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
LR129840	Streptococcus pneumoniae strain 4496 genome assembly, chromosome: 1	5 crisprs	NA	2	2	0	0

Cas Category Instructions

Results visualization

1. LR129840

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CRISPR-Cas detection and classification

Crispr_ID: LR129840_1

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LR129840_1

130751-130846

Orphan

Consensus_repeat	Method
AATGTGTAAGATTTTTATATATAA	CRISPRCasFinder

1 spacers

The CRISPR arrays of LR129840_1

>merge|LR129840|1|130751-130846|CRISPRCasFinder
AATGTGTAAGATTTTTATATATAATTTTTCTACACATACATTGTACATCTAAAAGAAAGCCCTGTCAAGAGAAATGTGTAAAATTTTTATATATAA

>LR129840|1|1|130751-130846|CRISPRCasFinder
AATGTGTAAGATTTTTATATATAA	TTTTTCTACACATACATTGTACATCTAAAAGAAAGCCCTGTCAAGAGA
AATGTGTAAAATTTTTATATATAA

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Crispr_ID: LR129840_2

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LR129840_2

1100821-1100900

Orphan

Consensus_repeat	Method
TTCTGGTGTCTGCCACCGCTTGGCCC	CRISPRCasFinder

1 spacers

The CRISPR arrays of LR129840_2

>merge|LR129840|2|1100821-1100900|CRISPRCasFinder
TTCTGGTGTCTGCCACCGCTTGGCCCGTACGTCCAAGATTGCTATCGGATTTTGTTCTGGTGTCCGCCACCGCTTGGCCC

>LR129840|2|2|1100821-1100900|CRISPRCasFinder
TTCTGGTGTCTGCCACCGCTTGGCCC	GTACGTCCAAGATTGCTATCGGATTTTG
TTCTGGTGTCCGCCACCGCTTGGCCC

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Crispr_ID: LR129840_3

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LR129840_3

1121175-1121287

Orphan

Consensus_repeat	Method
TCAATCAAGTTTCCATTTTCATCCACTCCTGTTGT	CRISPRCasFinder

1 spacers

The CRISPR arrays of LR129840_3

>merge|LR129840|3|1121175-1121287|CRISPRCasFinder
TCAATCAAGTTTCCATTTTCATCCACTCCTGTTGTACCTACTGGCTCAGTATATTCTGGGATGTCGTTAACAGGTGGTTCAATCAAGTTTCCATTTTCATCTACTCCTGTTGT

>LR129840|3|3|1121175-1121287|CRISPRCasFinder
TCAATCAAGTTTCCATTTTCATCCACTCCTGTTGT	ACCTACTGGCTCAGTATATTCTGGGATGTCGTTAACAGGTGGT
TCAATCAAGTTTCCATTTTCATCTACTCCTGTTGT

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Crispr_ID: LR129840_4

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LR129840_4

1264519-1264590

Orphan

Consensus_repeat	Method
ATTTACAAAATCAACCTCGCTCT	CRISPRCasFinder

1 spacers

The CRISPR arrays of LR129840_4

>merge|LR129840|4|1264519-1264590|CRISPRCasFinder
ATTTACAAAATCAACCTCGCTCTCTTATTTTTAGGCTCGGGAAAAAATGATTTACAAAATCAGCCTCGCTCT

>LR129840|4|4|1264519-1264590|CRISPRCasFinder
ATTTACAAAATCAACCTCGCTCT	CTTATTTTTAGGCTCGGGAAAAAATG
ATTTACAAAATCAGCCTCGCTCT

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Crispr_ID: LR129840_5

CRISPR_ID

CRISPR_location

CRISPR_type

Repeat_type

Spacer_info

Cas_protein_info

CRISPR-Cas_info

LR129840_5

1687759-1687908

Orphan

Consensus_repeat	Method
GTTGATGCCGATGTGCTT	CRT

3 spacers

The CRISPR arrays of LR129840_5

>merge|LR129840|5|1687759-1687908|CRT
GTTGATGCCGATGTGCTTGCACTTGTCGATGCGGACGTGCTTGCGCTTGTTGATGCTGACGTGCTTGCTGACGTACTTGCGCTTGTTGATGCCGATGTGCTTGCTGACGTGCTTGCTGAGGTCGACGCGCTTGTTGATGCCGATGTACTT

>LR129840|5|1|1687759-1687908|CRT
GTTGATGCCGATGTGCTT	GCACTTGTCGATGCGGACGTGCTTGCGCTT
GTTGATGCTGACGTGCTT	GCTGACGTACTTGCGCTT
GTTGATGCCGATGTGCTT	GCTGACGTGCTTGCTGAGGTCGACGCGCTT
GTTGATGCCGATGTACTT

