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Input and runtime details for job 3195732 (precomputed example)
Input Parameters
Sequence(s) | [.fa] | ||
Sequence type | Single Genome DNA (FASTA format) |
Genome information
DNA sequence completeness | complete |
Parameters concerning CRISPR arrays
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 3195732 (server version trunk)
Job Submitted & Queued | @ Fri Dec 18 07:37:00 CET 2020 | ||
CRISPRloci Started | @ Fri Dec 18 07:37:09 CET 2020 | ||
CRISPRloci Finished & Post-Processing | @ Fri Dec 18 07:50:33 CET 2020 | ||
Job Completed | @ Fri Dec 18 07:50:55 CET 2020 |
DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3195732&toolName=CRISPRloci ( 30 days expiry )
Description of the job
Synechocystis sp. PCC 6803 plasmid pSYSA (NC_005230)
CRISPR Array Summary
Sort by selecting a column name.
[Download Table Data]
ID | Start | End | Length | Consensus repeat | Repeat Length | Average Spacer Length | Number of spacers | Strand | Category | subtype |
---|---|---|---|---|---|---|---|---|---|---|
CRISPR1 | 16310 | 19901 | 3592 | GTTTCAGTCCCGATCGCCGGGATTAGTAGAAGGAAAG | 37 | 35 | 49 | Reversed | Bona-fide | I-D |
CRISPR2 | 68499 | 72778 | 4280 | GTTTCAGTCCCCTGACGGGGAAAAGAGGGTGTTGAAC | 37 | 38 | 56 | Reversed | Bona-fide | III-D |
CRISPR3 | 90105 | 92958 | 2854 | GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAAC | 36 | 38 | 38 | Forward | Bona-fide | III-B |
CRISPR Details for selection from above
Summary of Self-targeting
Sort by selecting a column name.
[Download Table Data]
#mismatches | Spacer.Len | SpacerID | ArrayID | Spacer.Start.Alin | Spacer.End.Align | Start-Area.selftargets | End-Area.selftargets | Category | Detail |
---|---|---|---|---|---|---|---|---|---|
31 | 44 | S11 | Array_2 | 13 | 1 | 67759 | 67771 | GenomicRegion | GenomicRegion |
28 | 41 | S12 | Array2 | 18 | 5 | 30803 | 30816 | ProphageRegion | ProphageRegion |
22 | 35 | S11 | Array_1 | 18 | 5 | 27874 | 27887 | GenomicRegion | GenomicRegion |
26 | 42 | S9 | Array_2 | 18 | 1 | 86963 | 86980 | CasgeneRegion | cas10_III-B(Prot98) |
25 | 39 | S19 | Array_3 | 18 | 4 | 20508 | 20522 | GenomicRegion | GenomicRegion |
21 | 37 | S22 | Array_2 | 19 | 1 | 52095 | 52113 | CasgeneRegion | csx1_III-D(Prot70) |
25 | 40 | S21 | Array_2 | 19 | 1 | 75183 | 75201 | GenomicRegion | GenomicRegion |
24 | 37 | S56 | Array_2 | 21 | 8 | 67892 | 67905 | GenomicRegion | GenomicRegion |
31 | 44 | S38 | Array_2 | 21 | 8 | 24892 | 24905 | GenomicRegion | GenomicRegion |
18 | 36 | S26 | Array1 | 22 | 1 | 35435 | 35456 | ProphageRegion | ProphageRegion |
18 | 35 | S3 | Array_2 | 22 | 2 | 14491 | 14511 | CasgeneRegion | cas4_I-D(Prot15) |
27 | 41 | S5 | Array_2 | 22 | 7 | 82523 | 82538 | CasgeneRegion | cmr5_III-B(Prot94) |
17 | 34 | S7 | Array_1 | 23 | 2 | 76778 | 76799 | GenomicRegion | GenomicRegion |
20 | 36 | S16 | Array_1 | 23 | 4 | 14029 | 14048 | CasgeneRegion | cas6_I-D(Prot14) |
19 | 36 | S33 | Array_2 | 23 | 1 | 85891 | 85913 | CasgeneRegion | cas10_III-B(Prot98) |
22 | 37 | S52 | Array_2 | 23 | 5 | 9838 | 9856 | CasgeneRegion | cas10d_I-D(Prot11) |
