Difference between revisions of "Blasting Spacers for Our Genome"
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== Blasting Spacers == | == Blasting Spacers == | ||
| + | |||
| + | |||
| + | [[EXPLORATION OF THE IMPORTANT FINDINGS]] | ||
| + | |||
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. | 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. | ||
| Line 11: | Line 15: | ||
'''Spacer Two''': TCCTACGACCTCGTCGGCGTCAACGGCTGGCCCGA | '''Spacer Two''': TCCTACGACCTCGTCGGCGTCAACGGCTGGCCCGA | ||
| + | |||
| + | [[Image:spacer2.jpg]] | ||
| + | |||
| + | Archaeal BJ1 virus complete genome: [http://www.biomedcentral.com/content/pdf/1471-2164-8-410.pdf Good Article] | ||
| + | |||
| + | [[Image:spacer2222.jpg]] | ||
| + | |||
| + | This is the protein sequence location that this match comes from in the virus: | ||
| + | |||
| + | [[Image:archaealvirus.jpg]] | ||
| + | |||
| + | Blasted this little sequence alignment section. . . did not get any significant viral alignments except its own | ||
| + | |||
| + | Did blastp to determine if hypothetical protein in archaeal BJ1 virus had hits in other viruses: | ||
| + | |||
| + | [[Image:blastp4.jpg]] | ||
| + | |||
| + | |||
| + | The rest of the hits are bacteria and are in coding protein sequences such as ABC transporter and ATP-binding protein. | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Spacer Three: CACCCTACAACAGGTGAAATCTACCAGACAAAAGA | Spacer Three: CACCCTACAACAGGTGAAATCTACCAGACAAAAGA | ||
[[Image:spacer3.jpg]] | [[Image:spacer3.jpg]] | ||
| + | |||
| + | All of these hits are bacteria and the bacteria hits are part of coding proteins such as conserved hypothetical protein; putative membrane protein, which I did a blastp for and found no viral matches | ||
Spacer Four: TCACCCAAGCGCAAGCAACAGCTGATCGAGGACCTG | Spacer Four: TCACCCAAGCGCAAGCAACAGCTGATCGAGGACCTG | ||
[[Image:spacer4.jpg]] | [[Image:spacer4.jpg]] | ||
| + | |||
| + | Hits come from prokaryotes and is from a coding segment | ||
Spacer Five: GCGACGGCGGCCAGTTCCGCGAGGGCGGGAAGGTCC | Spacer Five: GCGACGGCGGCCAGTTCCGCGAGGGCGGGAAGGTCC | ||
| Line 32: | Line 52: | ||
[[Image:spacer5.jpg]] | [[Image:spacer5.jpg]] | ||
| − | Spacer Six: TGCGAGTGTTGCGGGGAACCGACTCGGGTAGGCCAG | + | The following hits are the only significant hits that come from a prokaryote but are n a coding segment of DNA |
| − | + | ||
| − | [[Image:spacer6.jpg]] | + | '''Spacer Six''': TGCGAGTGTTGCGGGGAACCGACTCGGGTAGGCCAG |
| + | |||
| + | [[Image:spacer6.jpg]] | ||
| + | |||
| + | Aligns with something in our genome. . . NOT another spacer but a segment of DNA that flanks two genes and is non-coding. . . | ||
Spacer Seven: ACGGTTTCGCTACCACCATCGCCACCAGCAACTGCCG | Spacer Seven: ACGGTTTCGCTACCACCATCGCCACCAGCAACTGCCG | ||
[[Image:spacer8.jpg]] | [[Image:spacer8.jpg]] | ||
| + | |||
| + | Hit from a prokaryote that is in its coding region | ||
Spacer Eight: GACGAGTATGCCAACCGGCTCGTGAGCGGGCGC | Spacer Eight: GACGAGTATGCCAACCGGCTCGTGAGCGGGCGC | ||
| Line 47: | Line 73: | ||
[[Image:spacer9.jpg]] | [[Image:spacer9.jpg]] | ||
| + | |||
| + | Hit from prokaryote that is in its coding region | ||
