Difference between revisions of "Blasting Spacers for Our Genome"
Karicheson (talk | contribs) (→Blasting Spacers) |
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Spacer One: TCCGAGACGTGTTCCCTCTCTAGCTGTGCATCTTCC | Spacer One: TCCGAGACGTGTTCCCTCTCTAGCTGTGCATCTTCC | ||
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Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC | Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC | ||
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Spacer Three: GATCCGGAATATGAAGTGACGAACGATCCGGATACGG | Spacer Three: GATCCGGAATATGAAGTGACGAACGATCCGGATACGG | ||
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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?? | ||
Revision as of 17:15, 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.
Spacer One: TGCGTCGTCCGGTGGCCGTCAATAAATGTCGCAAGGG
No significant hits. . . lowest E-value is 25
Matches by chance!
Spacer Two: TCCTACGACCTCGTCGGCGTCAACGGCTGGCCCGA
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
This image is only part of it. . .
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
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
Spacer Ten: ACTCACTGGATTATGACCCCTACAACGAGGGCGTCA
No significant hits. . . lowest E-value is 1.5
Spacer Eleven: GGATCTCGATCGTTGTAGTATCCATAGCTGCTATACC
Spacer Twelve: GAAGTAACGCAACTCCAGTGAGCGCTACTGAGAGCCC
No significant hits. . . lowest E-value is 1.6
Spacer Thirteen:CCGATCACGCCCTGCCGATACTGGTAGTTCGCGATA
Spacer Fourteen: TCGTCGGCCGGCTCGTCGGCCGACGTGGACTTGC
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
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
Spacer Twenty-Six: TCAAAGCGAGCCTCGAACGCGACGACGAAGATATG
Spacer Twenty 27: TCCTCCTTGTACCCACGGTCTTGCCGATCCATCCCG
No significant hits . . . lowest E-value is 6.0
Spacer Twenty-Eight: GACTGGCGTGTTGCCGTTCAGGCCGGCGTTGATCCCG
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
Spacer Thirty-Three:GTTGTGTGAGGTATGCGATGGACACCACCGATCACG
No significant hits . . . lowest E-value is 6
CRISPR Two Spacers:
Spacer One: TCCGAGACGTGTTCCCTCTCTAGCTGTGCATCTTCC
Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC
Spacer Three: GATCCGGAATATGAAGTGACGAACGATCCGGATACGG
Spacer Four:
Spacer Five:
Spacer Six:
Spacer Seven:
Spacer Eight:
Spacer Nine:
Spacer Ten:
Spacer Eleven:
Spacer Twelve:
Spacer Thirteen:
Spacer Fourteen:
Spacer Fifteen:
Spacer Sixteen:
Spacer Seventeen:
Spacer Eighteen:
Spacer Nineteen:
Spacer Twenty:
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:
Spacer Forty-Two:
Spacer Forty-Three:
Spacer Forty-Four:
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??
