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CRISPRloci 3195732

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

? 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 array21
? Max. repeat length in the array55
? Min. spacer length in the array18
? Max. spacer length in the array78
? Min. number of repeats in the array3
? Max. edit distance for evaluated array enhancement6
? Max. number of identical spacers in the array4
? Max. number of consecutive identical spacers in the array3
? Max. length of the spacer's margin for the degenerated search30

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 cassette2

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)

? Overview of CRISPR-Cas system on the genome

Zoom:     Download CRISPR-Cas system    
Zoom:     Download
Legend

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

[Download Data]

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
9 32 S1 Array_1 31 1 50583 50613 GenomicRegion GenomicRegion
10 37 S1 Array3 36 1 34555 34590 ProphageRegion ProphageRegion
12 33 S2 Array_1 32 1 28663 28694 GenomicRegion GenomicRegion
12 41 S27 Array_2 40 2 8298 8334 CasgeneRegion cas3_I-D(Prot10)
13 36 S15 Array_2 34 2 57426 57458 CasgeneRegion csm3_III-D(Prot74)
14 35 S23 Array_1 34 6 52165 52193 CasgeneRegion csx1_III-D(Prot70)
14 35 S3 Array_1 26 2 78970 78994 GenomicRegion GenomicRegion
14 36 S28 Array_1 33 3 12657 12687 CasgeneRegion csc1_I-D(Prot13)
14 38 S45 Array_1 36 2 53132 53166 CasgeneRegion csm6_III-D(Prot71)
14 37 S53 Array_2 36 6 9031 9061 CasgeneRegion cas10d_I-D(Prot11)
14 36 S22 Array_3 32 1 100595 100626 GenomicRegion GenomicRegion
15 36 S16 Array_3 33 4 14772 14801 CasgeneRegion cas4_I-D(Prot15)
16 37 S12 Array_1 31 2 30258 30287 GenomicRegion GenomicRegion
16 36 S23 Array_2 30 2 61912 61940 CasgeneRegion cas10_III-D(Prot76)
16 38 S10 Array_2 35 8 7634 7661 CasgeneRegion cas3_I-D(Prot10)
16 38 S13 Array_2 32 2 11366 11396 CasgeneRegion cas10d_I-D(Prot11)
16 37 S29 Array_3 34 5 74194 74223 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)
16 38 S35 Array_3 37 4 30557 30590 GenomicRegion GenomicRegion
16 40 S17 Array_3 36 5 12218 12249 CasgeneRegion csc2_I-D(Prot12)
16 40 S25 Array_3 38 4 8040 8074 CasgeneRegion cas3_I-D(Prot10)
17 38 S25 Array1 31 2 38671 38700 ProphageRegion ProphageRegion
17 34 S15 Array_1 33 12 3317 3338 GenomicRegion GenomicRegion
17 34 S47 Array_1 25 4 100467 100488 GenomicRegion GenomicRegion
17 34 S7 Array_1 23 2 76778 76799 GenomicRegion GenomicRegion
17 35 S22 Array_1 24 1 62145 62168 CasgeneRegion cas10_III-D(Prot76)
17 36 S10 Array_1 34 10 80708 80732 CasgeneRegion cmr6_III-B(Prot93)
17 36 S27 Array_1 33 9 29126 29150 GenomicRegion GenomicRegion
17 36 S31 Array_1 30 6 44999 45023 GenomicRegion GenomicRegion
17 36 S32 Array_1 25 1 66112 66136 CasgeneRegion cas2_III-D(Prot81)
17 36 S9 Array_1 34 10 80708 80732 CasgeneRegion cmr6_III-B(Prot93)
17 36 S12 Array_3 30 5 11024 11049 CasgeneRegion cas10d_I-D(Prot11)
17 37 S6 Array_3 28 1 99613 99640 GenomicRegion GenomicRegion
