CRISPRimmunity

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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
CP031238	Haemophilus haemolyticus strain M28486 chromosome, complete genome	3 crisprs	NA	0	5	0	0

Cas Category Instructions

Results visualization

1. CP031238

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CRISPR-Cas detection and classification

Crispr_ID: CP031238_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

CP031238_1

184272-184396

Orphan

Consensus_repeat	Method
CCGCATTTACCTTCTGCGGCTTT	CRISPRCasFinder

2 spacers

The CRISPR arrays of CP031238_1

>merge|CP031238|1|184272-184396|CRISPRCasFinder
CCGCATTTACCTTCACCACATTTACCTTCTGCAGCTTTTGGTTTGCTCGCACCGCATTTACCTTCTGCGGCTTTCGTTTCGTTTGCACCACATTTGCCTTCTCCGCATTTACCTTCTGCAGCTTT

>CP031238|1|1|184272-184396|CRISPRCasFinder
CCGCATTTACCTTCACCACATTT	ACCTTCTGCAGCTTTTGGTTTGCTCGCA
CCGCATTTACCTTCTGCGGCTTT	CGTTTCGTTTGCACCACATTTGCCTTCT
CCGCATTTACCTTCTGCAGCTTT

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Crispr_ID: CP031238_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

CP031238_2

1204030-1204462

Orphan

Consensus_repeat	Method
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACCA	PILER-CR
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	CRISPRCasFinder
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	CRT

6 spacers

The CRISPR arrays of CP031238_2

>merge|CP031238|2|1204030-1204462|PILER-CR,CRISPRCasFinder,CRT
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACTAAAATTTTAGGCACGTTATTAAGACTTGGTAACTCGCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACCAAGTATTAGTGCCGGGTGCGGTGGGATTGATGCGCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACTATGCCTTTCTTCAGCTCAAGGTAGAGGCATTAAGCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACCAGTTATTATGCTATTTATTAGCAAAAAAAGAAAAAGCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACCAACGTATCTTATATCCACCGACAAACAGGTGTATGCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACAAAAAAGGCGCGAAAACGGGAAGGCTTTTTCCTTGCAGCCATCTTCGGGTGGCTGTGTGTTGAAAC

>CP031238|2|1|1204030-1204398|PILER-CR
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACTA	AAATTTTAGGCACGTTATTAAGACTTGGTAACTC
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACCA	AGTATTAGTGCCGGGTGCGGTGGGATTGATGC
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACTA	TGCCTTTCTTCAGCTCAAGGTAGAGGCATTAA
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACCA	GTTATTATGCTATTTATTAGCAAAAAAAGAAAAA
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACCA	ACGTATCTTATATCCACCGACAAACAGGTGTAT
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAACAA

>CP031238|2|2|1204030-1204462|CRISPRCasFinder
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	TAAAATTTTAGGCACGTTATTAAGACTTGGTAACTC
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	CAAGTATTAGTGCCGGGTGCGGTGGGATTGATGC
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	TATGCCTTTCTTCAGCTCAAGGTAGAGGCATTAA
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	CAGTTATTATGCTATTTATTAGCAAAAAAAGAAAAA
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	CAACGTATCTTATATCCACCGACAAACAGGTGTAT
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	AAAAAAGGCGCGAAAACGGGAAGGCTTTTTCCTT
GCAGCCATCTTCGGGTGGCTGTGTGTTGAAAC

>CP031238|2|1|1204030-1204462|CRT
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	TAAAATTTTAGGCACGTTATTAAGACTTGGTAACTC
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	CAAGTATTAGTGCCGGGTGCGGTGGGATTGATGC
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	TATGCCTTTCTTCAGCTCAAGGTAGAGGCATTAA
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	CAGTTATTATGCTATTTATTAGCAAAAAAAGAAAAA
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	CAACGTATCTTATATCCACCGACAAACAGGTGTAT
GCAGCCGCCTTCGCGCGGCTGTGTGTTGAAAC	AAAAAAGGCGCGAAAACGGGAAGGCTTTTTCCTT
GCAGCCATCTTCGGGTGGCTGTGTGTTGAAAC

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Crispr_ID: CP031238_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

CP031238_3

1592751-1592899

Orphan

Consensus_repeat	Method
TTGGAGCGGGAAACGAGGCTCGAACTCGCGACCCCGACCTTGGCAAGGT	CRISPRCasFinder

