Use this CRT formatted CRISPR data
ORGANISM: gi|134103876|gb|EF434469.1| Streptococcus thermophilus strain DGCC7710 CRISPR1 locus genomic sequence Bases: 2225 CRISPR 1 Range: 38 - 2184 POSITION REPEAT SPACER -------- ------------------------------------ ----------------------------- 38 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC TGTTTGACAGCAAATCAAGATTCGAATTGT [ 36, 30 ] 104 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC AATGACGAGGAGCTATTGGCACAACTTACA [ 36, 30 ] 170 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC CGATTTGACAATCTGCTGACCACTGTTATC [ 36, 30 ] 236 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC ACACTTGGCAGGCTTATTACTCAACAGCGA [ 36, 30 ] 302 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC CTGTTCCTTGTTCTTTTGTTGTATCTTTTC [ 36, 30 ] 368 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC TTCATTCTTCCGTTTTTGTTTGCGAATCCT [ 36, 30 ] 434 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC GCTGGCGAGGAAACGAACAAGGCCTCAACA [ 36, 30 ] 500 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC CATAGAGTGGAAAACTAGAAACAGATTCAA [ 36, 30 ] 566 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC ATAATGCCGTTGAATTACACGGCAAGGTCA [ 36, 30 ] 632 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC GAGCGAGCTCGAAATAATCTTAATTACAAG [ 36, 30 ] 698 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC GTTCGCTAGCGTCATGTGGTAACGTATTTA [ 36, 30 ] 764 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC GGCGTCCCAATCCTGATTAATACTTACTCG [ 36, 30 ] 830 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC AACACAGCAAGACAAGAGGATGATGCTATG [ 36, 30 ] 896 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC CGACACAAGAACGTATGCAAGAGTTCAAG [ 36, 29 ] 961 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC ACAATTCTTCATCCGGTAACTGCTCAAGTG [ 36, 30 ] 1027 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC AATTAAGGGCATAGAAAGGGAGACAACATG [ 36, 30 ] 1093 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC CGATATTTAAAATCATTTTCATAACTTCAT [ 36, 30 ] 1159 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC GCAGTATCAGCAAGCAAGCTGTTAGTTACT [ 36, 30 ] 1225 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC ATAAACTATGAAATTTTATAATTTTTAAGA [ 36, 30 ] 1291 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC AATAATTTATGGTATAGCTTAATATCATTG [ 36, 30 ] 1357 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC TGCATCGAGCACGTTCGAGTTTACCGTTTC [ 36, 30 ] 1423 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC TCTATATCGAGGTCAACTAACAATTATGCT [ 36, 30 ] 1489 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC AATCGTTCAAATTCTGTTTTAGGTACATTT [ 36, 30 ] 1555 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC AATCAATACGACAAGAGTTAAAATGGTCTT [ 36, 30 ] 1621 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC GCTTAGCTGTCCAATCCACGAACGTGGATG [ 36, 30 ] 1687 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC CAACCAACGGTAACAGCTACTTTTTACAGT [ 36, 30 ] 1753 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC ATAACTGAAGGATAGGAGCTTGTAAAGTCT [ 36, 30 ] 1819 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC TAATGCTACATCTCAAAGGATGATCCCAGA [ 36, 30 ] 1885 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC AAGTAGTTGATGACCTCTACAATGGTTTAT [ 36, 30 ] 1951 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC ACCTAGAAGCATTTGAGCGTATATTGATTG [ 36, 30 ] 2017 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC AATTTTGCCCCTTCTTTGCCCCTTGACTAG [ 36, 30 ] 2083 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC ACCATTAGCAATCATTTGTGCCCATTGAGT [ 36, 30 ] 2149 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAGT -------- ------------------------------------ ----------------------------- Repeats: 33 Average Length: 36 Average Length: 29 Time to find repeats: 11 ms
Use this CRISPR_Detect formatted CRISPR data