18 36 S26 Array1 22 1 35435 35456 ProphageRegion ProphageRegion
18 35 S1 Array2 33 12 34207 34228 ProphageRegion ProphageRegion
18 41 S36 Array2 37 7 33139 33168 ProphageRegion ProphageRegion
18 37 S10 Array3 26 3 33312 33335 ProphageRegion ProphageRegion
18 40 S5 Array3 34 4 33904 33934 ProphageRegion ProphageRegion
18 36 S36 Array_1 34 13 58558 58579 CasgeneRegion csm3_III-D(Prot75)
18 36 S49 Array_1 27 7 85650 85670 CasgeneRegion cas10_III-B(Prot98)
18 37 S6 Array_1 35 10 96811 96836 GenomicRegion GenomicRegion
18 38 S18 Array_1 31 5 48144 48170 GenomicRegion GenomicRegion
18 38 S20 Array_1 31 5 48144 48170 GenomicRegion GenomicRegion
18 38 S21 Array_1 28 1 97100 97127 GenomicRegion GenomicRegion
18 38 S48 Array_1 36 11 21290 21315 GenomicRegion GenomicRegion
18 38 S4 Array_1 28 1 12992 13019 CasgeneRegion csc1_I-D(Prot13)
18 38 S5 Array_1 29 2 62575 62602 CasgeneRegion cas10_III-D(Prot76)
18 35 S3 Array_2 22 2 14491 14511 CasgeneRegion cas4_I-D(Prot15)
18 36 S8 Array_2 34 11 88701 88724 CasgeneRegion cas1_III-B(Prot100)
18 37 S24 Array_2 36 10 94163 94189 GenomicRegion GenomicRegion
18 37 S14 Array_3 31 7 4659 4683 GenomicRegion GenomicRegion
18 37 S4 Array_3 28 2 84076 84102 CasgeneRegion cmr3_III-B(Prot97)
19 36 S39 Array_1 31 9 101207 101229 GenomicRegion GenomicRegion
19 36 S40 Array_1 31 9 101207 101229 GenomicRegion GenomicRegion
19 37 S38 Array_1 33 11 73712 73734 GenomicRegion GenomicRegion
19 37 S42 Array_1 36 15 6818 6839 CasgeneRegion cas3_I-D(Prot10)
19 36 S33 Array_2 23 1 85891 85913 CasgeneRegion cas10_III-B(Prot98)
19 37 S18 Array_2 32 8 50276 50300 GenomicRegion GenomicRegion
19 37 S20 Array_2 32 8 50276 50300 GenomicRegion GenomicRegion
19 39 S44 Array_2 28 3 84194 84219 CasgeneRegion cmr3_III-B(Prot97)
19 41 S28 Array_2 39 8 73156 73187 GenomicRegion GenomicRegion
19 43 S54 Array_2 41 6 8225 8260 CasgeneRegion cas3_I-D(Prot10)
19 38 S8 Array_3 36 11 7261 7286 CasgeneRegion cas3_I-D(Prot10)
20 36 S16 Array_1 23 4 14029 14048 CasgeneRegion cas6_I-D(Prot14)
20 36 S41 Array_1 32 13 25314 25333 GenomicRegion GenomicRegion
20 37 S37 Array_1 25 5 93770 93790 GenomicRegion GenomicRegion
20 35 S26 Array_2 32 14 5789 5807 CasgeneRegion wyl_I-D(Prot9)
20 38 S29 Array_2 28 5 43284 43307 GenomicRegion GenomicRegion
20 46 S4 Array_2 43 6 66561 66598 GenomicRegion GenomicRegion
20 40 S21 Array_3 39 15 82816 82840 CasgeneRegion cmr4_III-B(Prot95)
20 41 S38 Array_3 32 3 20950 20979 GenomicRegion GenomicRegion
21 38 S9 Array3 29 7 37695 37717 ProphageRegion ProphageRegion
21 35 S29 Array_1 34 19 50558 50573 GenomicRegion GenomicRegion
21 35 S35 Array_1 25 9 75204 75220 GenomicRegion GenomicRegion
21 37 S8 Array_1 32 15 8323 8340 CasgeneRegion cas3_I-D(Prot10)
21 38 S46 Array_1 24 1 43610 43633 GenomicRegion GenomicRegion
21 36 S37 Array_2 33 15 50333 50351 GenomicRegion GenomicRegion
21 37 S14 Array_2 31 11 53605 53625 CasgeneRegion csm6_III-D(Prot71)
21 37 S22 Array_2 19 1 52095 52113 CasgeneRegion csx1_III-D(Prot70)
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