Spacer Ten: ACTCACTGGATTATGACCCCTACAACGAGGGCGTCA | Spacer Ten: ACTCACTGGATTATGACCCCTACAACGAGGGCGTCA | ||
| Line 52: | Line 80: | ||
No significant hits . . . lowest E-value is 1.4 | No significant hits . . . lowest E-value is 1.4 | ||
| − | Spacer Eleven: GGATCTCGATCGTTGTAGTATCCATAGCTGCTATACC | + | '''Spacer Eleven''': GGATCTCGATCGTTGTAGTATCCATAGCTGCTATACC |
| − | + | ||
| − | [[Image:spacer11.jpg]] | + | [[Image:spacer11.jpg]] |
| + | |||
| + | Hits from gene segment in prokaryote or promoter sequence because flanking two genes | ||
Spacer Twelve: GAAGTAACGCAACTCCAGTGAGCGCTACTGAGAGCCC | Spacer Twelve: GAAGTAACGCAACTCCAGTGAGCGCTACTGAGAGCCC | ||
| Line 64: | Line 94: | ||
[[Image:spacer132.jpg]] | [[Image:spacer132.jpg]] | ||
| − | + | Hit from prokaryote in gene segment | |
| − | [[Image:spacer142.jpg]] | + | '''Spacer Fourteen''': TCGTCGGCCGGCTCGTCGGCCGACGTGGACTTGC |
| + | |||
| + | [[Image:spacer142.jpg]] | ||
| + | |||
| + | first hit from prokaryote gene region | ||
| + | |||
| + | 2nd hit: from [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=FSHC5VSU01S&log%24=nuclalign&blast_rank=3&list_uids=163716581 virus] | ||
| + | |||
| + | [[Image:spacer14more.jpg]] | ||
| + | |||
| + | this virus when you blast it. . . it infects pathogens, bacteria and plant. . .maybe archaea too???? | ||
Spacer Fifteen: AGTAGGTCTAATGTCTCTCTGTCGTCTATCAGCCCCG | Spacer Fifteen: AGTAGGTCTAATGTCTCTCTGTCGTCTATCAGCCCCG | ||
| Line 79: | Line 119: | ||
[[Image:spacer17.jpg]] | [[Image:spacer17.jpg]] | ||
| + | |||
| + | Bad hit from prokaryote coding sequence | ||
Spacer Eighteen: AAATACGATCCTGCGGTGACGCTACGTCCGGGGCAGC | Spacer Eighteen: AAATACGATCCTGCGGTGACGCTACGTCCGGGGCAGC | ||
| Line 99: | Line 141: | ||
[[Image:spacer22.jpg]] | [[Image:spacer22.jpg]] | ||
| + | |||
| + | Hit from prokaryote in gene segment | ||
Spacer Twenty-Three: GTCTAGCCCAGTCTGGTCGGGGTGGTCGGCAGGATCGG | Spacer Twenty-Three: GTCTAGCCCAGTCTGGTCGGGGTGGTCGGCAGGATCGG | ||
[[Image:spacer23.jpg]] | [[Image:spacer23.jpg]] | ||
| + | |||
| + | Bad -values= throw out | ||
Spacer Twenty-Four: CACTCCTCATATGTCTGTTCGAGCAGCGGGACGTG | Spacer Twenty-Four: CACTCCTCATATGTCTGTTCGAGCAGCGGGACGTG | ||
| Line 108: | Line 154: | ||
[[Image:spacer24.jpg]] | [[Image:spacer24.jpg]] | ||
| − | + | Hit from prokaryote in gene segment | |
| − | [[Image:spacer252.jpg]] | + | '''Spacer Twenty-Five''': ACCGTTGCCGCCGATCGGCAGCGAGCCGGTGATGTGT |
| + | |||
| + | [[Image:spacer252.jpg]] | ||
| + | |||
| + | Hits from prokaryotes in flanking sequence or in gene sequence. . . check to see if this is in spacer!! | ||
| + | |||
| + | [[Image:spacer26more.jpg]] | ||
Spacer Twenty-Six: TCAAAGCGAGCCTCGAACGCGACGACGAAGATATG | Spacer Twenty-Six: TCAAAGCGAGCCTCGAACGCGACGACGAAGATATG | ||
[[Image:spacer262.jpg]] | [[Image:spacer262.jpg]] | ||
| + | |||
| + | Hits from prokaryotes in gene segment | ||
Spacer Twenty-Seven: TCCTCCTTGTACCCACGGTCTTGCCGATCCATCCCG | Spacer Twenty-Seven: TCCTCCTTGTACCCACGGTCTTGCCGATCCATCCCG | ||
| Line 123: | Line 177: | ||
[[Image:spacer28.jpg]] | [[Image:spacer28.jpg]] | ||
| + | |||
| + | Hits from prokaryotes in gene segment | ||