Array 3 2937206-2935917 **** Predicted by CRISPRDetect 2.3 *** >gi|NC_008463.1|ref|NC_008463-NZ_AABQ07000000 NZ_AABQ07000001 NZ_AABQ07000002|Pseudomonas aeruginosa UCBPP-PA14, complete genome. Array_Orientation: Reverse Position Repeat %id Spacer Repeat_Sequence Spacer_Sequence Insertion/Deletion ========== ====== ====== ====== ============================ ================================= ================== 2937206 28 100.0 32 ............................ ATCAGCCGGACGTTGTAGTAGTCGAGCGCGGT 2937146 28 100.0 33 ............................ GCCGGGTGGTGACTTCTGGACGGCGTTCGTCAA 2937085 28 100.0 32 ............................ GACCTGGTTTTGGCCGACACAGTGGCTGCGAC 2937025 28 100.0 32 ............................ CGGTCCTGCCAGTACTGCGGCAGGATCTGGTC 2936965 28 100.0 32 ............................ AGCCTGGCGCCCTTCGAGTCCATCCAGCCCGG 2936905 28 100.0 32 ............................ CATCCAATTCGCCGATCCGGCGCAAGCGCCCG 2936845 28 100.0 32 ............................ ACGAAGCAGATCGCCGAATGCGGCGTCAGCGC 2936785 28 100.0 32 ............................ GTGGGTGCAAATCGCGATTCTGGTCGCGTCGT 2936725 28 100.0 32 ............................ TGAATATCAGCCTGCAAAGCGTCGTCGTAGTA 2936665 28 100.0 32 ............................ AAGCCGGGCCGATGTTCGAGCCTGGCTGCGTG 2936605 28 100.0 32 ............................ TGGACAATGCGCAGCCCAGGCGCTGGATTTAC 2936545 28 100.0 32 ............................ ATGCGAGGCTGATCGAGGTGCGCGGTTCTGTT 2936485 28 100.0 32 ............................ GTGCGCGGATGGCTGGTATCTCGAGCACGATT 2936425 28 100.0 32 ............................ AGGCAAACAACGGAAAGATCACCACCGAAGGC 2936365 28 100.0 32 ............................ AACGAAACAGGCCCAGCACAGCCGCTTGATAA 2936305 28 100.0 32 ............................ ACAAGACGCTCATCGACGGCAGCATCGAGACG 2936245 28 100.0 32 ............................ AAGGTGACGATGCACAGCTGTTGCGCGCGGTT 2936185 28 100.0 32 ............................ ATCCTCGAACAGCCCGGGTTCGGTCGCCTCCA 2936125 28 100.0 32 ............................ AGGAGTTTGCGGCCCCGCTCCCTGCGGCTCTC 2936065 28 100.0 32 ............................ TTCACGGCGGGCTTGATGTCCGCGTCTACCTG 2936005 28 100.0 32 ............................ TTGCCGAGTACGATGCCTGATACATGAATCCA 2935945 28 100.0 0 ............................ | ========== ====== ====== ====== ============================ ================================= ================== 22 28 100.0 32 GTTCACTGCCGTGTAGGCAGCTAAGAAA # Left flank : GCGCCCGAACGGCACGGTTGATCGCCGTCCCGGTCCTCGCGAAACGGCCGCCAATTGCCCGAAGCTTCCGACCCTTTTTTCGGACGATTTCTTACGCCCTTATAAATCAGCAAGTTACGAGACCTCGAAAAAAGAGGGTTTCTGGCGGGAAAAACTCGGTATTTCTTTTTCCTTCAAATGGTTATAGGTTTTCGGAGCTA # Right flank : CTCGAACCCACCTCGGCCACAACAGCCGCCGGGTTCGCTGCCGTCTAGGCAGAACCACCCTCCCCATCCCACTACCAAACATCCGAATATAAAGTTCCTACCCCGCCCGCCAGCCTCGCCCGTCCACGACAATGTGCCTCGCTTGGAAGCTCACGCTCCTCACACAGACGAAAACGGGGTAGCGGCAATCGGCCATATCC # Questionable array : NO Score: 8.03 # Score Detail : 1:0, 2:3, 3:0, 4:1.00, 5:0, 6:1, 7:1.03, 8:1, 9:1, # Score Legend : 1: cas, 2: likely_repeat, 3: motif_match, 4: overall_repeat_identity, 5: one_repeat_cluster, 6: exp_repeat_length, 7:exp_spacer_length, 8: spacer_identity, 9: log(total repeats) - log(total mutated repeats), # Primary repeat : GTTCACTGCCGTGTAGGCAGCTAAGAAA # Alternate repeat : NA # Directional analysis summary from each method: # Motif ATTGAAA(N) match prediction: NA Score: 0/4.5 # A,T distribution in repeat prediction: R [6,8] Score: 0.37/0.37 # Reference repeat match prediction: R [matched GTTCACTGCCGTGTAGGCAGCTAAGAAA with 100% identity] Score: 4.5/4.5 # Secondary Structural analysis prediction: R [-7.70,-8.00] Score: 0.37/0.37 # Array degeneracy analysis prediction: NA [0-0] Score: 0/0.41 # AT richness analysis in flanks prediction: R [31.7-60.0]%AT Score: 0.27/0.27 # Longer leader analysis prediction: NA # ---------------------------------------------------------------------------- # Final direction: R [0,5.51 Confidence: HIGH] # Identified Cas genes: NA # Array family : I-F [Matched known repeat from this family], //
Use this CRISPRFinder formatted CRISPR data.