1 spacers

The CRISPR arrays of CP031238_3

>merge|CP031238|3|1592751-1592899|CRISPRCasFinder
TTGGAGCGGGAAACGAGGCTCGAACTCGCGACCCCGACCTTGGCAAGGTCGTGCTCTACCAACTGAGCTATTCCCGCAATAATGCTTCTATAATGTGAAATTGGAGCGGGAAACGAGGCTCGAACTCGCGACCCCAACCTTGGCAAGGT

>CP031238|3|3|1592751-1592899|CRISPRCasFinder
TTGGAGCGGGAAACGAGGCTCGAACTCGCGACCCCGACCTTGGCAAGGT	CGTGCTCTACCAACTGAGCTATTCCCGCAATAATGCTTCTATAATGTGAAA
TTGGAGCGGGAAACGAGGCTCGAACTCGCGACCCCAACCTTGGCAAGGT

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
CP031238_2	2.3\|1204198\|32\|CP031238\|PILER-CR	1204198-1204229	32	NC_004846	Haemophilus influenzae biotype aegyptius plasmid pF3031, complete sequence	21080-21111	1	0.969
CP031238_2	2.3\|1204198\|32\|CP031238\|PILER-CR	1204198-1204229	32	NC_004058	Haemophilus influenzae biotype aegyptius BPF plasmid pF3028, complete sequence	21026-21057	1	0.969
CP031238_2	2.8\|1204196\|34\|CP031238\|CRISPRCasFinder,CRT	1204196-1204229	34	NC_004846	Haemophilus influenzae biotype aegyptius plasmid pF3031, complete sequence	21078-21111	1	0.971
CP031238_2	2.8\|1204196\|34\|CP031238\|CRISPRCasFinder,CRT	1204196-1204229	34	NC_004058	Haemophilus influenzae biotype aegyptius BPF plasmid pF3028, complete sequence	21024-21057	1	0.971
CP031238_2	2.3\|1204198\|32\|CP031238\|PILER-CR	1204198-1204229	32	NC_021776	Vibrio phage vpms1, complete genome	13492-13523	4	0.875
CP031238_2	2.2\|1204132\|32\|CP031238\|PILER-CR	1204132-1204163	32	NZ_CP017590	Pantoea stewartii subsp. stewartii DC283 plasmid pDSJ09, complete sequence	90020-90051	7	0.781
CP031238_2	2.3\|1204198\|32\|CP031238\|PILER-CR	1204198-1204229	32	MN693487	Marine virus AFVG_25M100, complete genome	25461-25492	7	0.781
CP031238_2	2.2\|1204132\|32\|CP031238\|PILER-CR	1204132-1204163	32	NZ_CP024882	Citrobacter freundii strain AR_0022 plasmid unitig_1_pilon, complete sequence	5462-5493	8	0.75
CP031238_2	2.2\|1204132\|32\|CP031238\|PILER-CR	1204132-1204163	32	NZ_CP032180	Citrobacter freundii strain AR_0116 plasmid unnamed2, complete sequence	135220-135251	8	0.75
CP031238_2	2.2\|1204132\|32\|CP031238\|PILER-CR	1204132-1204163	32	NZ_CP037863	Citrobacter sp. LY-1 plasmid unnamed2, complete sequence	100858-100889	8	0.75
CP031238_2	2.3\|1204198\|32\|CP031238\|PILER-CR	1204198-1204229	32	KX171213	Staphylococcus phage vB_SscM-2, complete genome	21309-21340	8	0.75
CP031238_2	2.3\|1204198\|32\|CP031238\|PILER-CR	1204198-1204229	32	NC_047767	Staphylococcus phage vB_SscM-1, complete genome	21309-21340	8	0.75
CP031238_2	2.3\|1204198\|32\|CP031238\|PILER-CR	1204198-1204229	32	MN694586	Marine virus AFVG_250M370, complete genome	24703-24734	8	0.75
CP031238_2	2.4\|1204264\|34\|CP031238\|PILER-CR	1204264-1204297	34	NZ_CP013615	Clostridium perfringens strain JP838 plasmid pJFP838A, complete sequence	197435-197468	9	0.735
CP031238_2	2.4\|1204264\|34\|CP031238\|PILER-CR	1204264-1204297	34	NZ_CP020064	Klebsiella pneumoniae strain AR_0117 plasmid unitig_3, complete sequence	55534-55567	9	0.735
CP031238_2	2.4\|1204264\|34\|CP031238\|PILER-CR	1204264-1204297	34	NZ_CP013238	Clostridium butyricum strain CDC_51208 plasmid pNPD4_2, complete sequence	520728-520761	9	0.735
CP031238_2	2.4\|1204264\|34\|CP031238\|PILER-CR	1204264-1204297	34	NZ_CP021753	Klebsiella pneumoniae strain AR_0113 plasmid unitig_2, complete sequence	16750-16783	9	0.735
CP031238_2	2.4\|1204264\|34\|CP031238\|PILER-CR	1204264-1204297	34	NZ_CP008791	Klebsiella oxytoca KONIH1 plasmid pKPC-727, complete sequence	197115-197148	9	0.735
CP031238_2	2.4\|1204264\|34\|CP031238\|PILER-CR	1204264-1204297	34	KY940546	Klebsiella pneumoniae plasmid pUCLA3, complete sequence	50067-50100	9	0.735
CP031238_2	2.4\|1204264\|34\|CP031238\|PILER-CR	1204264-1204297	34	NZ_CP021545	Klebsiella pneumoniae strain AR_0112 plasmid tig00000001, complete sequence	100139-100172	9	0.735
CP031238_2	2.4\|1204264\|34\|CP031238\|PILER-CR	1204264-1204297	34	NZ_CP006922	Klebsiella pneumoniae 30684/NJST258_2 plasmid pNJST258C1, complete sequence	28495-28528	9	0.735
CP031238_2	2.4\|1204264\|34\|CP031238\|PILER-CR	1204264-1204297	34	NZ_CP021857	Klebsiella pneumoniae strain AR_0125 plasmid tig00000002_pilon, complete sequence	88558-88591	9	0.735
CP031238_2	2.7\|1204130\|34\|CP031238\|CRISPRCasFinder,CRT	1204130-1204163	34	NZ_CP024882	Citrobacter freundii strain AR_0022 plasmid unitig_1_pilon, complete sequence	5460-5493	9	0.735
CP031238_2	2.7\|1204130\|34\|CP031238\|CRISPRCasFinder,CRT	1204130-1204163	34	NZ_CP032180	Citrobacter freundii strain AR_0116 plasmid unnamed2, complete sequence	135218-135251	9	0.735
CP031238_2	2.7\|1204130\|34\|CP031238\|CRISPRCasFinder,CRT	1204130-1204163	34	NZ_CP037863	Citrobacter sp. LY-1 plasmid unnamed2, complete sequence	100858-100891	9	0.735
CP031238_2	2.4\|1204264\|34\|CP031238\|PILER-CR	1204264-1204297	34	NZ_LR134421	Legionella adelaidensis strain NCTC12735 genome assembly, plasmid: 12	16316-16349	11	0.676