21 37 S13 Array_3 36 17 26912 26931 GenomicRegion GenomicRegion
21 37 S2 Array_3 25 6 47533 47552 GenomicRegion GenomicRegion
21 42 S15 Array_3 36 9 222 249 GenomicRegion GenomicRegion
22 43 S39 Array2 32 6 31974 32000 ProphageRegion ProphageRegion
22 35 S11 Array_1 18 5 27874 27887 GenomicRegion GenomicRegion
22 36 S43 Array_1 32 18 42967 42981 GenomicRegion GenomicRegion
22 40 S44 Array_1 31 5 79806 79832 GenomicRegion GenomicRegion
22 37 S52 Array_2 23 5 9838 9856 CasgeneRegion cas10d_I-D(Prot11)
22 40 S25 Array_2 33 11 29530 29552 GenomicRegion GenomicRegion
22 40 S45 Array_2 39 13 26750 26776 GenomicRegion GenomicRegion
22 41 S17 Array_2 38 14 103071 103095 GenomicRegion GenomicRegion
22 41 S19 Array_2 38 14 103071 103095 GenomicRegion GenomicRegion
22 36 S33 Array_3 35 19 97246 97262 GenomicRegion GenomicRegion
22 38 S23 Array_3 32 12 29362 29382 GenomicRegion GenomicRegion
22 40 S26 Array_3 26 5 80454 80475 CasgeneRegion cmr6_III-B(Prot93)
23 42 S17 Array_1 27 3 38824 38848 GenomicRegion GenomicRegion
23 42 S19 Array_1 27 3 38824 38848 GenomicRegion GenomicRegion
23 41 S40 Array_2 40 16 54234 54258 CasgeneRegion csm3_III-D(Prot72)
23 40 S28 Array_3 25 3 2882 2904 GenomicRegion GenomicRegion
24 39 S24 Array1 28 10 37975 37993 ProphageRegion ProphageRegion
24 37 S56 Array_2 21 8 67892 67905 GenomicRegion GenomicRegion
24 39 S41 Array_2 37 19 95598 95616 GenomicRegion GenomicRegion
24 45 S46 Array_2 35 5 89646 89676 CasgeneRegion cas2_III-B(Prot101)
24 40 S36 Array_3 39 20 77249 77268 GenomicRegion GenomicRegion
24 41 S24 Array_3 31 10 45779 45800 GenomicRegion GenomicRegion
24 43 S31 Array_3 30 6 86204 86228 CasgeneRegion cas10_III-B(Prot98)
24 48 S34 Array_3 36 2 49364 49398 GenomicRegion GenomicRegion
25 37 S34 Array_1 27 15 98193 98205 GenomicRegion GenomicRegion
25 40 S21 Array_2 19 1 75183 75201 GenomicRegion GenomicRegion
25 46 S7 Array_2 39 12 85489 85516 CasgeneRegion cas10_III-B(Prot98)
25 39 S19 Array_3 18 4 20508 20522 GenomicRegion GenomicRegion
25 47 S27 Array_3 46 12 74443 74477 GenomicRegion GenomicRegion
26 40 S48 Array_2 29 14 78563 78578 GenomicRegion GenomicRegion
26 40 S50 Array_2 29 14 78563 78578 GenomicRegion GenomicRegion
26 42 S9 Array_2 18 1 86963 86980 CasgeneRegion cas10_III-B(Prot98)
27 40 S30 Array_2 30 16 9297 9311 CasgeneRegion cas10d_I-D(Prot11)
27 41 S5 Array_2 22 7 82523 82538 CasgeneRegion cmr5_III-B(Prot94)
27 42 S43 Array_2 24 8 28458 28474 GenomicRegion GenomicRegion
27 47 S2 Array_2 30 5 39973 39998 GenomicRegion GenomicRegion
27 42 S32 Array_3 37 19 89961 89979 GenomicRegion GenomicRegion
28 41 S12 Array2 18 5 30803 30816 ProphageRegion ProphageRegion
29 46 S32 Array2 27 6 36609 36630 ProphageRegion ProphageRegion
31 44 S11 Array_2 13 1 67759 67771 GenomicRegion GenomicRegion
31 44 S38 Array_2 21 8 24892 24905 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

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Results are computed with CRISPRloci version 1.1.0
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