Input and runtime details for job 5825354 (precomputed example)

Input Parameters

	Sequence(s)		[.fa]
	Sequence type		Virus DNA/RNA sequence(s) (FASTA format)

Genome information

DNA sequence completeness

complete

Parameters concerning CRISPR arrays

	CRISPR array orientation prediction		Yes
	ML model to use		all
	Detect the IS-element		Yes
	Compute degenerated repeat		Yes
	Fast run mode		No
	Enhancement of the predicted array		Yes
	Enhancement of the start and end of the array		Yes
	Min. repeat length in the array		21
	Max. repeat length in the array		55
	Min. spacer length in the array		18
	Max. spacer length in the array		78
	Min. number of repeats in the array		3
	Max. edit distance for evaluated array enhancement		6
	Max. number of identical spacers in the array		4
	Max. number of consecutive identical spacers in the array		3
	Max. length of the spacer's margin for the degenerated search		30

Parameters concerning Cas genes

	ML model to run		combination of both
	Select the classifiers		ERT
	Select the regressors		ERT
	Max. number of contiguous gaps in a cassette		2

Parameters for CRISPR repeat input

Hit sensitivity (e-value threshold)

0.01

Parameters for Virus DNA/RNA input

Hit sensitivity (e-value threshold)

0.000001

Job ID 5825354 (server version trunk)

	Job Submitted & Queued		@ Thu Dec 17 15:33:36 CET 2020
	CRISPRloci Started		@ Thu Dec 17 15:33:54 CET 2020
	CRISPRloci Finished & Post-Processing		@ Thu Dec 17 15:34:25 CET 2020
	Job Completed		@ Thu Dec 17 15:34:29 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5825354&toolName=CRISPRloci ( 30 days expiry )

Description of the job

Genomic region of of Sulfolobus islandicus rod-shaped virus 8 (NC_034623)

Overview of CRISPR-Cas system on the genome

Zoom: Download CRISPR-Cas system

Zoom: Download

Viral DNA Results

Sort by selecting a column name. [Download Table Data]