1. spacer 2.3|1204198|32|CP031238|PILER-CR matches to NC_004846 (Haemophilus influenzae biotype aegyptius plasmid pF3031, complete sequence) position: , mismatch: 1, identity: 0.969

tgcctttcttcagctcaaggtagaggcattaa	CRISPR spacer
tgcctttcttctgctcaaggtagaggcattaa	Protospacer
*********** ********************

2. spacer 2.3|1204198|32|CP031238|PILER-CR matches to NC_004058 (Haemophilus influenzae biotype aegyptius BPF plasmid pF3028, complete sequence) position: , mismatch: 1, identity: 0.969

tgcctttcttcagctcaaggtagaggcattaa	CRISPR spacer
tgcctttcttctgctcaaggtagaggcattaa	Protospacer
*********** ********************

3. spacer 2.8|1204196|34|CP031238|CRISPRCasFinder,CRT matches to NC_004846 (Haemophilus influenzae biotype aegyptius plasmid pF3031, complete sequence) position: , mismatch: 1, identity: 0.971

tatgcctttcttcagctcaaggtagaggcattaa	CRISPR spacer
tatgcctttcttctgctcaaggtagaggcattaa	Protospacer
************* ********************

4. spacer 2.8|1204196|34|CP031238|CRISPRCasFinder,CRT matches to NC_004058 (Haemophilus influenzae biotype aegyptius BPF plasmid pF3028, complete sequence) position: , mismatch: 1, identity: 0.971

tatgcctttcttcagctcaaggtagaggcattaa	CRISPR spacer
tatgcctttcttctgctcaaggtagaggcattaa	Protospacer
************* ********************

5. spacer 2.3|1204198|32|CP031238|PILER-CR matches to NC_021776 (Vibrio phage vpms1, complete genome) position: , mismatch: 4, identity: 0.875

-tgcctttcttcagctcaaggtagaggcattaa	CRISPR spacer
atgcctatc-tcagctgaaggtagcggcattaa	Protospacer
 ***** ** ****** ******* ********

