Welcome to CRISPRTarget

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) ):

A. Paste entire content of a CRISPR array file e.g. CRT, CRISPRDetect, CRISPRFinder or CRISPRCasFinder (json) :

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:

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:

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 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 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.

Best with Chrome