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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
CP012345 Salmonella enterica subsp. enterica serovar Choleraesuis str. ATCC 10708 plasmid pCFSAN000679_01, complete sequence 0 crisprs cas14j 0 0 1 0
CP012344 Salmonella enterica subsp. enterica serovar Choleraesuis str. ATCC 10708, complete genome 2 crisprs PD-DExK,WYL,cas3,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,cas14j 0 5 8 0

Results visualization

1. CP012345
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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 34135 : 41039 8 Escherichia_phage(33.33%) transposase NA
Acr ID Acr position Acr size Homology with known anti Neighbor HTH/AcRanker Neighbor Aca In prophage Protospacer in prophage
2. CP012344
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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP012344_2 900681-901136 TypeI-E I-E
7 spacers
cas3

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CRISPR_ID CRISPR_location CRISPR_type Repeat_type Spacer_info Cas_protein_info CRISPR-Cas_info
CP012344_3 918575-918908 TypeI-E I-E
5 spacers
cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas3

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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
CP012344_2 2.3|900832|32|CP012344|PILER-CR,CRISPRCasFinder,CRT 900832-900863 32 NZ_CP029832 Azospirillum ramasamyi strain M2T2B2 plasmid unnamed2, complete sequence 167172-167203 8 0.75
CP012344_2 2.3|900832|32|CP012344|PILER-CR,CRISPRCasFinder,CRT 900832-900863 32 NC_016586 Azospirillum lipoferum 4B plasmid AZO_p2, complete sequence 405399-405430 8 0.75
CP012344_2 2.4|900893|32|CP012344|PILER-CR,CRISPRCasFinder,CRT 900893-900924 32 NZ_CP049914 Vibrio sp. HDW18 plasmid p_unnamed1, complete sequence 234396-234427 8 0.75
CP012344_2 2.4|900893|32|CP012344|PILER-CR,CRISPRCasFinder,CRT 900893-900924 32 NC_018688 Bacillus thuringiensis MC28 plasmid pMC319, complete sequence 85616-85647 8 0.75
CP012344_3 3.6|918604|32|CP012344|CRISPRCasFinder,CRT 918604-918635 32 NZ_CP022021 Listeria monocytogenes strain FDA709873-33 plasmid pCFSAN021445, complete sequence 72705-72736 9 0.719
CP012344_3 3.6|918604|32|CP012344|CRISPRCasFinder,CRT 918604-918635 32 NZ_CP041212 Listeria monocytogenes strain LMP18-H2446 plasmid pCFSAN074383, complete sequence 56906-56937 9 0.719
CP012344_3 3.6|918604|32|CP012344|CRISPRCasFinder,CRT 918604-918635 32 NC_022045 Listeria monocytogenes strain N1-011A plasmid, complete sequence 76500-76531 9 0.719
CP012344_3 3.6|918604|32|CP012344|CRISPRCasFinder,CRT 918604-918635 32 NZ_CP014251 Listeria monocytogenes strain CFSAN010068 plasmid pCFSAN010068_01, complete sequence 30149-30180 9 0.719
CP012344_3 3.6|918604|32|CP012344|CRISPRCasFinder,CRT 918604-918635 32 NC_003383 Listeria innocua Clip11262 plasmid pLI100, complete sequence 23028-23059 9 0.719
CP012344_3 3.6|918604|32|CP012344|CRISPRCasFinder,CRT 918604-918635 32 NZ_MH382833 Listeria welshimeri strain 40/07 plasmid pLIS1, complete sequence 11753-11784 9 0.719
CP012344_3 3.6|918604|32|CP012344|CRISPRCasFinder,CRT 918604-918635 32 NZ_CP020834 Listeria monocytogenes strain CFSAN004330 plasmid pCFSAN004330, complete sequence 35903-35934 9 0.719
CP012344_2 2.3|900832|32|CP012344|PILER-CR,CRISPRCasFinder,CRT 900832-900863 32 NZ_CP053711 Acetobacteraceae bacterium strain PAMC 26569 plasmid unnamed4, complete sequence 113090-113121 10 0.688
CP012344_2 2.6|901015|32|CP012344|PILER-CR,CRISPRCasFinder,CRT 901015-901046 32 NZ_CP046164 Vibrio sp. THAF191c plasmid pTHAF191c_c, complete sequence 362233-362264 10 0.688
CP012344_2 2.6|901015|32|CP012344|PILER-CR,CRISPRCasFinder,CRT 901015-901046 32 NZ_CP046067 Vibrio sp. THAF191d plasmid pTHAF191d_c, complete sequence 110732-110763 10 0.688
CP012344_2 2.6|901015|32|CP012344|PILER-CR,CRISPRCasFinder,CRT 901015-901046 32 NZ_CP009266 Vibrio coralliilyticus strain OCN014 plasmid pOCN014, complete sequence 36435-36466 10 0.688
CP012344_2 2.6|901015|32|CP012344|PILER-CR,CRISPRCasFinder,CRT 901015-901046 32 NZ_CP045357 Vibrio sp. THAF64 plasmid pTHAF64_b, complete sequence 217923-217954 10 0.688
CP012344_2 2.6|901015|32|CP012344|PILER-CR,CRISPRCasFinder,CRT 901015-901046 32 MN693596 Marine virus AFVG_25M324, complete genome 45600-45631 10 0.688
CP012344_3 3.10|918848|32|CP012344|CRISPRCasFinder,CRT 918848-918879 32 NC_016113 Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCAT, complete sequence 1151729-1151760 10 0.688
CP012344_3 3.10|918848|32|CP012344|CRISPRCasFinder,CRT 918848-918879 32 NC_017585 Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCATT, complete sequence 661429-661460 10 0.688

