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 PILER-CR formatted CRISPR data
pilercr v1.02 By Robert C. Edgar EF434469.fasta: 1 putative CRISPR arrays found. DETAIL REPORT Array 1 >gi|134103876|gb|EF434469.1| Streptococcus thermophilus strain DGCC7710 CRISPR1 locus genomic sequence Pos Repeat %id Spacer Left flank Repeat Spacer ========== ====== ====== ====== ========== ==================================== ====== 38 36 100.0 30 TTCATTTGAG .................................... TGTTTGACAGCAAATCAAGATTCGAATTGT 104 36 100.0 30 TTCGAATTGT .................................... AATGACGAGGAGCTATTGGCACAACTTACA 170 36 100.0 30 ACAACTTACA .................................... CGATTTGACAATCTGCTGACCACTGTTATC 236 36 100.0 30 CACTGTTATC .................................... ACACTTGGCAGGCTTATTACTCAACAGCGA 302 36 100.0 30 TCAACAGCGA .................................... CTGTTCCTTGTTCTTTTGTTGTATCTTTTC 368 36 100.0 30 GTATCTTTTC .................................... TTCATTCTTCCGTTTTTGTTTGCGAATCCT 434 36 100.0 30 TGCGAATCCT .................................... GCTGGCGAGGAAACGAACAAGGCCTCAACA 500 36 100.0 30 GGCCTCAACA .................................... CATAGAGTGGAAAACTAGAAACAGATTCAA 566 36 100.0 30 ACAGATTCAA .................................... ATAATGCCGTTGAATTACACGGCAAGGTCA 632 36 100.0 30 GGCAAGGTCA .................................... GAGCGAGCTCGAAATAATCTTAATTACAAG 698 36 100.0 30 TAATTACAAG .................................... GTTCGCTAGCGTCATGTGGTAACGTATTTA 764 36 100.0 30 AACGTATTTA .................................... GGCGTCCCAATCCTGATTAATACTTACTCG 830 36 100.0 30 TACTTACTCG .................................... AACACAGCAAGACAAGAGGATGATGCTATG 896 36 100.0 29 TGATGCTATG .................................... CGACACAAGAACGTATGCAAGAGTTCAAG 961 36 100.0 30 AGAGTTCAAG .................................... ACAATTCTTCATCCGGTAACTGCTCAAGTG 1027 36 100.0 30 TGCTCAAGTG .................................... AATTAAGGGCATAGAAAGGGAGACAACATG 1093 36 100.0 30 AGACAACATG .................................... CGATATTTAAAATCATTTTCATAACTTCAT 1159 36 100.0 30 ATAACTTCAT .................................... GCAGTATCAGCAAGCAAGCTGTTAGTTACT 1225 36 100.0 30 GTTAGTTACT .................................... ATAAACTATGAAATTTTATAATTTTTAAGA 1291 36 100.0 30 ATTTTTAAGA .................................... AATAATTTATGGTATAGCTTAATATCATTG 1357 36 100.0 30 AATATCATTG .................................... TGCATCGAGCACGTTCGAGTTTACCGTTTC 1423 36 100.0 30 TTACCGTTTC .................................... TCTATATCGAGGTCAACTAACAATTATGCT 1489 36 100.0 30 CAATTATGCT .................................... AATCGTTCAAATTCTGTTTTAGGTACATTT 1555 36 100.0 30 AGGTACATTT .................................... AATCAATACGACAAGAGTTAAAATGGTCTT 1621 36 100.0 30 AAATGGTCTT .................................... GCTTAGCTGTCCAATCCACGAACGTGGATG 1687 36 100.0 30 AACGTGGATG .................................... CAACCAACGGTAACAGCTACTTTTTACAGT 1753 36 100.0 30 TTTTTACAGT .................................... ATAACTGAAGGATAGGAGCTTGTAAAGTCT 1819 36 100.0 30 TGTAAAGTCT .................................... TAATGCTACATCTCAAAGGATGATCCCAGA 1885 36 100.0 30 TGATCCCAGA .................................... AAGTAGTTGATGACCTCTACAATGGTTTAT 1951 36 100.0 30 AATGGTTTAT .................................... ACCTAGAAGCATTTGAGCGTATATTGATTG 2017 36 100.0 30 ATATTGATTG .................................... AATTTTGCCCCTTCTTTGCCCCTTGACTAG 2083 36 100.0 CCTTGACTAG .................................... ACCATTAGCA ========== ====== ====== ====== ========== ==================================== 32 36 29 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC SUMMARY BY SIMILARITY Array Sequence Position Length # Copies Repeat Spacer + Consensus ===== ================ ========== ========== ======== ====== ====== = ========= 1 gi|134103876|gb| 38 2081 32 36 29 + GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC SUMMARY BY POSITION >gi|134103876|gb|EF434469.1| Streptococcus thermophilus strain DGCC7710 CRISPR1 locus genomic sequence Array Sequence Position Length # Copies Repeat Spacer Distance Consensus ===== ================ ========== ========== ======== ====== ====== ========== ========= 1 gi|134103876|gb| 38 2081 32 36 29 GTTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC
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 CRT, PILER-CR and CRISPRFinder ):
OR
A. Paste entire content of a CRISPR array file (sample CRISPR array files
CRT
,
PILER-CR
and
CRISPRFinder
) :
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:
2. Select target database(s)
Select database(s) from the list containing the target/protospacer sequences:
Genbank-Environmental
Genbank-Phage (default)
RefSeq-Bacteria (note:large > 30 min )
RefSeq-Archaea
RefSeq-Plasmid (default)
RefSeq-Viral
Genbank-Viral
Islandviewer
IMGVR (default)
HuVirDB
PHAST
CAMERA selection
Test
Test2
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
(can be changed after the output is generated)
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.