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
LS483448	Streptococcus pneumoniae strain 4041STDY6836167 genome assembly, chromosome: 1	2 crisprs	NA	0	1	0	0

Cas Category Instructions

Results visualization

1. LS483448

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CRISPR-Cas detection and classification

Crispr_ID: LS483448_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LS483448_1

11280-11381

Orphan

Consensus_repeat	Method
GTTGTTTCTTATACAGTTTTTCTTG	CRISPRCasFinder

1 spacers

The CRISPR arrays of LS483448_1

>merge|LS483448|1|11280-11381|CRISPRCasFinder
GTTGTTTCTTATACAGTTTTTCTTGCCTACAGCCTCATGCTCTCGGTCGCCAAACTTCTGAGCGTGGGGCTTTTTGAGTTGTTTCTTATACAGTTTTTTCTT

>LS483448|1|1|11280-11381|CRISPRCasFinder
GTTGTTTCTTATACAGTTTTTCTTG	CCTACAGCCTCATGCTCTCGGTCGCCAAACTTCTGAGCGTGGGGCTTTTTGA
GTTGTTTCTTATACAGTTTTTTCTT

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Crispr_ID: LS483448_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LS483448_2

141563-141658

Orphan

Consensus_repeat	Method
AATGTGTAAGATTTTTATATATAA	CRISPRCasFinder

1 spacers

The CRISPR arrays of LS483448_2

>merge|LS483448|2|141563-141658|CRISPRCasFinder
AATGTGTAAGATTTTTATATATAATTTTTCTACACATACATTGTACATCTAAAAGAAAGCCCTGTCAAGAGAAATGTGTAAAATTTTTATATATAA

>LS483448|2|2|141563-141658|CRISPRCasFinder
AATGTGTAAGATTTTTATATATAA	TTTTTCTACACATACATTGTACATCTAAAAGAAAGCCCTGTCAAGAGA
AATGTGTAAAATTTTTATATATAA

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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
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448629	Streptococcus satellite phage Javan742, complete genome	5187-5238	0	1.0
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448646	Streptococcus satellite phage Javan758, complete genome	5186-5237	0	1.0
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448432	Streptococcus satellite phage Javan327, complete genome	4489-4540	1	0.981
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448612	Streptococcus satellite phage Javan725, complete genome	3457-3508	3	0.942
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448495	Streptococcus satellite phage Javan434, complete genome	5542-5593	3	0.942
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448410	Streptococcus satellite phage Javan298, complete genome	3649-3700	3	0.942
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448614	Streptococcus satellite phage Javan727, complete genome	7482-7533	4	0.923
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448623	Streptococcus satellite phage Javan736, complete genome	6059-6110	4	0.923
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448630	Streptococcus satellite phage Javan743, complete genome	7931-7982	4	0.923
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448647	Streptococcus satellite phage Javan759, complete genome	10291-10342	5	0.904
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448643	Streptococcus satellite phage Javan755, complete genome	6646-6697	5	0.904
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448649	Streptococcus satellite phage Javan760, complete genome	4331-4382	5	0.904
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448616	Streptococcus satellite phage Javan729, complete genome	8547-8598	5	0.904
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448627	Streptococcus satellite phage Javan740, complete genome	7031-7082	5	0.904
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	KT337367	Streptococcus phage phiARI0826b, partial genome	32391-32442	7	0.865
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	KT337369	Streptococcus phage phiARI0831b, partial genome	29445-29496	7	0.865
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	FR671407	Streptococcus phage 34117	36073-36124	7	0.865
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	NC_024361	Streptococcus phage DCC1738, complete sequence	36829-36880	7	0.865
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	NC_024357	Streptococcus phage K13, complete sequence	37797-37848	7	0.865
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448640	Streptococcus satellite phage Javan752, complete genome	3884-3935	7	0.865
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448634	Streptococcus satellite phage Javan747, complete genome	2570-2621	7	0.865
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448986	Streptococcus phage Javan570, complete genome	1517-1568	8	0.846
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448455	Streptococcus satellite phage Javan364, complete genome	3323-3374	8	0.846
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448445	Streptococcus satellite phage Javan344, complete genome	5150-5201	9	0.827
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448555	Streptococcus satellite phage Javan592, complete genome	3565-3616	11	0.788
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448547	Streptococcus satellite phage Javan572, complete genome	3566-3617	11	0.788
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448535	Streptococcus satellite phage Javan550, complete genome	3566-3617	11	0.788
LS483448_1	1.1\|11305\|52\|LS483448\|CRISPRCasFinder	11305-11356	52	MK448544	Streptococcus satellite phage Javan564, complete genome	2943-2994	11	0.788

1. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448629 (Streptococcus satellite phage Javan742, complete genome) position: , mismatch: 0, identity: 1.0

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	Protospacer
****************************************************

2. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448646 (Streptococcus satellite phage Javan758, complete genome) position: , mismatch: 0, identity: 1.0

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	Protospacer
****************************************************

3. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448432 (Streptococcus satellite phage Javan327, complete genome) position: , mismatch: 1, identity: 0.981

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
cctacagcctcacgctctcggtcgccaaacttctgagcgtggggctttttga	Protospacer
************.***************************************

4. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448612 (Streptococcus satellite phage Javan725, complete genome) position: , mismatch: 3, identity: 0.942

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
tctacagcctcatgctctcggtcgccaaatttctgaacgtggggctttttga	Protospacer
.****************************.******.***************

5. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448495 (Streptococcus satellite phage Javan434, complete genome) position: , mismatch: 3, identity: 0.942

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
cctacagcctcatgctctcggtcgccaaatttctgagcatggggctttttaa	Protospacer
*****************************.********.***********.*

6. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448410 (Streptococcus satellite phage Javan298, complete genome) position: , mismatch: 3, identity: 0.942

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
cctacagcctcatgctctcggtcgccaaatttctgagcatggggctttttaa	Protospacer
*****************************.********.***********.*

7. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448614 (Streptococcus satellite phage Javan727, complete genome) position: , mismatch: 4, identity: 0.923

cctaca-gcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
-tcacatgcctcacgctctcggtcgccaaacttctgagcgtggggctttttga	Protospacer
 ..*** ******.***************************************

8. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448623 (Streptococcus satellite phage Javan736, complete genome) position: , mismatch: 4, identity: 0.923

cctaca-gcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
-tcacatgcctcatgctctcggtcgccaaacttctgagcgtgggtctttttga	Protospacer
 ..*** ************************************* ********

9. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448630 (Streptococcus satellite phage Javan743, complete genome) position: , mismatch: 4, identity: 0.923

cctaca-gcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
-tcacatgcctcacgctctcggtcgccaaacttctgagcgtggggctttttga	Protospacer
 ..*** ******.***************************************

10. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448647 (Streptococcus satellite phage Javan759, complete genome) position: , mismatch: 5, identity: 0.904

cctaca-gcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
-tcacatgcctcatgctctcggtcgccaaacttctgagcgtggggcttttttg	Protospacer
 ..*** ******************************************** .

11. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448643 (Streptococcus satellite phage Javan755, complete genome) position: , mismatch: 5, identity: 0.904

cctaca-gcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
-tcacatgcctcatgctctcggtcgccaaatttctgagcgtgggtctttttga	Protospacer
 ..*** ***********************.************* ********

12. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448649 (Streptococcus satellite phage Javan760, complete genome) position: , mismatch: 5, identity: 0.904

cctaca-gcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
-ccacatgcctcacgctctcggtcgccaaacttctgagcgtggggctttttac	Protospacer
 *.*** ******.*************************************.

13. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448616 (Streptococcus satellite phage Javan729, complete genome) position: , mismatch: 5, identity: 0.904

cctaca-gcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
-tcacatgcctcatgctctcggtcgccaaatttctgagcgtgggtctttttga	Protospacer
 ..*** ***********************.************* ********

14. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448627 (Streptococcus satellite phage Javan740, complete genome) position: , mismatch: 5, identity: 0.904

cctaca-gcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
-tcacatgcctcacgctctcggtcgccaaacttctgagcgtgggtctttttga	Protospacer
 ..*** ******.****************************** ********

15. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to KT337367 (Streptococcus phage phiARI0826b, partial genome) position: , mismatch: 7, identity: 0.865

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
gtactagcctcatgctctcggtcgccaaacttctgagcgtggggcttttttt	Protospacer
 .  .*********************************************

16. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to KT337369 (Streptococcus phage phiARI0831b, partial genome) position: , mismatch: 7, identity: 0.865

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
gtactagcctcatgctctcggtcgccaaacttctgagcgtggggcttttttt	Protospacer
 .  .*********************************************

17. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to FR671407 (Streptococcus phage 34117) position: , mismatch: 7, identity: 0.865

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
ctcctagcctcacgctctcggtcgccaaacttctgagcgtggggcttttttg	Protospacer
*.. .*******.************************************* .

18. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to NC_024361 (Streptococcus phage DCC1738, complete sequence) position: , mismatch: 7, identity: 0.865

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
ctcctagcctcacgctctcggtcgccaaacttctgagcgtggggcttttttg	Protospacer
*.. .*******.************************************* .

19. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to NC_024357 (Streptococcus phage K13, complete sequence) position: , mismatch: 7, identity: 0.865

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
ctcctagcctcacgctctcggtcgccaaacttctgagcgtggggcttttttg	Protospacer
*.. .*******.************************************* .

20. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448640 (Streptococcus satellite phage Javan752, complete genome) position: , mismatch: 7, identity: 0.865

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
tcgcatgcctcatgctctcggtcgccaaatttctgagcgtgggtctttttga	Protospacer
.*    ***********************.************* ********

21. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448634 (Streptococcus satellite phage Javan747, complete genome) position: , mismatch: 7, identity: 0.865

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
tcgcatgcctcatgctctcggtcgccaaatttctgagcgtgggtctttttga	Protospacer
.*    ***********************.************* ********

22. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448986 (Streptococcus phage Javan570, complete genome) position: , mismatch: 8, identity: 0.846

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
tagcttgcctcacgctctcggtcgccaaacttctgagcgtggggctttttta	Protospacer
.   . ******.************************************* *

23. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448455 (Streptococcus satellite phage Javan364, complete genome) position: , mismatch: 8, identity: 0.846

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
tgaagttcctcacgctctcggtcgccaaatttctgagcgtggggctttttga	Protospacer
.  *   *****.****************.**********************

24. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448445 (Streptococcus satellite phage Javan344, complete genome) position: , mismatch: 9, identity: 0.827

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
aggatatcctcacactctcggtcgccaaacttctgagcgtggggcttttttg	Protospacer
   *.* *****..************************************ .

25. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448555 (Streptococcus satellite phage Javan592, complete genome) position: , mismatch: 11, identity: 0.788

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
gtaattgcctcatgctctcggtcgcctaatttctgagcgtggggctttggtt	Protospacer
 . *. ******************** **.******************

26. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448547 (Streptococcus satellite phage Javan572, complete genome) position: , mismatch: 11, identity: 0.788

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
gtaattgcctcatgctctcggtcgcctaatttctgagcgtggggctttggtt	Protospacer
 . *. ******************** **.******************

27. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448535 (Streptococcus satellite phage Javan550, complete genome) position: , mismatch: 11, identity: 0.788

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
gtaattgcctcatgctctcggtcgcctaatttctgagcgtggggctttggtt	Protospacer
 . *. ******************** **.******************

28. spacer 1.1|11305|52|LS483448|CRISPRCasFinder matches to MK448544 (Streptococcus satellite phage Javan564, complete genome) position: , mismatch: 11, identity: 0.788

cctacagcctcatgctctcggtcgccaaacttctgagcgtggggctttttga	CRISPR spacer
gtaattgcctcatgctctcggtcgcctaatttctgagcgtggggctttggtt	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