17 | 35 | S22 | Array_1 | 24 | 1 | 62145 | 62168 | CasgeneRegion | cas10_III-D(Prot76) |
21 | 38 | S46 | Array_1 | 24 | 1 | 43610 | 43633 | GenomicRegion | GenomicRegion |
27 | 42 | S43 | Array_2 | 24 | 8 | 28458 | 28474 | GenomicRegion | GenomicRegion |
17 | 34 | S47 | Array_1 | 25 | 4 | 100467 | 100488 | GenomicRegion | GenomicRegion |
17 | 36 | S32 | Array_1 | 25 | 1 | 66112 | 66136 | CasgeneRegion | cas2_III-D(Prot81) |
20 | 37 | S37 | Array_1 | 25 | 5 | 93770 | 93790 | GenomicRegion | GenomicRegion |
21 | 35 | S35 | Array_1 | 25 | 9 | 75204 | 75220 | GenomicRegion | GenomicRegion |
21 | 37 | S2 | Array_3 | 25 | 6 | 47533 | 47552 | GenomicRegion | GenomicRegion |
23 | 40 | S28 | Array_3 | 25 | 3 | 2882 | 2904 | GenomicRegion | GenomicRegion |
18 | 37 | S10 | Array3 | 26 | 3 | 33312 | 33335 | ProphageRegion | ProphageRegion |
14 | 35 | S3 | Array_1 | 26 | 2 | 78970 | 78994 | GenomicRegion | GenomicRegion |
22 | 40 | S26 | Array_3 | 26 | 5 | 80454 | 80475 | CasgeneRegion | cmr6_III-B(Prot93) |
29 | 46 | S32 | Array2 | 27 | 6 | 36609 | 36630 | ProphageRegion | ProphageRegion |
18 | 36 | S49 | Array_1 | 27 | 7 | 85650 | 85670 | CasgeneRegion | cas10_III-B(Prot98) |
23 | 42 | S17 | Array_1 | 27 | 3 | 38824 | 38848 | GenomicRegion | GenomicRegion |
23 | 42 | S19 | Array_1 | 27 | 3 | 38824 | 38848 | GenomicRegion | GenomicRegion |
25 | 37 | S34 | Array_1 | 27 | 15 | 98193 | 98205 | GenomicRegion | GenomicRegion |
24 | 39 | S24 | Array1 | 28 | 10 | 37975 | 37993 | ProphageRegion | ProphageRegion |
18 | 38 | S21 | Array_1 | 28 | 1 | 97100 | 97127 | GenomicRegion | GenomicRegion |
18 | 38 | S4 | Array_1 | 28 | 1 | 12992 | 13019 | CasgeneRegion | csc1_I-D(Prot13) |
19 | 39 | S44 | Array_2 | 28 | 3 | 84194 | 84219 | CasgeneRegion | cmr3_III-B(Prot97) |
20 | 38 | S29 | Array_2 | 28 | 5 | 43284 | 43307 | GenomicRegion | GenomicRegion |
17 | 37 | S6 | Array_3 | 28 | 1 | 99613 | 99640 | GenomicRegion | GenomicRegion |
18 | 37 | S4 | Array_3 | 28 | 2 | 84076 | 84102 | CasgeneRegion | cmr3_III-B(Prot97) |
21 | 38 | S9 | Array3 | 29 | 7 | 37695 | 37717 | ProphageRegion | ProphageRegion |
18 | 38 | S5 | Array_1 | 29 | 2 | 62575 | 62602 | CasgeneRegion | cas10_III-D(Prot76) |
26 | 40 | S48 | Array_2 | 29 | 14 | 78563 | 78578 | GenomicRegion | GenomicRegion |
26 | 40 | S50 | Array_2 | 29 | 14 | 78563 | 78578 | GenomicRegion | GenomicRegion |
17 | 36 | S31 | Array_1 | 30 | 6 | 44999 | 45023 | GenomicRegion | GenomicRegion |
16 | 36 | S23 | Array_2 | 30 | 2 | 61912 | 61940 | CasgeneRegion | cas10_III-D(Prot76) |
27 | 40 | S30 | Array_2 | 30 | 16 | 9297 | 9311 | CasgeneRegion | cas10d_I-D(Prot11) |
27 | 47 | S2 | Array_2 | 30 | 5 | 39973 | 39998 | GenomicRegion | GenomicRegion |
17 | 36 | S12 | Array_3 | 30 | 5 | 11024 | 11049 | CasgeneRegion | cas10d_I-D(Prot11) |
24 | 43 | S31 | Array_3 | 30 | 6 | 86204 | 86228 | CasgeneRegion | cas10_III-B(Prot98) |
17 | 38 | S25 | Array1 | 31 | 2 | 38671 | 38700 | ProphageRegion | ProphageRegion |
9 | 32 | S1 | Array_1 | 31 | 1 | 50583 | 50613 | GenomicRegion | GenomicRegion |
16 | 37 | S12 | Array_1 | 31 | 2 | 30258 | 30287 | GenomicRegion | GenomicRegion |