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Self-targeting detection

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_ID	Protospacer_location	Mismatch	Identity
LR129840_5	5.1\|1687777\|30\|LR129840\|CRT	1687777-1687806	30	LR129840.1	1685743-1685772	0	1.0
LR129840_5	5.2\|1687825\|18\|LR129840\|CRT	1687825-1687842	18	LR129840.1	1687909-1687926	1	0.944
LR129840_5	5.2\|1687825\|18\|LR129840\|CRT	1687825-1687842	18	LR129840.1	1682683-1682700	2	0.889
LR129840_5	5.2\|1687825\|18\|LR129840\|CRT	1687825-1687842	18	LR129840.1	1682947-1682964	2	0.889
LR129840_5	5.2\|1687825\|18\|LR129840\|CRT	1687825-1687842	18	LR129840.1	1683649-1683666	2	0.889
LR129840_5	5.2\|1687825\|18\|LR129840\|CRT	1687825-1687842	18	LR129840.1	1683745-1683762	2	0.889
LR129840_5	5.2\|1687825\|18\|LR129840\|CRT	1687825-1687842	18	LR129840.1	1685755-1685772	2	0.889
LR129840_5	5.2\|1687825\|18\|LR129840\|CRT	1687825-1687842	18	LR129840.1	1686025-1686042	2	0.889
LR129840_5	5.2\|1687825\|18\|LR129840\|CRT	1687825-1687842	18	LR129840.1	1686121-1686138	2	0.889

1. spacer 5.1|1687777|30|LR129840|CRT matches to position: 1685743-1685772, mismatch: 0, identity: 1.0

gcacttgtcgatgcggacgtgcttgcgctt	CRISPR spacer
gcacttgtcgatgcggacgtgcttgcgctt	Protospacer
******************************

2. spacer 5.2|1687825|18|LR129840|CRT matches to position: 1687909-1687926, mismatch: 1, identity: 0.944

gctgacgtacttgcgctt	CRISPR spacer
gctgacgtgcttgcgctt	Protospacer
********.*********

3. spacer 5.2|1687825|18|LR129840|CRT matches to position: 1682683-1682700, mismatch: 2, identity: 0.889

gctgacgtacttgcgctt	CRISPR spacer
gctgacgcacttgtgctt	Protospacer
*******.*****.****

4. spacer 5.2|1687825|18|LR129840|CRT matches to position: 1682947-1682964, mismatch: 2, identity: 0.889

gctgacgtacttgcgctt	CRISPR spacer
gctgacgcacttgtgctt	Protospacer
*******.*****.****

5. spacer 5.2|1687825|18|LR129840|CRT matches to position: 1683649-1683666, mismatch: 2, identity: 0.889

gctgacgtacttgcgctt	CRISPR spacer
gctgacgcacttgtgctt	Protospacer
*******.*****.****

6. spacer 5.2|1687825|18|LR129840|CRT matches to position: 1683745-1683762, mismatch: 2, identity: 0.889

gctgacgtacttgcgctt	CRISPR spacer
gctgacgcacttgtgctt	Protospacer
*******.*****.****

7. spacer 5.2|1687825|18|LR129840|CRT matches to position: 1685755-1685772, mismatch: 2, identity: 0.889

gctgacgtacttgcgctt	CRISPR spacer
gcggacgtgcttgcgctt	Protospacer
** *****.*********

8. spacer 5.2|1687825|18|LR129840|CRT matches to position: 1686025-1686042, mismatch: 2, identity: 0.889

gctgacgtacttgcgctt	CRISPR spacer
gctgacgcacttgtgctt	Protospacer
*******.*****.****

9. spacer 5.2|1687825|18|LR129840|CRT matches to position: 1686121-1686138, mismatch: 2, identity: 0.889

gctgacgtacttgcgctt	CRISPR spacer
gctgacgcacttgtgctt	Protospacer
*******.*****.****

