Blasting Spacers for Our Genome

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Revision as of 17:39, 10 November 2009 by Karicheson (talk | contribs) (Blasting Spacers)
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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


Spacer Ten: CGGGAAGACCACGACCGCCCGCGCCCTCCAGTTCGA

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

Spacer Eleven: GGCTTCTACGTCGGCAACCGGACCGAGGACGGCGATG

Spacer Twelve: AAGTACGCCTCGATCATCAACGGCGTCCGGGCTGT


Spacer Thirteen: GATGCTGTTGAGCTCGTAGCGATCCCACTCGGCGT

Spacer Fourteen: AGCCCTTGTGCAATGATCGGGAGTGCAATCCGACC

Spacer Fifteen: TCAGGCGAGTTGTCGGACGAACAGCTTGAAGCGTGT

Spacer Sixteen: TCGTCGAGCGGCAGGCCGCCGACCGCTACGGGCTG

Spacer Seventeen: CGACACGGTCGAAGATGCTGGCAGCTCGCGAATCGC

Spacer Eighteen: GGATCTCGACGGCCGCGTGGCCGTGCATCTCGGGGTC

Spacer Nineteen: AACGCTTCAACGCGCTCTATTGACCGAGCGTATCG

Spacer Twenty: AGATCTCGCGGATAAGCTGCCCCCGCCCTCCCATGAG

Spacer Twenty-One:

Spacer Twenty-Two:

Spacer Twenty-Three:

Spacer Twenty-Four:

Spacer Twenty-Five:

Spacer Twenty-Six:

Spacer Twenty-Seven:

Spacer Twenty-Eight:

Spacer Twenty-Nine:

Spacer Thirty:

Spacer Thirty-One:

Spacer Thirty-Two:

Spacer Thirty-Three:

Spacer Thirty-Four:

Spacer Thirty-Five:

Spacer Thirty-Six:

Spacer Thirty-Seven:

Spacer Thirty-Eight:

Spacer Thirty-Nine:

Spacer Forty:

Spacer Forty-One:

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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??