Difference between revisions of "CRISPR info"

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(BLASTing CRISPRs)
 
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== CRISPRs from JGI: ==
+
[[Direct Repeats]]
  
ID: Halomicrobium mukohataei DSM 12286, ''unfinished sequence'': NZ_ABTY01000001<br>
+
[[Blasting Spacers for Our Genome]]
Start Potision: 1000310<br>
 
End Position: 1002443<br>
 
CRISPR length: 2133
 
  
 +
[[Spacers for Other Species]]
  
ID: Halomicrobium mukohataei DSM 12286, ''unfinished sequenc''e: NZ_ABTY01000002<br>
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[[Blasting Spacers for Haloferax mediterranei]]
Start Position: 201627 <br>
 
End Position: 204293<br>
 
CRISPR length: 2666
 
  
== Found on CRISPRFInder: ==
+
[[CRISPR-associated Proteins]]
 
 
'''Two confirmed CRISPRs:'''
 
 
 
CRISPR id : tmp_1_Crispr_12<br>
 
START crispr position : 2723382 <br>
 
END crispr position : 2725579 <br>
 
Crispr length : 2197 <br>
 
DR consensus : GTTTCAGACGGACCCTTGTGGGATTGAAGC DR length : 30<br>
 
Number of spacers : 33<br>
 
 
 
 
 
CRISPR id : tmp_2_Crispr_1<br>
 
START crispr position : 31920<br>
 
END crispr position : 34849<br>
 
Crispr length : 2929<br>
 
DR consensus : GCTTCAATCCCACAAGGGTCCGTCTGAAAC DR length : 30<br>
 
Number of spacers : 44<br>
 
 
 
 
 
 
 
'''11 Questionable CRISPRs:'''
 
 
 
CRISPR id : tmp_1_PossibleCrispr_1<br>
 
START crispr position : 451036<br>
 
END crispr position : 451146<br>
 
Crispr length : 110<br>
 
DR consensus : CCTCGACCGTGTCGGCCGCGCCGCC DR length : 25<br>
 
Number of spacers : 1<br>
 
 
 
 
 
CRISPR id : tmp_1_PossibleCrispr_2<br>
 
START crispr position : 451266<br>
 
END crispr position : 451422<br>
 
Crispr length : 156<br>
 
DR consensus : CCTCGACCGTGTCGGCCGCGCCGCC DR length : 25<br>
 
Number of spacers : 2<br>
 
 
 
 
 
CRISPR id : tmp_1_PossibleCrispr_3<br>
 
START crispr position : 723910<br>
 
END crispr position : 724040<br>
 
Crispr length : 130<br>
 
DR consensus : CCGCCCGAACACGCCGGTCCCGACCACGAGAACGAGAC DR length : 38<br>
 
Number of spacers : 1<br>
 
 
 
 
 
RISPR id : tmp_1_PossibleCrispr_4<br>
 
START crispr position : 775514<br>
 
END crispr position : 775595<br>
 
Crispr length : 81<br>
 
DR consensus : TGATTCGCCCAGCGAGCGCGTTCGTG DR length : 26<br>
 
Number of spacers : 1<br>
 
 
 
 
 
CRISPR id : tmp_1_PossibleCrispr_5<br>
 
START crispr position : 1587713<br>
 
END crispr position : 1587871
 
Crispr length : 158<br>
 
DR consensus : TCGAAGGGGCTGTCGCTGTCGGTG DR length : 24<br>
 
Number of spacers : 2<br>
 
 
 
 
 
CRISPR id : tmp_1_PossibleCrispr_6<br>
 
START crispr position : 1635784<br>
 
END crispr position : 1635940<br>
 
Crispr length : 156<br>
 
DR consensus : CCTCGACCGTGTCGGCCGCGCCGCC DR length : 25<br>
 
Number of spacers : 2<br>
 
 
 
 
 
CRISPR id : tmp_1_PossibleCrispr_7<br>
 
START crispr position : 1733154<br>
 
END crispr position : 1733268<br>
 
Crispr length : 114<br>
 
DR consensus : GTTCGCCGGACCGTGTGGGTGTCG DR length : 24<br>
 
Number of spacers : 2<br>
 
 
 
 
 
CRISPR id : tmp_1_PossibleCrispr_8<br>
 
START crispr position : 2087618<br>
 
END crispr position : 2087725<br>
 
Crispr length : 107<br>
 
DR consensus : AGCGCCGGGCGACGACGGGCCAGC DR length : 24<br>
 
Number of spacers : 1<br>
 
 
 
 
 
CRISPR id : tmp_1_PossibleCrispr_9<br>
 
START crispr position : 2127953<br>
 
END crispr position : 2128039<br>
 
Crispr length : 86<br>
 
DR consensus : CGCTCGCTTCGAGGGCCGACACTCGCT DR length : 27<br>
 
Number of spacers : 1<br>
 
 
 
 
 
CRISPR id : tmp_1_PossibleCrispr_10<br>
 
START crispr position : 2206888<br>
 
END crispr position : 2206968<br>
 
Crispr length : 80<br>
 
DR consensus : CAGTCCAGTGAGGCGTCTCGTCGTCG DR length : 26<br>
 
Number of spacers : 1<br>
 
 
 
 
 
CRISPR id : tmp_1_PossibleCrispr_11<br>
 
START crispr position : 2293949<br>
 
END crispr position : 2294199<br>
 
Crispr length : 250<br>
 
DR consensus : CGTTCGCAGCAAAACGGGCCGGAAGGGATTTGAACC DR length : 36<br>
 
Number of spacers : 2<br>
 
 
 
== BLASTing CRISPRs ==
 
 
 
I Blasted the two confirmed direct repeat (DR) sequences found by CRISPR Finder in order to see if these repeats are found in any other archaea.
 
 
 
DR sequences: 1. GTTTCAGACGGACCCTTGTGGGATTGAAGC    2. GCTTCAATCCCACAAGGGTCCGTCTGAAAC
 
 
 
For both DRs 1 and 2 had top hits with the three archaeal species with which we commonly compare H. mukohataei:
 
# Haloarcula marismortui
 
# Halorhabdus utahensis
 
# Natronomonas pharaonis
 
 
 
[[Image:CRISPRCompare102909.png|600px|thumb|center]]
 

Latest revision as of 17:02, 19 November 2009

Direct Repeats

Blasting Spacers for Our Genome

Spacers for Other Species

Blasting Spacers for Haloferax mediterranei

CRISPR-associated Proteins