6. spacer 2.2|1204132|32|CP031238|PILER-CR matches to NZ_CP017590 (Pantoea stewartii subsp. stewartii DC283 plasmid pDSJ09, complete sequence) position: , mismatch: 7, identity: 0.781

agtattagt----gccgggtgcggtgggattgatgc	CRISPR spacer
----tcactgacggccgggtgcggtggtattgatgc	Protospacer
    *.* *    ************** ********

7. spacer 2.3|1204198|32|CP031238|PILER-CR matches to MN693487 (Marine virus AFVG_25M100, complete genome) position: , mismatch: 7, identity: 0.781

tgcctttcttcagctcaaggtagaggcattaa	CRISPR spacer
ttccttcgttcagctcaaggtagagaatttac	Protospacer
* ****. *****************.  ***

8. spacer 2.2|1204132|32|CP031238|PILER-CR matches to NZ_CP024882 (Citrobacter freundii strain AR_0022 plasmid unitig_1_pilon, complete sequence) position: , mismatch: 8, identity: 0.75

agtattagtgccgggtgcggtgggattgatgc	CRISPR spacer
tccctcaatgccggctgcggtggcattgatgc	Protospacer
  . *.*.****** ******** ********

9. spacer 2.2|1204132|32|CP031238|PILER-CR matches to NZ_CP032180 (Citrobacter freundii strain AR_0116 plasmid unnamed2, complete sequence) position: , mismatch: 8, identity: 0.75

agtattagtgccgggtgcggtgggattgatgc	CRISPR spacer
tccctcaatgccggctgcggtggcattgatgc	Protospacer
  . *.*.****** ******** ********

10. spacer 2.2|1204132|32|CP031238|PILER-CR matches to NZ_CP037863 (Citrobacter sp. LY-1 plasmid unnamed2, complete sequence) position: , mismatch: 8, identity: 0.75

agtattagtgccgggtgcggtgggattgatgc	CRISPR spacer
tccctcaatgccggctgcggtggcattgatgc	Protospacer
  . *.*.****** ******** ********

11. spacer 2.3|1204198|32|CP031238|PILER-CR matches to KX171213 (Staphylococcus phage vB_SscM-2, complete genome) position: , mismatch: 8, identity: 0.75

tgcctttcttcagctcaaggtagaggcattaa	CRISPR spacer
ttagttatatcagttcaaggtagaggtattaa	Protospacer
*   ** . ****.************.*****

12. spacer 2.3|1204198|32|CP031238|PILER-CR matches to NC_047767 (Staphylococcus phage vB_SscM-1, complete genome) position: , mismatch: 8, identity: 0.75

tgcctttcttcagctcaaggtagaggcattaa	CRISPR spacer
ttagttatatcagttcaaggtagaggtattaa	Protospacer
*   ** . ****.************.*****

13. spacer 2.3|1204198|32|CP031238|PILER-CR matches to MN694586 (Marine virus AFVG_250M370, complete genome) position: , mismatch: 8, identity: 0.75

tgcctttcttcagctcaaggtagaggcattaa	CRISPR spacer
ttccttcgttcagctcaaggtagagaattttc	Protospacer
* ****. *****************.  **

14. spacer 2.4|1204264|34|CP031238|PILER-CR matches to NZ_CP013615 (Clostridium perfringens strain JP838 plasmid pJFP838A, complete sequence) position: , mismatch: 9, identity: 0.735

gttattatgctatttattagcaaaaaaagaaaaa	CRISPR spacer
cttttaatgctatttattagcaaaaaccttttaa	Protospacer
 ** * ********************      **

15. spacer 2.4|1204264|34|CP031238|PILER-CR matches to NZ_CP020064 (Klebsiella pneumoniae strain AR_0117 plasmid unitig_3, complete sequence) position: , mismatch: 9, identity: 0.735

gttattatgctatttattagcaaaaaaagaaaaa	CRISPR spacer
atcattattctttttattagcaaaaaacagaact	Protospacer
.*.***** ** *************** ..**

16. spacer 2.4|1204264|34|CP031238|PILER-CR matches to NZ_CP013238 (Clostridium butyricum strain CDC_51208 plasmid pNPD4_2, complete sequence) position: , mismatch: 9, identity: 0.735

gttattatgctatttattagcaaaaaaagaaaaa	CRISPR spacer
agcatcttcatatgtattagcaaaaacagaaaaa	Protospacer
. .**. *  *** ************ *******