ID	Start	End	Acc.Nr	ArrayID	Array.Loc	Array.Size	Organism	Num.Host.Spacers	e-Value	Input.Viral.Genome	SpacerID	Spacer.Start	Spacer.Align.End	Spacer.Strand	Spacer.Length	BlastBitscore	Blast.Percent.Identity	Length.Hybrid.Region	Region.Matched.Hybrid	Seq.Spacer.Aligned	Seq.Target.Aligned	DB.Spacer.Seq
Protospacer1	193	233	AE006641	8	1811198_1815558	66 Spacers	Sulfolobus-solfataricus-P2	17	3e-11	NC_034623.1	S_349637	1	41	minus	41	63.4	97.561	82	0.975609756097561	CCAAATAATAATTGGAGCGGTGCAAAAAATTCAAAATTCCA	CCAAATATTAATTGGAGCGGTGCAAAAAATTCAAAATTCCA	TGGAATTTTGAATTTTTTGCACCGCTCCAATTATTATTTGG
Protospacer2	193	233	ACUK01000127	1	210_4570	66 Spacers	Saccharolobus-solfataricus-98/2-contig127	17	3e-11	NC_034623.1	S_290200	1	41	plus	41	63.4	97.561	82	0.975609756097561	CCAAATAATAATTGGAGCGGTGCAAAAAATTCAAAATTCCA	CCAAATATTAATTGGAGCGGTGCAAAAAATTCAAAATTCCA	CCAAATAATAATTGGAGCGGTGCAAAAAATTCAAAATTCCA
Protospacer3	6950	6990	LOBW01000074	1	77_4353	66 Spacers	Thermocladium-sp.-ECH_B-100231	17	3.34e-12	NC_034623.1	S_522292	1	41	plus	41	66.6	100.0	82	1.0	AATACAATTTTCAATTCCAGTTGATAGAGTTGAATTTATAG	AATACAATTTTCAATTCCAGTTGATAGAGTTGAATTTATAG	AATACAATTTTCAATTCCAGTTGATAGAGTTGAATTTATAG
Protospacer4	7797	7837	LOBW01000074	1	77_4353	66 Spacers	Thermocladium-sp.-ECH_B-100231	17	3e-11	NC_034623.1	S_522329	1	41	plus	41	63.4	97.561	82	0.975609756097561	ATAAAAAAAATCGTAACTTATGACGTTTTAAAATTCGTCTT	ATAAAAAAAATCGTAACTTATGACATTTTAAAATTCGTCTT	ATAAAAAAAATCGTAACTTATGACGTTTTAAAATTCGTCTT
Protospacer5	9083	9128	AE006641	7	1809772_1811222	22 Spacers	Sulfolobus-solfataricus-P2	2	1.0000000000000001e-11	NC_034623.1	S_349578	1	46	minus	48	65.0	93.478	94	0.9148936170212766	GTATCCATATTCAATAATGCATTAACTCCAAGTGTTGTGGTATCTT	GTATCCATATTCAATAATGCATTAATTCCAAGAGTTGTAGTATCTT	AAGATACCACAACACTTGGAGTTAATGCATTATTGAATATGGATACAT
Protospacer6	9614	9652	LOBW01000074	1	77_4353	66 Spacers	Thermocladium-sp.-ECH_B-100231	17	2.19e-08	NC_034623.1	S_522302	1	39	minus	39	53.9	92.30799999999999	78	0.9230769230769232	TATGCTATGAATCACAAGCTAAACAGATCTGAAGTAATT	TATGCTATGAATCATAAATTAAACAGATCTGAAGTAATT	AATTACTTCAGATCTGTTTAGCTTGTGATTCATAGCATA
Protospacer7	11288	11328	CP011056	5	2557814_2558227	6 Spacers	Saccharolobus-solfataricus-strain-SARC-C-chromosome	5	2.43e-09	NC_034623.1	S_89373	1	41	minus	41	57.1	92.68299999999999	82	0.9268292682926829	TCAGAATATGGAATAACTGGGCCTAACAGAGCTATTTACCA	TCAGAATATGGAATTACTGGTCCTAACAGAGCCATTTACCA	TGGTAAATAGCTCTGTTAGGCCCAGTTATTCCATATTCTGA
Protospacer8	11288	11328	ACUK01000010	1	2373_2786	6 Spacers	Saccharolobus-solfataricus-98/2-contig10	5	2.43e-09	NC_034623.1	S_290040	1	41	minus	41	57.1	92.68299999999999	82	0.9268292682926829	TCAGAATATGGAATAACTGGGCCTAACAGAGCTATTTACCA	TCAGAATATGGAATTACTGGTCCTAACAGAGCCATTTACCA	TGGTAAATAGCTCTGTTAGGCCCAGTTATTCCATATTCTGA
Protospacer9	11288	11328	CP011057	5	2557814_2558227	6 Spacers	Sulfolobus-solfataricus-strain-SULA	5	2.43e-09	NC_034623.1	S_66801	1	41	minus	41	57.1	92.68299999999999	82	0.9268292682926829	TCAGAATATGGAATAACTGGGCCTAACAGAGCTATTTACCA	TCAGAATATGGAATTACTGGTCCTAACAGAGCCATTTACCA	TGGTAAATAGCTCTGTTAGGCCCAGTTATTCCATATTCTGA
