Difference between revisions of "Blasting Spacers for Our Genome"

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(Blasting Spacers)
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Spacer Thirteen: GATGCTGTTGAGCTCGTAGCGATCCCACTCGGCGT
 
Spacer Thirteen: GATGCTGTTGAGCTCGTAGCGATCCCACTCGGCGT

Revision as of 17:45, 10 November 2009

Blasting Spacers

CRISPR one results from CRISPR finder are shown below. I blasted all of the spacers using the nr/nt database and the results are shown below.

CrisperOne.jpg


Spacer One: TGCGTCGTCCGGTGGCCGTCAATAAATGTCGCAAGGG

No significant hits. . . lowest E-value is 25

Matches by chance!

Spacer Two: TCCTACGACCTCGTCGGCGTCAACGGCTGGCCCGA

SpacerTwo.jpg

Spacer Three: CACCCTACAACAGGTGAAATCTACCAGACAAAAGA

No significant hits. . . lowest E-value is 0.36

Spacer Four: TCACCCAAGCGCAAGCAACAGCTGATCGAGGACCTG

No significant hits. . . lowest E-value is 0.36

Spacer Five: GCGACGGCGGCCAGTTCCGCGAGGGCGGGAAGGTCC

SpacerFive.jpg

This image is only part of it. . .

SpacerFiveTwo.jpg

NOTE: lots of hits from each organism- indicates that multiple parts have been incorporated into our species' spacers. . . interesting to study what genes have been inserted

Spacer Six: TGCGAGTGTTGCGGGGAACCGACTCGGGTAGGCCAG

SpacerSix.jpg

No viral insertions in this spacer

Spacer Seven: ACGGTTTCGCTACCACCATCGCCACCAGCAACTGCCG

No significant hits. . . lowest E-value is 0.41

Spacer Eight: GACGAGTATGCCAACCGGCTCGTGAGCGGGCGC

No significant hits. . . lowest E-value is 4.9

E-values not good- no significant hits!