Spacer Twenty-Nine: CTCAGCAGCAGTCAACGGCATTTTATACACCTTGT | Spacer Twenty-Nine: CTCAGCAGCAGTCAACGGCATTTTATACACCTTGT | ||
| Line 130: | Line 186: | ||
Spacer Thirty: CACCCCTTCCGGGGAGACGAGGAAACCCCGGACGA | Spacer Thirty: CACCCCTTCCGGGGAGACGAGGAAACCCCGGACGA | ||
| − | [[Image:spacer30.jpg]] | + | [[Image:spacer30.jpg]] |
| + | |||
| + | Bad e-value and top hit is a bunch of gene from bacteria | ||
Spacer Thirty-One: GTCACGCTGTCTGACGATATGGCTGACCAGGTGC | Spacer Thirty-One: GTCACGCTGTCTGACGATATGGCTGACCAGGTGC | ||
[[Image:spacer31.jpg]] | [[Image:spacer31.jpg]] | ||
| + | |||
| + | Hit from prokaryotes in gene segment | ||
Spacer Thirty-Two: CACTCCTGGGCGGCCTCATCGGCGGCCATCGTC | Spacer Thirty-Two: CACTCCTGGGCGGCCTCATCGGCGGCCATCGTC | ||
| Line 140: | Line 200: | ||
[[Image:spacer322.jpg]] | [[Image:spacer322.jpg]] | ||
| − | Spacer Thirty-Three:GTTGTGTGAGGTATGCGATGGACACCACCGATCACG | + | Hit from prokaryotes in gene segment |
| + | |||
| + | Spacer Thirty-Three: GTTGTGTGAGGTATGCGATGGACACCACCGATCACG | ||
No significant hits . . . lowest E-value is 1.4 | No significant hits . . . lowest E-value is 1.4 | ||
| Line 152: | Line 214: | ||
[[Image:crispr3.jpg]] | [[Image:crispr3.jpg]] | ||
| − | + | Spacer One: TCCGAGACGTGTTCCCTCTCTAGCTGTGCATCTTCC | |
| − | + | Hits from prokaryote in gene segment | |
Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC | Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC | ||
| Line 160: | Line 222: | ||
No significant hits . . . lowest E-value is 1.5 | No significant hits . . . lowest E-value is 1.5 | ||
| − | + | Spacer Three: GATCCGGAATATGAAGTGACGAACGATCCGGATACGG | |
[[Image:crispr2spacer3.jpg]] | [[Image:crispr2spacer3.jpg]] | ||
| − | + | E-values not good and prokaryotes | |
| + | |||
| + | Spacer Four: TCGACGAGATCGGCGCGAACTCGTTCGCTGATACT | ||
[[Image:crispr2spacer4.jpg]] | [[Image:crispr2spacer4.jpg]] | ||
| + | |||
| + | Hits from prokaryote in gene segment | ||
'''Spacer Five''': TCGGGGACCGAGACGACGGGGCCGGGTGCTGTCT | '''Spacer Five''': TCGGGGACCGAGACGACGGGGCCGGGTGCTGTCT | ||
| + | |||
| + | [[Image:crispr2spacer5.jpg]] | ||
| + | |||
| + | Hit from a [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=FW14AEYZ01S&log%24=nucltop&blast_rank=3&list_uids=255927524 virus] (same virus even though | ||
| + | called different names): | ||
| + | |||
| + | [[Image:crispr2spacer5more.jpg]] | ||
| − | + | Spacer Six: CCGGAGGGGCCGCTGCGTGGGTGATCTGGAGAGAAGA | |
| − | + | [[Image:crispr2spacer6.jpg]] | |
| − | + | E-values not good and from prokaryotes | |
Spacer Seven: GTTGCGTGAGCTAGCGAAACACCGAGTCCGTGTGAT | Spacer Seven: GTTGCGTGAGCTAGCGAAACACCGAGTCCGTGTGAT | ||
| Line 180: | Line 253: | ||
No significant hits . . . lowest E-value is 5.5 | No significant hits . . . lowest E-value is 5.5 | ||
| − | + | Spacer Eight: ACGGAAATCCAGCCGATCACCCTCCGAGAGGAGAGG | |
[[Image:crispr2spacer8.jpg]] | [[Image:crispr2spacer8.jpg]] | ||
| + | |||
| + | Hit from prokaryote in gene segment | ||
Spacer Nine: CGGACATTCAGAAGCGCCTGACTAACCGCATGGCT | Spacer Nine: CGGACATTCAGAAGCGCCTGACTAACCGCATGGCT | ||
| Line 189: | Line 264: | ||