17. spacer 2.4|1204264|34|CP031238|PILER-CR matches to NZ_CP021753 (Klebsiella pneumoniae strain AR_0113 plasmid unitig_2, complete sequence) position: , mismatch: 9, identity: 0.735

gttattatgctatttattagcaaaaaaagaaaaa	CRISPR spacer
atcattattctttttattagcaaaaaacagaact	Protospacer
.*.***** ** *************** ..**

18. spacer 2.4|1204264|34|CP031238|PILER-CR matches to NZ_CP008791 (Klebsiella oxytoca KONIH1 plasmid pKPC-727, complete sequence) position: , mismatch: 9, identity: 0.735

gttattatgctatttattagcaaaaaaagaaaaa	CRISPR spacer
atcattattctttttattagcaaaaaacagaact	Protospacer
.*.***** ** *************** ..**

19. spacer 2.4|1204264|34|CP031238|PILER-CR matches to KY940546 (Klebsiella pneumoniae plasmid pUCLA3, complete sequence) position: , mismatch: 9, identity: 0.735

gttattatgctatttattagcaaaaaaagaaaaa	CRISPR spacer
atcattattctttttattagcaaaaaacagaact	Protospacer
.*.***** ** *************** ..**

20. spacer 2.4|1204264|34|CP031238|PILER-CR matches to NZ_CP021545 (Klebsiella pneumoniae strain AR_0112 plasmid tig00000001, complete sequence) position: , mismatch: 9, identity: 0.735

gttattatgctatttattagcaaaaaaagaaaaa	CRISPR spacer
atcattattctttttattagcaaaaaacagaact	Protospacer
.*.***** ** *************** ..**

21. spacer 2.4|1204264|34|CP031238|PILER-CR matches to NZ_CP006922 (Klebsiella pneumoniae 30684/NJST258_2 plasmid pNJST258C1, complete sequence) position: , mismatch: 9, identity: 0.735

gttattatgctatttattagcaaaaaaagaaaaa	CRISPR spacer
atcattattctttttattagcaaaaaacagaact	Protospacer
.*.***** ** *************** ..**

22. spacer 2.4|1204264|34|CP031238|PILER-CR matches to NZ_CP021857 (Klebsiella pneumoniae strain AR_0125 plasmid tig00000002_pilon, complete sequence) position: , mismatch: 9, identity: 0.735

gttattatgctatttattagcaaaaaaagaaaaa	CRISPR spacer
atcattattctttttattagcaaaaaacagaact	Protospacer
.*.***** ** *************** ..**

23. spacer 2.7|1204130|34|CP031238|CRISPRCasFinder,CRT matches to NZ_CP024882 (Citrobacter freundii strain AR_0022 plasmid unitig_1_pilon, complete sequence) position: , mismatch: 9, identity: 0.735

caagtattagtgccgggtgcggtgggattgatgc	CRISPR spacer
cctccctcaatgccggctgcggtggcattgatgc	Protospacer
*   . *.*.****** ******** ********

24. spacer 2.7|1204130|34|CP031238|CRISPRCasFinder,CRT matches to NZ_CP032180 (Citrobacter freundii strain AR_0116 plasmid unnamed2, complete sequence) position: , mismatch: 9, identity: 0.735

caagtattagtgccgggtgcggtgggattgatgc	CRISPR spacer
cctccctcaatgccggctgcggtggcattgatgc	Protospacer
*   . *.*.****** ******** ********

25. spacer 2.7|1204130|34|CP031238|CRISPRCasFinder,CRT matches to NZ_CP037863 (Citrobacter sp. LY-1 plasmid unnamed2, complete sequence) position: , mismatch: 9, identity: 0.735

caagtattagtgccgggtgcggtgggattgatgc	CRISPR spacer
cctccctcaatgccggctgcggtggcattgatgc	Protospacer
*   . *.*.****** ******** ********

26. spacer 2.4|1204264|34|CP031238|PILER-CR matches to NZ_LR134421 (Legionella adelaidensis strain NCTC12735 genome assembly, plasmid: 12) position: , mismatch: 11, identity: 0.676

gttattatgctatttattagcaaaaaaagaaaaa	CRISPR spacer
aaatcgaaattatttattaactaaaaaagaaaaa	Protospacer
.   . * ..*********.* ************

Prophage detection

Region	Region Position	Protein_number	Hit_taxonomy	Key_proteins	Att_site	Prophage annotation

Anti-CRISPR protein detection

Acr ID	Acr position	Acr size	Homology with known anti	Neighbor HTH/AcRanker	Neighbor Aca	In prophage	Protospacer in prophage