Protospacer10	11288	11328	CP011055	5	2557814_2558227	6 Spacers	Saccharolobus-solfataricus-strain-SARC-B-chromosome	5	2.43e-09	NC_034623.1	S_89054	1	41	minus	41	57.1	92.68299999999999	82	0.9268292682926829	TCAGAATATGGAATAACTGGGCCTAACAGAGCTATTTACCA	TCAGAATATGGAATTACTGGTCCTAACAGAGCCATTTACCA	TGGTAAATAGCTCTGTTAGGCCCAGTTATTCCATATTCTGA
Protospacer11	11289	11328	AE006641	6	1744006_1744418	6 Spacers	Sulfolobus-solfataricus-P2	5	7.290000000000001e-09	NC_034623.1	S_349559	1	40	minus	40	55.5	92.5	80	0.925	CAGAATATGGAATAACTGGGCCTAACAGAGCTATTTACCA	CAGAATATGGAATTACTGGTCCTAACAGAGCCATTTACCA	TGGTAAATAGCTCTGTTAGGCCCAGTTATTCCATATTCTG
Protospacer12	13294	13331	AE006641	8	1811198_1815558	66 Spacers	Sulfolobus-solfataricus-P2	17	6.559999999999999e-08	NC_034623.1	S_349621	3	40	minus	40	52.3	92.105	78	0.8974358974358975	TATTAAAAGAATGATGAATAAGTTATAATTCTTTTTTT	TATACAAAGAATGATGAAAAAGTTATAATTCTTTTTTT	ATAAAAAAAGAATTATAACTTATTCATCATTCTTTTAATA
Protospacer13	13294	13331	ACUK01000127	1	210_4570	66 Spacers	Saccharolobus-solfataricus-98/2-contig127	17	6.559999999999999e-08	NC_034623.1	S_290216	1	38	plus	40	52.3	92.105	78	0.8974358974358975	TATTAAAAGAATGATGAATAAGTTATAATTCTTTTTTT	TATACAAAGAATGATGAAAAAGTTATAATTCTTTTTTT	TATTAAAAGAATGATGAATAAGTTATAATTCTTTTTTTAT
Protospacer14	15867	15908	ACUK01000096	1	4104_11436	115 Spacers	Saccharolobus-solfataricus-98/2-contig96	2	7.290000000000001e-09	NC_034623.1	S_290152	1	42	minus	42	55.5	90.476	84	0.9047619047619048	TTGAACTTGTAGAAATTGTTCATATGAAACAGCATAATTTTC	TTGGACTTGTAAAAATTGTTCATATGAAACTGCATAATTCTC	GAAAATTATGCTGTTTCATATGAACAATTTCTACAAGTTCAA
Protospacer15	15867	15908	CP011057	1	2112739_2120133	116 Spacers	Sulfolobus-solfataricus-strain-SULA	6	7.290000000000001e-09	NC_034623.1	S_66521	1	42	plus	42	55.5	90.476	84	0.9047619047619048	TTGAACTTGTAGAAATTGTTCATATGAAACAGCATAATTTTC	TTGGACTTGTAAAAATTGTTCATATGAAACTGCATAATTCTC	TTGAACTTGTAGAAATTGTTCATATGAAACAGCATAATTTTC
Protospacer16	15867	15908	CP011055	1	2112739_2120133	116 Spacers	Saccharolobus-solfataricus-strain-SARC-B-chromosome	6	7.290000000000001e-09	NC_034623.1	S_88774	1	42	plus	42	55.5	90.476	84	0.9047619047619048	TTGAACTTGTAGAAATTGTTCATATGAAACAGCATAATTTTC	TTGGACTTGTAAAAATTGTTCATATGAAACTGCATAATTCTC	TTGAACTTGTAGAAATTGTTCATATGAAACAGCATAATTTTC
Protospacer17	15867	15908	CP011056	1	2112739_2120133	116 Spacers	Saccharolobus-solfataricus-strain-SARC-C-chromosome	6	7.290000000000001e-09	NC_034623.1	S_89093	1	42	plus	42	55.5	90.476	84	0.9047619047619048	TTGAACTTGTAGAAATTGTTCATATGAAACAGCATAATTTTC	TTGGACTTGTAAAAATTGTTCATATGAAACTGCATAATTCTC	TTGAACTTGTAGAAATTGTTCATATGAAACAGCATAATTTTC
Protospacer18	17866	17901	AE006641	1	1233466_1239960	102 Spacers	Sulfolobus-solfataricus-P2	1	8.1e-10	NC_034623.1	S_349278	1	36	minus	36	58.6	100.0	72	1.0	TAATTTGATGAATTTTAGACAATCTGGAAAATATTA	TAATTTGATGAATTTTAGACAATCTGGAAAATATTA	TAATATTTTCCAGATTGTCTAAAATTCATCAAATTA
Protospacer19	17948	17982	AE006641	8	1811198_1815558	66 Spacers	Sulfolobus-solfataricus-P2	17	2.19e-08	NC_034623.1	S_349586	6	40	minus	40	53.9	97.14299999999999	75	0.9066666666666666	ATAAGAATTCCAGTTTCTGGAACTGGAAAACAACC	ATAAGAATTCCAGTTTCTGGAACTGGAAAACAGCC	AAAGCGGTTGTTTTCCAGTTCCAGAAACTGGAATTCTTAT