1. spacer 2.3|900832|32|CP012344|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP029832 (Azospirillum ramasamyi strain M2T2B2 plasmid unnamed2, complete sequence) position: , mismatch: 8, identity: 0.75

gcccgcctgtcgctgtacgccggggcggcata	CRISPR spacer
cgcggcctgtcgctgtccgccgcggcggggga	Protospacer
  * ************ ***** ***** . *

2. spacer 2.3|900832|32|CP012344|PILER-CR,CRISPRCasFinder,CRT matches to NC_016586 (Azospirillum lipoferum 4B plasmid AZO_p2, complete sequence) position: , mismatch: 8, identity: 0.75

gcccgcctgtcgctgtacgccggggcggcata	CRISPR spacer
cgcggcctgtcgctgtccgccgcggcggggga	Protospacer
  * ************ ***** ***** . *

3. spacer 2.4|900893|32|CP012344|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP049914 (Vibrio sp. HDW18 plasmid p_unnamed1, complete sequence) position: , mismatch: 8, identity: 0.75

----ccatttttgatcatctcctccagcctgctgag	CRISPR spacer
ggtaaca----cgatcgtctcttccagcctgctgag	Protospacer
     **    .****.****.**************

4. spacer 2.4|900893|32|CP012344|PILER-CR,CRISPRCasFinder,CRT matches to NC_018688 (Bacillus thuringiensis MC28 plasmid pMC319, complete sequence) position: , mismatch: 8, identity: 0.75

ccatttttgatcatctcctccagcctgctgag	CRISPR spacer
taatttttgttcatctcttccagccttatcat	Protospacer
. ******* *******.********  * * 

5. spacer 3.6|918604|32|CP012344|CRISPRCasFinder,CRT matches to NZ_CP022021 (Listeria monocytogenes strain FDA709873-33 plasmid pCFSAN021445, complete sequence) position: , mismatch: 9, identity: 0.719

ctgcatattcacgcctcactccagcacactgg--	CRISPR spacer
tgccatattcacgccacactcca--acaacgatt	Protospacer
.  ************ *******  *** .*.  

6. spacer 3.6|918604|32|CP012344|CRISPRCasFinder,CRT matches to NZ_CP041212 (Listeria monocytogenes strain LMP18-H2446 plasmid pCFSAN074383, complete sequence) position: , mismatch: 9, identity: 0.719

ctgcatattcacgcctcactccagcacactgg--	CRISPR spacer
tgccatattcacgccacactcca--acaacgatt	Protospacer
.  ************ *******  *** .*.  

7. spacer 3.6|918604|32|CP012344|CRISPRCasFinder,CRT matches to NC_022045 (Listeria monocytogenes strain N1-011A plasmid, complete sequence) position: , mismatch: 9, identity: 0.719

ctgcatattcacgcctcactccagcacactgg--	CRISPR spacer
tgccatattcacgccacactcca--acaacgatt	Protospacer
.  ************ *******  *** .*.  

8. spacer 3.6|918604|32|CP012344|CRISPRCasFinder,CRT matches to NZ_CP014251 (Listeria monocytogenes strain CFSAN010068 plasmid pCFSAN010068_01, complete sequence) position: , mismatch: 9, identity: 0.719

ctgcatattcacgcctcactccagcacactgg--	CRISPR spacer
tgccatattcacgccacactcca--acaacgatt	Protospacer
.  ************ *******  *** .*.  

9. spacer 3.6|918604|32|CP012344|CRISPRCasFinder,CRT matches to NC_003383 (Listeria innocua Clip11262 plasmid pLI100, complete sequence) position: , mismatch: 9, identity: 0.719

ctgcatattcacgcctcactccagcacactgg--	CRISPR spacer
tgccatattcacgccacactcca--acaacgatt	Protospacer
.  ************ *******  *** .*.  

10. spacer 3.6|918604|32|CP012344|CRISPRCasFinder,CRT matches to NZ_MH382833 (Listeria welshimeri strain 40/07 plasmid pLIS1, complete sequence) position: , mismatch: 9, identity: 0.719

ctgcatattcacgcctcactccagcacactgg--	CRISPR spacer
tgccatattcacgccacactcca--acaacgatt	Protospacer
.  ************ *******  *** .*.  

11. spacer 3.6|918604|32|CP012344|CRISPRCasFinder,CRT matches to NZ_CP020834 (Listeria monocytogenes strain CFSAN004330 plasmid pCFSAN004330, complete sequence) position: , mismatch: 9, identity: 0.719

ctgcatattcacgcctcactccagcacactgg--	CRISPR spacer
tgccatattcacgccacactcca--acaacgatt	Protospacer
.  ************ *******  *** .*.  