Spacer Nine: TGGTAGGCGTCGTAGGTGTTCGTGGCGAGCGTGTC

SpacerNine.jpg

Spacer Ten: ACTCACTGGATTATGACCCCTACAACGAGGGCGTCA

No significant hits. . . lowest E-value is 1.5

Spacer Eleven: GGATCTCGATCGTTGTAGTATCCATAGCTGCTATACC

SpacerEleven.jpg

Spacer Twelve: GAAGTAACGCAACTCCAGTGAGCGCTACTGAGAGCCC

No significant hits. . . lowest E-value is 1.6

Spacer Thirteen:CCGATCACGCCCTGCCGATACTGGTAGTTCGCGATA

Spacer13.jpg

Spacer Fourteen: TCGTCGGCCGGCTCGTCGGCCGACGTGGACTTGC

Spacer14.jpg

Spacer Fifteen: AGTAGGTCTAATGTCTCTCTGTCGTCTATCAGCCCCG

No significant hits. . . lowest E-value is 1.6

Spacer Sixteen: GCTCTCCGGTGTCACAGGTCAGGTCACGGTCTCCGC

No significant hits . . . lowest E-value is 1.5

Spacer Seventeen: ACGGACAAGTCATCCACCCGCCAGTATCTCCCGGT

No significant hits . . . lowest E-value is 1.4

Spacer Eighteen: AAATACGATCCTGCGGTGACGCTACGTCCGGGGCAGC

No significant hits . . . lowest E-value is 6.4

Spacer Nineteen: CAGATGTGGGGTCTGTGGCCACAGTCTAACATCTCT

Spacer19.jpg

Spacer Twenty: CCTGATAACGGACTCTTGTAGGTCCGTTAGGTCGT

No significant hits . . . lowest E-value is 22

Spacer Twenty-One: AAAAATGAGTGACGTAGACATTCGGCAAAATGCCGG

No significant hits . . . lowest E-value is 6

Spacer Twenty-Two: CAGCAGCGAAACGAGCCGTCCGTCCTTTTGAGACA

No significant hits . . . lowest E-value is 1.2

Spacer Twenty-Three: GTCTAGCCCAGTCTGGTCGGGGTGGTCGGCAGGATCGG

No significant hits . . . lowest E-value is 0.43

Spacer Twenty-Four: CACTCCTCATATGTCTGTTCGAGCAGCGGGACGTG

No significant hits . . . lowest E-value is 1.4

Spacer Twenty-Five: ACCGTTGCCGCCGATCGGCAGCGAGCCGGTGATGTGT

Spacer25.jpg

Spacer Twenty-Six: TCAAAGCGAGCCTCGAACGCGACGACGAAGATATG

Spacer26.jpg

Spacer Twenty 27: TCCTCCTTGTACCCACGGTCTTGCCGATCCATCCCG

No significant hits . . . lowest E-value is 6.0

Spacer Twenty-Eight: GACTGGCGTGTTGCCGTTCAGGCCGGCGTTGATCCCG

File:Spacer27.jpg

Spacer Twenty-Nine: CTCAGCAGCAGTCAACGGCATTTTATACACCTTGT

No significant hits . . . lowest E-value is 0.36

Spacer Thirty: CACCCCTTCCGGGGAGACGAGGAAACCCCGGACGA

No significant hits . . . lowest E-value is 1.4

Spacer Thirty-One: GTCACGCTGTCTGACGATATGGCTGACCAGGTGC

No significant hits . . . lowest E-value is 1.3

Spacer Thirty-Two: CACTCCTGGGCGGCCTCATCGGCGGCCATCGTC

Spacer32.jpg

Spacer Thirty-Three:GTTGTGTGAGGTATGCGATGGACACCACCGATCACG

No significant hits . . . lowest E-value is 6



CRISPR Two Spacers: CHANGED parameters to be 1.-1 match/mistatch to make it less intense. . . also excluded eukaryotes NOW

Crisprtwo.jpg Crispr3.jpg

Spacer One: TCCGAGACGTGTTCCCTCTCTAGCTGTGCATCTTCC

LOTS of Hits!!!!

Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC

No significant hits . . . lowest E-value is 1.5

Spacer Three: GATCCGGAATATGAAGTGACGAACGATCCGGATACGG

Crispr2spacer3.jpg

Spacer Four: TCGACGAGATCGGCGCGAACTCGTTCGCTGATACT

Crispr2spacer4.jpg

Spacer Five: TCGGGGACCGAGACGACGGGGCCGGGTGCTGTCT

Crispr2spacer5.jpg

Spacer Six: CCGGAGGGGCCGCTGCGTGGGTGATCTGGAGAGAAGA

Crispr2spacer6.jpg

Spacer Seven: GTTGCGTGAGCTAGCGAAACACCGAGTCCGTGTGAT

No significant hits . . . lowest E-value is 5.5

Spacer Eight: ACGGAAATCCAGCCGATCACCCTCCGAGAGGAGAGG

Crispr2spacer8.jpg

Spacer Nine: CGGACATTCAGAAGCGCCTGACTAACCGCATGGCT

No significant hits . . . lowest E-value is 5.2

Spacer Ten: CGGGAAGACCACGACCGCCCGCGCCCTCCAGTTCGA

Crispr2spacer10.jpg

Spacer Eleven: GGCTTCTACGTCGGCAACCGGACCGAGGACGGCGATG

Crispr2spacer11.jpg

Spacer Twelve: AAGTACGCCTCGATCATCAACGGCGTCCGGGCTGT

Crispr2spacer12.jpg


Spacer Thirteen: GATGCTGTTGAGCTCGTAGCGATCCCACTCGGCGT

Spacer Fourteen: AGCCCTTGTGCAATGATCGGGAGTGCAATCCGACC

Spacer Fifteen: TCAGGCGAGTTGTCGGACGAACAGCTTGAAGCGTGT

Spacer Sixteen: TCGTCGAGCGGCAGGCCGCCGACCGCTACGGGCTG

Spacer Seventeen: CGACACGGTCGAAGATGCTGGCAGCTCGCGAATCGC

Spacer Eighteen: GGATCTCGACGGCCGCGTGGCCGTGCATCTCGGGGTC

Spacer Nineteen: AACGCTTCAACGCGCTCTATTGACCGAGCGTATCG

Spacer Twenty: AGATCTCGCGGATAAGCTGCCCCCGCCCTCCCATGAG

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Spacer Thirty:

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Spacer Forty:

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Other things i want to do:

  compare our species spacers with themselves
  look to see if these blast results show hits to any other halophiles
  look at spacer length and number between our species and others??
  any known viruses that infect halophiles??