18 | 38 | S18 | Array_1 | 31 | 5 | 48144 | 48170 | GenomicRegion | GenomicRegion |
18 | 38 | S20 | Array_1 | 31 | 5 | 48144 | 48170 | GenomicRegion | GenomicRegion |
19 | 36 | S39 | Array_1 | 31 | 9 | 101207 | 101229 | GenomicRegion | GenomicRegion |
19 | 36 | S40 | Array_1 | 31 | 9 | 101207 | 101229 | GenomicRegion | GenomicRegion |
22 | 40 | S44 | Array_1 | 31 | 5 | 79806 | 79832 | GenomicRegion | GenomicRegion |
21 | 37 | S14 | Array_2 | 31 | 11 | 53605 | 53625 | CasgeneRegion | csm6_III-D(Prot71) |
18 | 37 | S14 | Array_3 | 31 | 7 | 4659 | 4683 | GenomicRegion | GenomicRegion |
24 | 41 | S24 | Array_3 | 31 | 10 | 45779 | 45800 | GenomicRegion | GenomicRegion |
22 | 43 | S39 | Array2 | 32 | 6 | 31974 | 32000 | ProphageRegion | ProphageRegion |
12 | 33 | S2 | Array_1 | 32 | 1 | 28663 | 28694 | GenomicRegion | GenomicRegion |
20 | 36 | S41 | Array_1 | 32 | 13 | 25314 | 25333 | GenomicRegion | GenomicRegion |
21 | 37 | S8 | Array_1 | 32 | 15 | 8323 | 8340 | CasgeneRegion | cas3_I-D(Prot10) |
22 | 36 | S43 | Array_1 | 32 | 18 | 42967 | 42981 | GenomicRegion | GenomicRegion |
16 | 38 | S13 | Array_2 | 32 | 2 | 11366 | 11396 | CasgeneRegion | cas10d_I-D(Prot11) |
19 | 37 | S18 | Array_2 | 32 | 8 | 50276 | 50300 | GenomicRegion | GenomicRegion |
19 | 37 | S20 | Array_2 | 32 | 8 | 50276 | 50300 | GenomicRegion | GenomicRegion |
20 | 35 | S26 | Array_2 | 32 | 14 | 5789 | 5807 | CasgeneRegion | wyl_I-D(Prot9) |
14 | 36 | S22 | Array_3 | 32 | 1 | 100595 | 100626 | GenomicRegion | GenomicRegion |
16 | 38 | S11 | Array_3 | 32 | 1 | 7811 | 7842 | CasgeneRegion | cas3_I-D(Prot10) |
16 | 38 | S18 | Array_3 | 32 | 1 | 60246 | 60277 | CasgeneRegion | csm3_III-D(Prot75) |
20 | 41 | S38 | Array_3 | 32 | 3 | 20950 | 20979 | GenomicRegion | GenomicRegion |
22 | 38 | S23 | Array_3 | 32 | 12 | 29362 | 29382 | GenomicRegion | GenomicRegion |
18 | 35 | S1 | Array2 | 33 | 12 | 34207 | 34228 | ProphageRegion | ProphageRegion |
14 | 36 | S28 | Array_1 | 33 | 3 | 12657 | 12687 | CasgeneRegion | csc1_I-D(Prot13) |
17 | 34 | S15 | Array_1 | 33 | 12 | 3317 | 3338 | GenomicRegion | GenomicRegion |
17 | 36 | S27 | Array_1 | 33 | 9 | 29126 | 29150 | GenomicRegion | GenomicRegion |
19 | 37 | S38 | Array_1 | 33 | 11 | 73712 | 73734 | GenomicRegion | GenomicRegion |
21 | 36 | S37 | Array_2 | 33 | 15 | 50333 | 50351 | GenomicRegion | GenomicRegion |
22 | 40 | S25 | Array_2 | 33 | 11 | 29530 | 29552 | GenomicRegion | GenomicRegion |
15 | 36 | S16 | Array_3 | 33 | 4 | 14772 | 14801 | CasgeneRegion | cas4_I-D(Prot15) |
18 | 40 | S5 | Array3 | 34 | 4 | 33904 | 33934 | ProphageRegion | ProphageRegion |
14 | 35 | S23 | Array_1 | 34 | 6 | 52165 | 52193 | CasgeneRegion | csx1_III-D(Prot70) |
17 | 36 | S10 | Array_1 | 34 | 10 | 80708 | 80732 | CasgeneRegion | cmr6_III-B(Prot93) |
17 | 36 | S9 | Array_1 | 34 | 10 | 80708 | 80732 | CasgeneRegion | cmr6_III-B(Prot93) |
18 | 36 | S36 | Array_1 | 34 | 13 | 58558 | 58579 | CasgeneRegion | csm3_III-D(Prot75) |
21 | 35 | S29 | Array_1 | 34 | 19 | 50558 | 50573 | GenomicRegion | GenomicRegion |
13 | 36 | S15 | Array_2 | 34 | 2 | 57426 | 57458 | CasgeneRegion | csm3_III-D(Prot74) |