Protospacer20	17948	17982	ACUK01000127	1	210_4570	66 Spacers	Saccharolobus-solfataricus-98/2-contig127	17	2.19e-08	NC_034623.1	S_290251	1	35	plus	40	53.9	97.14299999999999	75	0.9066666666666666	ATAAGAATTCCAGTTTCTGGAACTGGAAAACAACC	ATAAGAATTCCAGTTTCTGGAACTGGAAAACAGCC	ATAAGAATTCCAGTTTCTGGAACTGGAAAACAACCGCTTT
Protospacer21	22384	22422	LOBW01000074	1	77_4353	66 Spacers	Thermocladium-sp.-ECH_B-100231	17	2.19e-08	NC_034623.1	S_522330	1	39	minus	39	53.9	92.30799999999999	78	0.9230769230769232	TATTTAAGTCCGCTTGAAGTTGATAGTGAAATTTACGAA	TATTTAAATCCATTTGAAGTTGATAGTGAAATTTACGAA	TTCGTAAATTTCACTATCAACTTCAAGCGGACTTAAATA
Protospacer22	23602	23639	ACUK01000271	1	17_1074	16 Spacers	Saccharolobus-solfataricus-98/2-contig274	1	8.1e-10	NC_034623.1	S_290365	4	41	plus	41	58.6	97.368	79	0.9367088607594936	GAAATTCAACTAACTGCACAAACTCCAACACTTTTAAG	GAAATTCAATTAACTGCACAAACTCCAACACTTTTAAG	AGTGAAATTCAACTAACTGCACAAACTCCAACACTTTTAAG
Protospacer23	23602	23639	AE006641	7	1809772_1811222	22 Spacers	Sulfolobus-solfataricus-P2	2	8.1e-10	NC_034623.1	S_349565	1	38	minus	41	58.6	97.368	79	0.9367088607594936	GAAATTCAACTAACTGCACAAACTCCAACACTTTTAAG	GAAATTCAATTAACTGCACAAACTCCAACACTTTTAAG	CTTAAAAGTGTTGGAGTTTGTGCAGTTAGTTGAATTTCACT
Protospacer24	23903	23943	CP002425	1	725209_732591	114 Spacers	Sulfolobus-islandicus-REY15A	2	3e-11	NC_034623.1	S_410889	1	41	minus	41	63.4	97.561	82	0.975609756097561	CAAATTCATCAATTACAATTTATATGTTTGTAAGAAATTCA	CAAATTCATCAATTACAATTTATATGTTTATAAGAAATTCA	TGAATTTCTTACAAACATATAAATTGTAATTGATGAATTTG
Protospacer25	24991	25030	ACUK01000127	1	210_4570	66 Spacers	Saccharolobus-solfataricus-98/2-contig127	17	6.559999999999999e-08	NC_034623.1	S_290222	1	40	minus	40	52.3	90.0	80	0.9	TTTAACTATGACTTTTCAGAATACAACAATTTCGCCAATT	TTTGACTATGACTTTTCAGAATACTACAATTTCACCGATT	AATTGGCGAAATTGTTGTATTCTGAAAAGTCATAGTTAAA
Protospacer26	24991	25030	AE006641	8	1811198_1815558	66 Spacers	Sulfolobus-solfataricus-P2	17	6.559999999999999e-08	NC_034623.1	S_349615	1	40	plus	40	52.3	90.0	80	0.9	TTTAACTATGACTTTTCAGAATACAACAATTTCGCCAATT	TTTGACTATGACTTTTCAGAATACTACAATTTCACCGATT	TTTAACTATGACTTTTCAGAATACAACAATTTCGCCAATT
Protospacer27	26287	26327	CP002425	1	725209_732591	114 Spacers	Sulfolobus-islandicus-REY15A	2	2.43e-09	NC_034623.1	S_410923	1	41	minus	41	57.1	92.68299999999999	82	0.9268292682926829	TACAAAATACGAATTCTCTATTATCATCAGTTATAAAAGTT	TACAAAATATAAATTCTTTATTATCATCAGTTATAAAAGTT	AACTTTTATAACTGATGATAATAGAGAATTCGTATTTTGTA
Protospacer28	26897	26940	AE006641	8	1811198_1815558	66 Spacers	Sulfolobus-solfataricus-P2	17	1.1100000000000001e-12	NC_034623.1	S_349640	1	44	minus	44	68.2	97.727	88	0.9772727272727272	ATATAAACTATATAATTACTAAGATTTTGTAAAATTATTCTTAC	ATATAAACTATATAATTGCTAAGATTTTGTAAAATTATTCTTAC	GTAAGAATAATTTTACAAAATCTTAGTAATTATATAGTTTATAT
Protospacer29	26897	26940	ACUK01000127	1	210_4570	66 Spacers	Saccharolobus-solfataricus-98/2-contig127	17	1.1100000000000001e-12	NC_034623.1	S_290197	1	44	plus	44	68.2	97.727	88	0.9772727272727272	ATATAAACTATATAATTACTAAGATTTTGTAAAATTATTCTTAC	ATATAAACTATATAATTGCTAAGATTTTGTAAAATTATTCTTAC	ATATAAACTATATAATTACTAAGATTTTGTAAAATTATTCTTAC
Protospacer30	28559	28597	CP011055	1	2112739_2120133	116 Spacers	Saccharolobus-solfataricus-strain-SARC-B-chromosome	6	2.19e-08	NC_034623.1	S_88803	1	39	plus	39	53.9	92.30799999999999	78	0.9230769230769232	ATCAATTTACGCCTTTTAGAAATCCAATTTCAATTATTC	ATCAATTTACCCCATTCAGAAATCCAATTTCAATTATTC	ATCAATTTACGCCTTTTAGAAATCCAATTTCAATTATTC
