgc	CRISPR spacer
acggcgcggcgtttacggtgagcgg	Protospacer
 ******** * ************ 

6. spacer 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder matches to NZ_CP022789 (Ralstonia solanacearum strain SL3175 plasmid unnamed, complete sequence) position: , mismatch: 4, identity: 0.84

tcggcgcgggggttacggtgagcgc	CRISPR spacer
acggcgcggcgtttacggtgagcgg	Protospacer
 ******** * ************ 

7. spacer 4.1|1953654|25|NZ_CP013254|CRISPRCasFinder matches to NC_015169 (Deinococcus proteolyticus MRP plasmid pDEIPR01, complete sequence) position: , mismatch: 5, identity: 0.8

tcggcgcgggggttacggtgagcgc	CRISPR spacer
ccggcgcgggggtcacggtgagaag	Protospacer
.************.******** . 

8. spacer 6.1|3184252|30|NZ_CP013254|CRISPRCasFinder matches to NZ_CP016083 (Streptomyces sp. SAT1 plasmid unnamed3, complete sequence) position: , mismatch: 6, identity: 0.8

----ggtctcccgcggcggacccacccggcgcgg	CRISPR spacer
ccgaggt----cgcggcggactcgcccggcgcgg	Protospacer
    ***    **********.*.**********

9. spacer 2.2|1742375|31|NZ_CP013254|PILER-CR matches to MT498053 (Streptomyces phage PHTowN, complete genome) position: , mismatch: 8, identity: 0.742

tcccgcaccgccaggactccagcacatcggg	CRISPR spacer
tcccgtaccgccagtactccagcgctctgat	Protospacer
*****.******** ********.* ..*. 

10. spacer 2.2|1742375|31|NZ_CP013254|PILER-CR matches to MK305891 (Streptomyces phage Gibson, complete genome) position: , mismatch: 8, identity: 0.742

tcccgcaccgccaggactccagcacatcggg	CRISPR spacer
tcccgtaccgccagtactccagcgctctgat	Protospacer
*****.******** ********.* ..*. 

11. spacer 2.2|1742375|31|NZ_CP013254|PILER-CR matches to MT897908 (Streptomyces phage ShakeNBake, complete genome) position: , mismatch: 8, identity: 0.742

tcccgcaccgccaggactccagcacatcggg	CRISPR spacer
tcccgtaccgccagtactccagcgctctgat	Protospacer
*****.******** ********.* ..*. 

12. spacer 5.1|2660472|34|NZ_CP013254|CRISPRCasFinder matches to GQ919031 (Streptomyces phage ZL12, complete genome) position: , mismatch: 8, identity: 0.765

cgggccgcggcccgatccaccggccggagccccg	CRISPR spacer
caagccgcggcctgatccaccggccggtcccgtc	Protospacer
*..*********.**************  ** . 

13. spacer 6.1|3184252|30|NZ_CP013254|CRISPRCasFinder matches to NZ_CP017756 (Cupriavidus malaysiensis strain USMAA1020 isolate pure plasmid unnamed1, complete sequence) position: , mismatch: 8, identity: 0.733

ggtctcccgcggcggacccacccggcgcgg	CRISPR spacer
gattgagttcggcagacccacccggcgcgg	Protospacer
*.*.   . ****.****************

14. spacer 2.2|1742375|31|NZ_CP013254|PILER-CR matches to NC_020056 (Anabaena cylindrica PCC 7122 plasmid pANACY.05, complete sequence) position: , mismatch: 9, identity: 0.71

tcccgcaccgccaggactccagcacatcggg	CRISPR spacer
tcctgcaccgcccggactccagcttccggta	Protospacer
***.******** ********** . . * .

15. spacer 5.1|2660472|34|NZ_CP013254|CRISPRCasFinder matches to NZ_CP007794 (Azospirillum brasilense strain Az39 plasmid AbAZ39_p1, complete sequence) position: , mismatch: 10, identity: 0.706

cgggccgcggcccgatccaccggccggagccccg	CRISPR spacer
ccgaaggcggcccgatccaccggcgggcgctggc	Protospacer
* *.  ****************** ** **.   

16. spacer 5.1|2660472|34|NZ_CP013254|CRISPRCasFinder matches to NZ_CP045721 (Pantoea eucalypti strain LMG 24197 plasmid unnamed1, complete sequence) position: , mismatch: 10, identity: 0.706

cgggccgcggcccgatccaccggccggagccccg	CRISPR spacer
aaggccgcgacccgttccaccggccgcacggtgg	Protospacer
 .*******.**** *********** *   . *

17. spacer 5.1|2660472|34|NZ_CP013254|CRISPRCasFinder matches to NZ_CP022517 (Pantoea vagans strain FBS135 plasmid pPant1, complete sequence) position: , mismatch: 10, identity: 0.706

cgggccgcggcccgatccaccggccggagccccg	CRISPR spacer
aaggccgcgacccgttccaccggccgcacggtgg	Protospacer
 .*******.**** *********** *   . *

Region Region Position Protein_number Hit_taxonomy Key_proteins Att_site Prophage annotation
DBSCAN-SWA_1 600767 : 672925 60 Mycobacterium_phage(17.65%) integrase,tRNA,protease,transposase attL 610252:610268|attR 662927:662943
DBSCAN-SWA_2 1456529 : 1466145 12 Bacillus_phage(25.0%) NA NA
DBSCAN-SWA_3 2102330 : 2109570 8 Orpheovirus(33.33%) tRNA NA
DBSCAN-SWA_4 2316394 : 2351510 27 Corynebacterium_phage(16.67%) transposase NA
DBSCAN-SWA_5 3311418 : 3372326 54 Mycobacterium_phage(42.86%) integrase,transposase,protease attL 3311873:3311889|attR 3374302:3374318
Acr ID Acr position Acr size Homology with known anti Neighbor HTH/AcRanker Neighbor Aca In prophage Protospacer in prophage