Difference between revisions of "Blasting Spacers for Our Genome"
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Spacer Twenty: AGATCTCGCGGATAAGCTGCCCCCGCCCTCCCATGAG | Spacer Twenty: AGATCTCGCGGATAAGCTGCCCCCGCCCTCCCATGAG | ||
| − | Spacer Twenty-One: | + | Spacer Twenty-One: CACTTCGAGCGGACTTTGGGCCACCCCGGAAAGTCAG |
| − | Spacer Twenty-Two: | + | Spacer Twenty-Two: CGATACGTCCGGGACGCCCGTGACGACCACCACTGC |
| − | Spacer Twenty-Three: | + | Spacer Twenty-Three: GGAGGAGCGGATGGACATGAGCGACACGACGATCCG |
| − | Spacer Twenty-Four: | + | Spacer Twenty-Four: GAGCATCTCTCCAATCAGCGGTCATCAACCGCGA |
| − | Spacer Twenty-Five: | + | Spacer Twenty-Five: AGTATCTGTCTACGCGATACCGCACCGTCAGAGTG |
| − | Spacer Twenty-Six: | + | Spacer Twenty-Six: TACGACCTTCCCACTGAGGGTCTTGAGCTAACGATT |
| − | Spacer Twenty-Seven: | + | Spacer Twenty-Seven: GCGACGTGCTTACCTCTGACGCCAATATTGACCTT |
| − | Spacer Twenty-Eight: | + | Spacer Twenty-Eight: TTCATCAAGAGGCACACAAGCATGGTGCGTCCAAA |
| − | Spacer Twenty-Nine: | + | Spacer Twenty-Nine: CTGGCCTACCCGAGTCGGTTCCCCGCAGCACTCGCA |
| − | Spacer Thirty: | + | Spacer Thirty: ACGATCGTCACCGACACCCTCGGGGCCGGCGGCGC |
| − | Spacer Thirty-One: | + | Spacer Thirty-One: GAAACGACCGAGACGCAAAGCGAGTTCACACAACTC |
| − | Spacer Thirty-Two: | + | Spacer Thirty-Two: TTAGATGATCAGGTAGCCTGCTACCAGTGCAGCTGC |
| − | Spacer Thirty-Three: | + | Spacer Thirty-Three: GAGACCCAGCTTTGCCTTCCAGGTGATCAGCTCGTA |
| − | Spacer Thirty-Four: | + | Spacer Thirty-Four: TCGAAGCGCTCGGTCGCGACGGAGACCAGCGACCAGCTG |
| − | Spacer Thirty-Five: | + | Spacer Thirty-Five: TGACGACCACACACACGAGGCCGTGCGTGTGCTTGTA |
| − | Spacer Thirty-Six: | + | Spacer Thirty-Six: CCACGTCCCGGTGACACGCAGCTCGGTGAGATCGC |
| − | Spacer Thirty-Seven: | + | Spacer Thirty-Seven: CATGGAGTCTTCAACATTTCATGGGCTGGGCTTGGCC |
| − | Spacer Thirty-Eight: | + | Spacer Thirty-Eight: CGCAACCCGACGATCGAGGACGGGCCGTCCCTGGA |
| − | Spacer Thirty-Nine: | + | Spacer Thirty-Nine: GCGTCGGACTGCGTCGATAGTGTTCGTGCTCATGTT |
| − | Spacer Forty: | + | Spacer Forty: CAGACTTCTACTGGAAGGCGAAAACTGAGAAGGCA |
| − | Spacer Forty-One: | + | Spacer Forty-One: TACGCTCGACGACCTCCGTCGTGCGCTCCAGAAGTCA |
| − | Spacer Forty-Two: | + | Spacer Forty-Two: GCGCTGCGGACGTGGTGTCAGAGGGGTTACCAGTAACT |
| − | Spacer Forty-Three: | + | Spacer Forty-Three: ACTCCGGGTACACTGGTGGCGATGCTCTACTCGCC |
| − | Spacer Forty-Four: | + | Spacer Forty-Four: ACACGTTTCTTTTTTTCAGGAGCCATCACTCACTC |
Revision as of 19:17, 11 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: CHANGED parameters to be 1.-1 match/mistatch to make it less intense. . . also excluded eukaryotes NOW
Spacer One: TCCGAGACGTGTTCCCTCTCTAGCTGTGCATCTTCC
LOTS of Hits!!!!
Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC
No significant hits . . . lowest E-value is 1.5
Spacer Three: GATCCGGAATATGAAGTGACGAACGATCCGGATACGG
Spacer Four: TCGACGAGATCGGCGCGAACTCGTTCGCTGATACT
Spacer Five: TCGGGGACCGAGACGACGGGGCCGGGTGCTGTCT
Spacer Six: CCGGAGGGGCCGCTGCGTGGGTGATCTGGAGAGAAGA
Spacer Seven: GTTGCGTGAGCTAGCGAAACACCGAGTCCGTGTGAT
No significant hits . . . lowest E-value is 5.5
Spacer Eight: ACGGAAATCCAGCCGATCACCCTCCGAGAGGAGAGG
Spacer Nine: CGGACATTCAGAAGCGCCTGACTAACCGCATGGCT
No significant hits . . . lowest E-value is 5.2
Spacer Ten: CGGGAAGACCACGACCGCCCGCGCCCTCCAGTTCGA
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: CACTTCGAGCGGACTTTGGGCCACCCCGGAAAGTCAG
Spacer Twenty-Two: CGATACGTCCGGGACGCCCGTGACGACCACCACTGC
Spacer Twenty-Three: GGAGGAGCGGATGGACATGAGCGACACGACGATCCG
Spacer Twenty-Four: GAGCATCTCTCCAATCAGCGGTCATCAACCGCGA
Spacer Twenty-Five: AGTATCTGTCTACGCGATACCGCACCGTCAGAGTG
Spacer Twenty-Six: TACGACCTTCCCACTGAGGGTCTTGAGCTAACGATT
Spacer Twenty-Seven: GCGACGTGCTTACCTCTGACGCCAATATTGACCTT
Spacer Twenty-Eight: TTCATCAAGAGGCACACAAGCATGGTGCGTCCAAA
Spacer Twenty-Nine: CTGGCCTACCCGAGTCGGTTCCCCGCAGCACTCGCA
Spacer Thirty: ACGATCGTCACCGACACCCTCGGGGCCGGCGGCGC
Spacer Thirty-One: GAAACGACCGAGACGCAAAGCGAGTTCACACAACTC
Spacer Thirty-Two: TTAGATGATCAGGTAGCCTGCTACCAGTGCAGCTGC
Spacer Thirty-Three: GAGACCCAGCTTTGCCTTCCAGGTGATCAGCTCGTA
Spacer Thirty-Four: TCGAAGCGCTCGGTCGCGACGGAGACCAGCGACCAGCTG
Spacer Thirty-Five: TGACGACCACACACACGAGGCCGTGCGTGTGCTTGTA
Spacer Thirty-Six: CCACGTCCCGGTGACACGCAGCTCGGTGAGATCGC
Spacer Thirty-Seven: CATGGAGTCTTCAACATTTCATGGGCTGGGCTTGGCC
Spacer Thirty-Eight: CGCAACCCGACGATCGAGGACGGGCCGTCCCTGGA
Spacer Thirty-Nine: GCGTCGGACTGCGTCGATAGTGTTCGTGCTCATGTT
Spacer Forty: CAGACTTCTACTGGAAGGCGAAAACTGAGAAGGCA
Spacer Forty-One: TACGCTCGACGACCTCCGTCGTGCGCTCCAGAAGTCA
Spacer Forty-Two: GCGCTGCGGACGTGGTGTCAGAGGGGTTACCAGTAACT
Spacer Forty-Three: ACTCCGGGTACACTGGTGGCGATGCTCTACTCGCC
Spacer Forty-Four: ACACGTTTCTTTTTTTCAGGAGCCATCACTCACTC
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??