18 | 36 | S8 | Array_2 | 34 | 11 | 88701 | 88724 | CasgeneRegion | cas1_III-B(Prot100) |
21 | 38 | S35 | Array_2 | 34 | 13 | 9243 | 9264 | CasgeneRegion | cas10d_I-D(Prot11) |
21 | 39 | S31 | Array_2 | 34 | 13 | 67471 | 67492 | GenomicRegion | GenomicRegion |
16 | 37 | S29 | Array_3 | 34 | 5 | 74194 | 74223 | GenomicRegion | GenomicRegion |
18 | 37 | S6 | Array_1 | 35 | 10 | 96811 | 96836 | GenomicRegion | GenomicRegion |
16 | 38 | S10 | Array_2 | 35 | 8 | 7634 | 7661 | CasgeneRegion | cas3_I-D(Prot10) |
24 | 45 | S46 | Array_2 | 35 | 5 | 89646 | 89676 | CasgeneRegion | cas2_III-B(Prot101) |
22 | 36 | S33 | Array_3 | 35 | 19 | 97246 | 97262 | GenomicRegion | GenomicRegion |
10 | 37 | S1 | Array3 | 36 | 1 | 34555 | 34590 | ProphageRegion | ProphageRegion |
14 | 38 | S45 | Array_1 | 36 | 2 | 53132 | 53166 | CasgeneRegion | csm6_III-D(Prot71) |
18 | 38 | S48 | Array_1 | 36 | 11 | 21290 | 21315 | GenomicRegion | GenomicRegion |
19 | 37 | S42 | Array_1 | 36 | 15 | 6818 | 6839 | CasgeneRegion | cas3_I-D(Prot10) |
14 | 37 | S53 | Array_2 | 36 | 6 | 9031 | 9061 | CasgeneRegion | cas10d_I-D(Prot11) |
18 | 37 | S24 | Array_2 | 36 | 10 | 94163 | 94189 | GenomicRegion | GenomicRegion |
16 | 40 | S17 | Array_3 | 36 | 5 | 12218 | 12249 | CasgeneRegion | csc2_I-D(Prot12) |
19 | 38 | S8 | Array_3 | 36 | 11 | 7261 | 7286 | CasgeneRegion | cas3_I-D(Prot10) |
21 | 37 | S13 | Array_3 | 36 | 17 | 26912 | 26931 | GenomicRegion | GenomicRegion |
21 | 42 | S15 | Array_3 | 36 | 9 | 222 | 249 | GenomicRegion | GenomicRegion |
24 | 48 | S34 | Array_3 | 36 | 2 | 49364 | 49398 | GenomicRegion | GenomicRegion |
18 | 41 | S36 | Array2 | 37 | 7 | 33139 | 33168 | ProphageRegion | ProphageRegion |
24 | 39 | S41 | Array_2 | 37 | 19 | 95598 | 95616 | GenomicRegion | GenomicRegion |
16 | 38 | S35 | Array_3 | 37 | 4 | 30557 | 30590 | GenomicRegion | GenomicRegion |
27 | 42 | S32 | Array_3 | 37 | 19 | 89961 | 89979 | GenomicRegion | GenomicRegion |
22 | 41 | S17 | Array_2 | 38 | 14 | 103071 | 103095 | GenomicRegion | GenomicRegion |
22 | 41 | S19 | Array_2 | 38 | 14 | 103071 | 103095 | GenomicRegion | GenomicRegion |
16 | 40 | S25 | Array_3 | 38 | 4 | 8040 | 8074 | CasgeneRegion | cas3_I-D(Prot10) |
19 | 41 | S28 | Array_2 | 39 | 8 | 73156 | 73187 | GenomicRegion | GenomicRegion |
22 | 40 | S45 | Array_2 | 39 | 13 | 26750 | 26776 | GenomicRegion | GenomicRegion |
25 | 46 | S7 | Array_2 | 39 | 12 | 85489 | 85516 | CasgeneRegion | cas10_III-B(Prot98) |
20 | 40 | S21 | Array_3 | 39 | 15 | 82816 | 82840 | CasgeneRegion | cmr4_III-B(Prot95) |
24 | 40 | S36 | Array_3 | 39 | 20 | 77249 | 77268 | GenomicRegion | GenomicRegion |
12 | 41 | S27 | Array_2 | 40 | 2 | 8298 | 8334 | CasgeneRegion | cas3_I-D(Prot10) |
23 | 41 | S40 | Array_2 | 40 | 16 | 54234 | 54258 | CasgeneRegion | csm3_III-D(Prot72) |
19 | 43 | S54 | Array_2 | 41 | 6 | 8225 | 8260 | CasgeneRegion | cas3_I-D(Prot10) |
20 | 46 | S4 | Array_2 | 43 | 6 | 66561 | 66598 | GenomicRegion | GenomicRegion |
25 | 47 | S27 | Array_3 | 46 | 12 | 74443 | 74477 | GenomicRegion | GenomicRegion |
CAS Protein Classification
Sort by selecting a column name.