MGE targeting detection<

CRISPR_ID	Spacer_Info	Spacer_region	Spacer_length	Hit_phage_ID	Hit_phage_def	Protospacer_location	Mismatch	Identity
LR129840_5	5.1\|1687777\|30\|LR129840\|CRT	1687777-1687806	30	MT701594	Streptomyces phage Spernnie, complete genome	42475-42504	6	0.8
LR129840_5	5.1\|1687777\|30\|LR129840\|CRT	1687777-1687806	30	KU197014	Xanthomonas phage XAJ2, complete genome	44358-44387	6	0.8
LR129840_5	5.1\|1687777\|30\|LR129840\|CRT	1687777-1687806	30	MN234216	Streptomyces phage Gilgamesh, complete genome	110357-110386	6	0.8
LR129840_5	5.3\|1687861\|30\|LR129840\|CRT	1687861-1687890	30	NZ_CP020040	Streptomyces sp. 3211 isolate 3 plasmid p3211-1, complete sequence	443145-443174	6	0.8
LR129840_5	5.1\|1687777\|30\|LR129840\|CRT	1687777-1687806	30	NZ_CP013104	Paraburkholderia caribensis strain MWAP64 plasmid 1, complete sequence	1079324-1079353	7	0.767
LR129840_5	5.1\|1687777\|30\|LR129840\|CRT	1687777-1687806	30	NZ_AP022593	Mycolicibacterium arabiense strain JCM 18538 plasmid pJCM18538, complete sequence	2135227-2135256	7	0.767
LR129840_5	5.1\|1687777\|30\|LR129840\|CRT	1687777-1687806	30	NZ_CP015867	Streptomyces parvulus strain 2297 plasmid pSPA1, complete sequence	424002-424031	8	0.733
LR129840_5	5.1\|1687777\|30\|LR129840\|CRT	1687777-1687806	30	MG962371	Mycobacterium phage LaterM, complete genome	53081-53110	8	0.733
LR129840_5	5.1\|1687777\|30\|LR129840\|CRT	1687777-1687806	30	KM677211	Mycobacterium phage Murucutumbu, complete genome	53625-53654	8	0.733

1. spacer 5.1|1687777|30|LR129840|CRT matches to MT701594 (Streptomyces phage Spernnie, complete genome) position: , mismatch: 6, identity: 0.8

gcacttgtcgatgcggacgtgcttgcgctt	CRISPR spacer
gtacttgttgttgcggacgtgcttgcgggc	Protospacer
*.******.* ****************  .

2. spacer 5.1|1687777|30|LR129840|CRT matches to KU197014 (Xanthomonas phage XAJ2, complete genome) position: , mismatch: 6, identity: 0.8

-gcacttgtcgatgcggacgtgcttgcgctt	CRISPR spacer
cgta-atgtcgatgtgaacgtgcttgcgctg	Protospacer
 *.*  ********.*.*************

3. spacer 5.1|1687777|30|LR129840|CRT matches to MN234216 (Streptomyces phage Gilgamesh, complete genome) position: , mismatch: 6, identity: 0.8

gcacttgtcgatgcggacgtgcttgcgctt	CRISPR spacer
gccgttgacgatgcggacgtgctggcgggt	Protospacer
**  *** *************** ***  *

4. spacer 5.3|1687861|30|LR129840|CRT matches to NZ_CP020040 (Streptomyces sp. 3211 isolate 3 plasmid p3211-1, complete sequence) position: , mismatch: 6, identity: 0.8

--gctgacgtgcttgctgaggtcgacgcgctt	CRISPR spacer
cagttg--gtgcatgctgaggtcgacgcgggt	Protospacer
  *.**  **** ****************  *

5. spacer 5.1|1687777|30|LR129840|CRT matches to NZ_CP013104 (Paraburkholderia caribensis strain MWAP64 plasmid 1, complete sequence) position: , mismatch: 7, identity: 0.767

gcacttgtcgatgcggacgtgcttgcgctt	CRISPR spacer
gcgcggcccgatgcggacgtgctcgcgctg	Protospacer
**.*   .***************.*****

6. spacer 5.1|1687777|30|LR129840|CRT matches to NZ_AP022593 (Mycolicibacterium arabiense strain JCM 18538 plasmid pJCM18538, complete sequence) position: , mismatch: 7, identity: 0.767

gcacttgtcgatgcggacgtgcttgcgctt	CRISPR spacer
gatcttgtcgaagcggacgtccttgctcca	Protospacer
*  ******** ******** ***** *.

7. spacer 5.1|1687777|30|LR129840|CRT matches to NZ_CP015867 (Streptomyces parvulus strain 2297 plasmid pSPA1, complete sequence) position: , mismatch: 8, identity: 0.733

gcacttgtcgatgcggacgtgcttgcgctt	CRISPR spacer
cgagttgtcgatgcggacatgcttgaggag	Protospacer
  * **************.****** *

8. spacer 5.1|1687777|30|LR129840|CRT matches to MG962371 (Mycobacterium phage LaterM, complete genome) position: , mismatch: 8, identity: 0.733

gcacttgtcgatgcggacgtgcttgcgctt	CRISPR spacer
gccgaggtcgatgcggaggtgcttgcgtcg	Protospacer
**    *********** *********..

9. spacer 5.1|1687777|30|LR129840|CRT matches to KM677211 (Mycobacterium phage Murucutumbu, complete genome) position: , mismatch: 8, identity: 0.733

gcacttgtcgatgcggacgtgcttgcgctt	CRISPR spacer
gccgacgtcgatgcggaggtgcttgcgtcg	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