######################################## # Program: Crispr Finder Program # Author: Ibtissem GRISSA # Rundate (GMT): - # Report_file: test_file ######################################## #======================================= # # Sequence: NC_004547 # Description: Erwinia carotovora subsp. atroseptica SCRI1043, complete genome # Length: 5064019 # Id: gi|50118965|ref|NC_004547.2| # #========================================================================= # Crispr Rank in the sequence: 1 # Crispr_begin_position: 4124152 Crispr_end_position: 4125860 # DR: TTTCTAAGCTGCCTGTACGGCAGTGAAC DR_length: 28 Number_of_spacers: 27 #========================================================================= Spacer_begin_position Spacer_length Spacer_sequence 4124180 33 GGGTTGCCTCGGCCTGAACAGCGATCTCGCGTG 4124241 32 TTGAAATTAGTGACGTGAGCAGAATCGTAAAC 4124301 32 CGATACTCGGATACGCTCCCAGACCTTATCGA 4124361 32 AACACGCCGCGCGATTTTGTCCACAATGCGCA 4124421 32 TGTCGAGCGCTGATTCGTCGGTCACTGGATAC 4124481 32 TCCATAGTCCTCGGAAGGGACGACGATGTGAC 4124541 32 CATTAATTGACGTCTCTCTATCAATTATCTGT 4124601 32 CCGAGCCTGTATTACAGGTGGTTATGGCGACA 4124661 32 ACGCTTGATATTGCTTATGGCGTGTTAGTTCA 4124721 32 GATCGGCAAAGATAATCAGGCACTCATCACCG 4124781 32 TGAATGAGCCGGCCAATCTATATCACTACACT 4124841 32 GGCGCGTCAGTGAAGTGGATGTATCCGTGCCA 4124901 32 GCGGGGGCTAATGTGTCTGAGGCTGGTAGATC 4124961 32 CCAGACCGCAGCAACTACCAGTTAGCTCAACA 4125021 32 GAGCAATTCGCGCATGAGTTCGCGTCTACGCT 4125081 32 GCGTTAGGCTCGTCGGTGTAGATCAACTTTCC 4125141 32 TCTTTGTAATCACCTGTACGGCTGGCCCACAC 4125201 32 TTACGGACGCAATCTATGTGCCGTGTAACGAT 4125261 32 ACGCTGCGTAAGCTGGCAACCGGTGAGGTGCA 4125321 32 TTTGTCCTTGAGCCTGACCGCTTCCGCCATCG 4125381 32 CTGTCGCAGTATTTGACCCACGACGTGATGCT 4125441 32 AGCTTGCGTTGCTCGTCTGTCAAATTGCGGGT 4125501 32 AGGCGATGGTGTCGTGGTCTGACCCTGCAAAC 4125561 32 AACCGTCGCTCGCTGGCCACTGTACGATTCGC 4125621 32 ACTCTGTTATTCCCCAACTGGCGTATGCCGAG 4125681 32 CCTGACGGCAACGCCGACGCCGATCCGACACA 4125741 32 AATCAATGGCTCAGGGGATTCTACAACCCTAA 4125801 32 GCATCCGTCCAGACCGTATCGATAGTCTCTGC #========================================================================= ########################################
News and updates
1. CRISPR RNA (crRNA) sequences to analyse
A. Upload a file containing the entire CRISPR array (supported formats are CRISPRDetect, CRT, PILER-CR, CRISPRFinder, CRISPRCasFinder (result.json) ):
OR
A. Paste entire content of a CRISPR array file e.g.
CRT
,
CRISPRDetect,
CRISPRFinder
or CRISPRCasFinder (json) :
OR
A. Upload just the spacers in FASTA (multiFASTA) format:
B. Remove redundant spacer sequences from your uploaded/pasted CRISPR(s):
C. Optional: Upload the FASTA sequence file which was used for generating the CRISPR prediction:
2. Select target database(s)
Select database(s) from the list containing the target/protospacer sequences:
ACLAME genes
Genbank-Environmental (note:large)
Genbank-Phage (default)
RefSeq-Archaea
RefSeq-Plasmid (default)
RefSeq-Viral
IMGVR (default)
Islandviewer
HuVirDB
PHAST
CAMERA selection
Test
OR
Upload a file containing putative target sequence(s) in FASTA/MultiFASTA format:
3. Parameters for the initial BLAST screen
Gap open: -
extend: -
Nucleotide match:
mismatch:
E-value:
Word size:
DB size:
Filter:
4.
Initial output display parameters
(Defaults to score a low cutoff of 20, 26/32 basepairs)
A. Spacer orientation to display
Show targets using the input sequence as the CRISPR RNA sequence.
Show the reverse complement (if the direction of transcription is unknown).
B. Order output based on spacer ID, rather than score
C. Cutoff score
D. Spacer match score
Match reward:
Mismatch penalty:
E. Scores for the 3' region of protospacer
(if relevant)(Help on types of CRISPRs and PAMs)
5' crRNA handle length (3' end flanking protospacer) :
|
Score for each base match
and mismatch
in handle.
Select PAM from the list
-----------------------
ALL PAMs
NGG (I-A,I-B)
CAT,CTT,CCT,CTC (I-E)
GAA (I-C)
GG (I-F)
OR give PAM in 5'--
--3' order.
|
PAM match score
Seed - require complementarity in the leading
bases except base
of the spacer and protospacer pair.
F. Scores for the 5' region of protospacer
(if relevant)
3' crRNA handle length (5' end flanking protospacer) :
|
Score for each base match
and mismatch
in handle.
Select PAM from the list
-----------------------
ALL PAMs
WTTCTNN (II-A)
TTTYRNNN (II-A)
CNCCN (II-B)
CCN (II-B)
OR give PAM in 5'--
--3' order.
|
PAM match score
Seed - require complementarity in the leading
bases except base(s)
of the spacer and protospacer pair.
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