Protospacer31	28559	28597	CP011057	1	2112739_2120133	116 Spacers	Sulfolobus-solfataricus-strain-SULA	6	2.19e-08	NC_034623.1	S_66550	1	39	plus	39	53.9	92.30799999999999	78	0.9230769230769232	ATCAATTTACGCCTTTTAGAAATCCAATTTCAATTATTC	ATCAATTTACCCCATTCAGAAATCCAATTTCAATTATTC	ATCAATTTACGCCTTTTAGAAATCCAATTTCAATTATTC
Protospacer32	28559	28597	ACUK01000096	1	4104_11436	115 Spacers	Saccharolobus-solfataricus-98/2-contig96	2	2.19e-08	NC_034623.1	S_290123	1	39	minus	39	53.9	92.30799999999999	78	0.9230769230769232	ATCAATTTACGCCTTTTAGAAATCCAATTTCAATTATTC	ATCAATTTACCCCATTCAGAAATCCAATTTCAATTATTC	GAATAATTGAAATTGGATTTCTAAAAGGCGTAAATTGAT
Protospacer33	28559	28597	CP011056	1	2112739_2120133	116 Spacers	Saccharolobus-solfataricus-strain-SARC-C-chromosome	6	2.19e-08	NC_034623.1	S_89122	1	39	plus	39	53.9	92.30799999999999	78	0.9230769230769232	ATCAATTTACGCCTTTTAGAAATCCAATTTCAATTATTC	ATCAATTTACCCCATTCAGAAATCCAATTTCAATTATTC	ATCAATTTACGCCTTTTAGAAATCCAATTTCAATTATTC
Protospacer34	32235	32276	ACUK01000127	1	210_4570	66 Spacers	Saccharolobus-solfataricus-98/2-contig127	17	8.1e-10	NC_034623.1	S_290226	1	42	minus	42	58.6	92.85700000000001	84	0.9285714285714286	AAACGATAAATTAGCACTATATTATAACTATGATTCTACACA	AAACGATAAATTAGCATTATATTATACCTATGATTCTTCACA	TGTGTAGAATCATAGTTATAATATAGTGCTAATTTATCGTTT
Protospacer35	32235	32276	AE006641	8	1811198_1815558	66 Spacers	Sulfolobus-solfataricus-P2	17	8.1e-10	NC_034623.1	S_349611	1	42	plus	42	58.6	92.85700000000001	84	0.9285714285714286	AAACGATAAATTAGCACTATATTATAACTATGATTCTACACA	AAACGATAAATTAGCATTATATTATACCTATGATTCTTCACA	AAACGATAAATTAGCACTATATTATAACTATGATTCTACACA
Protospacer36	32945	32985	LOBW01000074	1	77_4353	66 Spacers	Thermocladium-sp.-ECH_B-100231	17	3.34e-12	NC_034623.1	S_522333	1	41	minus	41	66.6	100.0	82	1.0	TGATATAAAATGACTGAATCACAAGGTAGAAAAATTAGATT	TGATATAAAATGACTGAATCACAAGGTAGAAAAATTAGATT	AATCTAATTTTTCTACCTTGTGATTCAGTCATTTTATATCA

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When using CRISPRloci please cite :

Omer S. Alkhnbashi, Alexander Mitrofanov, Robson Bonidia, Martin Raden, Van Dinh Tran, Florian Eggenhofer, Shiraz A. Shah, Ekrem ̈Öztürk, Victor A. Padilha, Danilo S. Sanches, Andre C.P.L.F. de Carvalho and Rolf Backofen
CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems
Nucleic Acids Research, 2021.
Alexander Mitrofanov, Omer S. Alkhnbashi, Sergey A. Shmakov, Kira S. Makarova, Eugene V. Koonin, and Rolf Backofen
CRISPRidentify: identification of CRISPR arrays using machine learning approach
Nucleic Acids Research, 49(4), e20, 2021.
Victor A. Padilha, Omer S. Alkhnbashi, Van Dinh Tran, Shiraz A. Shah, Andre C.P.L. de Carvalho and Rolf Backofen
Casboundary: automated definition of integral Cas cassettes
Bioinformatics, 2021.
Victor A. Padilha, Omer S. Alkhnbashi, Shiraz A. Shah, Andre C.P.L.F. de Carvalho and Rolf Backofen
CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems
Gigascience, 9(6), 2020.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CRISPRloci version 1.1.0

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