12. spacer 2.3|900832|32|CP012344|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP053711 (Acetobacteraceae bacterium strain PAMC 26569 plasmid unnamed4, complete sequence) position: , mismatch: 10, identity: 0.688

gcccgcctgtcgctgtacgccggggcggcata	CRISPR spacer
gcccgcctgtcgcagcacgccggtgaactgcg	Protospacer
************* *.******* * . ....

13. spacer 2.6|901015|32|CP012344|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP046164 (Vibrio sp. THAF191c plasmid pTHAF191c_c, complete sequence) position: , mismatch: 10, identity: 0.688

gtcaaataaatatgagtgaagaagccaaagcc	CRISPR spacer
ccgtagccaatatcagtgaagatgccaaagct	Protospacer
 .  *.. ***** ******** ********.

14. spacer 2.6|901015|32|CP012344|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP046067 (Vibrio sp. THAF191d plasmid pTHAF191d_c, complete sequence) position: , mismatch: 10, identity: 0.688

gtcaaataaatatgagtgaagaagccaaagcc	CRISPR spacer
ccgtagccaatatcagtgaagatgccaaagct	Protospacer
 .  *.. ***** ******** ********.

15. spacer 2.6|901015|32|CP012344|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP009266 (Vibrio coralliilyticus strain OCN014 plasmid pOCN014, complete sequence) position: , mismatch: 10, identity: 0.688

gtcaaataaatatgagtgaagaagccaaagcc	CRISPR spacer
ccgtagccaatatcagtgaagatgccaaagct	Protospacer
 .  *.. ***** ******** ********.

16. spacer 2.6|901015|32|CP012344|PILER-CR,CRISPRCasFinder,CRT matches to NZ_CP045357 (Vibrio sp. THAF64 plasmid pTHAF64_b, complete sequence) position: , mismatch: 10, identity: 0.688

gtcaaataaatatgagtgaagaagccaaagcc	CRISPR spacer
ccgtagccaatatcagtgaagatgccaaagct	Protospacer
 .  *.. ***** ******** ********.

17. spacer 2.6|901015|32|CP012344|PILER-CR,CRISPRCasFinder,CRT matches to MN693596 (Marine virus AFVG_25M324, complete genome) position: , mismatch: 10, identity: 0.688

gtcaaataaatatgagtgaagaagccaaagcc	CRISPR spacer
taggagcaaaaatgagtgaagaagcaaaagag	Protospacer
   .*..*** ************** ****  

18. spacer 3.10|918848|32|CP012344|CRISPRCasFinder,CRT matches to NC_016113 (Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCAT, complete sequence) position: , mismatch: 10, identity: 0.688

aggggcgttccgcagtcgacaagggctgaaaa	CRISPR spacer
ccgggcggtccgcagtcgacgagggtgaggga	Protospacer
  ***** ************.****. ....*

19. spacer 3.10|918848|32|CP012344|CRISPRCasFinder,CRT matches to NC_017585 (Streptomyces cattleya NRRL 8057 = DSM 46488 plasmid pSCATT, complete sequence) position: , mismatch: 10, identity: 0.688

aggggcgttccgcagtcgacaagggctgaaaa	CRISPR spacer
ccgggcggtccgcagtcgacgagggtgaggga	Protospacer
  ***** ************.****. ....*

Region Region Position Protein_number Hit_taxonomy Key_proteins Att_site Prophage annotation
DBSCAN-SWA_1 1155052 : 1200275 62 Salmonella_phage(75.81%) head,lysis,holin,tail NA
DBSCAN-SWA_2 1661765 : 1670934 9 Enterobacteria_phage(66.67%) tRNA NA
DBSCAN-SWA_3 1936669 : 1987227 51 Enterobacteria_phage(25.0%) integrase,protease,transposase,tail attL 1952687:1952702|attR 1984848:1984863
DBSCAN-SWA_4 2595895 : 2643853 62 Salmonella_phage(31.37%) tail,terminase,head,tRNA,capsid,portal,transposase,integrase,holin attL 2590781:2590800|attR 2639780:2639799
DBSCAN-SWA_5 2788929 : 2886941 101 Salmonella_phage(37.29%) lysis,tail,terminase,tRNA,protease,holin NA
DBSCAN-SWA_6 2938827 : 2946140 8 Ralstonia_phage(16.67%) integrase,protease attL 2933443:2933457|attR 2944876:2944890
DBSCAN-SWA_7 3533864 : 3574907 58 Salmonella_phage(51.79%) lysis,tail,terminase,protease,portal,coat,integrase,holin attL 3530612:3530657|attR 3571017:3571062
DBSCAN-SWA_8 4337696 : 4384662 49 Burkholderia_phage(42.86%) tail,plate,tRNA NA
Acr ID Acr position Acr size Homology with known anti Neighbor HTH/AcRanker Neighbor Aca In prophage Protospacer in prophage