[Download Table Data]
ID | Name | Subtype | Module | Cassette | Strand | Start | End | Length |
---|---|---|---|---|---|---|---|---|
Prot9 | wyl | I-D | interference | 2 | minus | 5340 | 6284 | 315 |
Prot10 | cas3 | I-D | interference | 2 | plus | 6349 | 8517 | 723 |
Prot11 | cas10d | I-D | interference | 2 | plus | 8531 | 11458 | 976 |
Prot12 | csc2 | I-D | interference | 2 | plus | 11524 | 12513 | 330 |
Prot13 | csc1 | I-D | interference | 2 | plus | 12674 | 13438 | 255 |
Prot14 | cas6 | I-D | processing | 2 | plus | 13441 | 14229 | 263 |
Prot15 | cas4 | I-D | adaptation | 2 | plus | 14222 | 14794 | 191 |
Prot16 | cas1 | I-D | adaptation | 2 | plus | 14804 | 15781 | 326 |
Prot17 | cas2 | I-D | adaptation | 2 | plus | 15813 | 16097 | 95 |
Prot70 | csx1 | III-D | interference | 3 | plus | 51537 | 52805 | 423 |
Prot71 | csm6 | III-D | interference | 3 | minus | 52881 | 53996 | 372 |
Prot72 | csm3 | III-D | interference | 3 | minus | 54005 | 56392 | 796 |
Prot73 | csx19 | III-D | interference | 3 | minus | 56394 | 56954 | 187 |
Prot74 | csm3 | III-D | interference | 3 | minus | 56954 | 58522 | 523 |
Prot75 | csm3 | III-D | interference | 3 | minus | 58527 | 60902 | 792 |
Prot76 | cas10 | III-D | interference | 3 | minus | 60905 | 62581 | 559 |
Prot77 | cas6 | III-D | processing | 3 | plus | 62911 | 64011 | 367 |
Prot78 | csx18 | III-D | interference | 3 | minus | 64005 | 64319 | 105 |
Prot79 | unknown | III-D | potential_cas | 3 | minus | 64316 | 64690 | 125 |
Prot80 | cas1 | III-D | adaptation | 3 | plus | 64822 | 65832 | 337 |
Prot81 | cas2 | III-D | adaptation | 3 | plus | 65842 | 66123 | 94 |
Prot93 | cmr6 | III-B | interference | 1 | minus | 80203 | 82140 | 646 |
Prot94 | cmr5 | III-B | interference | 1 | minus | 82196 | 82591 | 132 |
Prot95 | cmr4 | III-B | interference | 1 | minus | 82630 | 83409 | 260 |
Prot96 | unknown | III-B | potential_cas | 1 | plus | 83501 | 83881 | 127 |
Prot97 | cmr3 | III-B | interference | 1 | minus | 83905 | 85017 | 371 |
Prot98 | cas10 | III-B | interference | 1 | minus | 85199 | 88138 | 980 |
Prot99 | unknown | III-B | potential_cas | 1 | minus | 88253 | 88546 | 98 |
Prot100 | cas1 | III-B | adaptation | 1 | plus | 88627 | 89616 | 330 |
Prot101 | cas2 | III-B | adaptation | 1 | plus | 89620 | 89898 | 93 |
CAS Protein Sequence for selection from above
To search for conserved domains within the protein,
copy and paste its sequence to the
CD-search of NCBI.
(It is not possible to auto-fill the CD-search input form without job submission.)
(It is not possible to auto-fill the CD-search input form without job submission.)
Job resubmission
usability assessment
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