'''Spacer Ten''': CGGGAAGACCACGACCGCCCGCGCCCTCCAGTTCGA | '''Spacer Ten''': CGGGAAGACCACGACCGCCCGCGCCCTCCAGTTCGA | ||
| + | |||
| + | [[Image:crispr2spacer10.jpg]] | ||
| + | |||
| + | First hit from bacteria in gene segment. . . | ||
| + | |||
| + | Second hit is from another [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=FW1UZWFK01S&log%24=nuclalign&blast_rank=3&list_uids=125860746 archaea] in a conserved hypothetical protein. . . is this a true protein. . .?? | ||
| + | |||
| + | [[Image:crispr2spacer10more.jpg]] | ||
| − | + | Spacer Eleven: GGCTTCTACGTCGGCAACCGGACCGAGGACGGCGATG | |
| − | + | [[Image:crispr2spacer11.jpg]] | |
| − | + | Hit with significant e-value is from a bacteria in a gene segment | |
| − | + | Spacer Twelve: AAGTACGCCTCGATCATCAACGGCGTCCGGGCTGT | |
[[Image:crispr2spacer12.jpg]] | [[Image:crispr2spacer12.jpg]] | ||
| + | |||
| + | E-values no good and from a prokaryote in a gene | ||
Spacer Thirteen: GATGCTGTTGAGCTCGTAGCGATCCCACTCGGCGT | Spacer Thirteen: GATGCTGTTGAGCTCGTAGCGATCCCACTCGGCGT | ||
| Line 212: | Line 297: | ||
No significant hits . . . lowest E-value is 1.4 | No significant hits . . . lowest E-value is 1.4 | ||
| − | + | Spacer Sixteen: TCGTCGAGCGGCAGGCCGCCGACCGCTACGGGCTG | |
[[Image:crispr2spacer16.jpg]] | [[Image:crispr2spacer16.jpg]] | ||
| − | + | Hits from prokaryotes in gene segment | |
| + | |||
| + | Spacer Seventeen: CGACACGGTCGAAGATGCTGGCAGCTCGCGAATCGC | ||
[[Image:crispr2spacer17.jpg]] | [[Image:crispr2spacer17.jpg]] | ||
| − | + | Bad e-value | |
| + | |||
| + | Spacer Eighteen: GGATCTCGACGGCCGCGTGGCCGTGCATCTCGGGGTC | ||
[[Image:crispr2spacer18.jpg]] | [[Image:crispr2spacer18.jpg]] | ||
| + | |||
| + | Hit from prokaryote in gene segment | ||
Spacer Nineteen: AACGCTTCAACGCGCTCTATTGACCGAGCGTATCG | Spacer Nineteen: AACGCTTCAACGCGCTCTATTGACCGAGCGTATCG | ||
| Line 236: | Line 327: | ||
No significant hits . . . lowest E-value is 1.5 | No significant hits . . . lowest E-value is 1.5 | ||
| − | + | Spacer Twenty-Two: CGATACGTCCGGGACGCCCGTGACGACCACCACTGC | |
[[Image:crispr2spacer21.jpg]] | [[Image:crispr2spacer21.jpg]] | ||
| + | |||
| + | Bad e-value | ||
Spacer Twenty-Three: GGAGGAGCGGATGGACATGAGCGACACGACGATCCG | Spacer Twenty-Three: GGAGGAGCGGATGGACATGAGCGACACGACGATCCG | ||
| Line 244: | Line 337: | ||
No significant hits . . . lowest E-value is 1.4 | No significant hits . . . lowest E-value is 1.4 | ||
| − | + | Spacer Twenty-Four: GAGCATCTCTCCAATCAGCGGTCATCAACCGCGA | |
[[Image:crispr2spacer24.jpg]] | [[Image:crispr2spacer24.jpg]] | ||
| + | |||
| + | Hits from prokaryotes in gene segment | ||
Spacer Twenty-Five: AGTATCTGTCTACGCGATACCGCACCGTCAGAGTG | Spacer Twenty-Five: AGTATCTGTCTACGCGATACCGCACCGTCAGAGTG | ||
| Line 265: | Line 360: | ||
'''Spacer Twenty-Nine:''' CTGGCCTACCCGAGTCGGTTCCCCGCAGCACTCGCA | '''Spacer Twenty-Nine:''' CTGGCCTACCCGAGTCGGTTCCCCGCAGCACTCGCA | ||
| + | |||
| + | [[Image:crispr2spacer29.jpg]] | ||
| − | + | Spacer Thirty: ACGATCGTCACCGACACCCTCGGGGCCGGCGGCGC | |
| − | + | [[Image:crispr2spacer30.jpg]] | |
| − | + | Hits from prokaryotes in gene segment | |
Spacer Thirty-One: GAAACGACCGAGACGCAAAGCGAGTTCACACAACTC | Spacer Thirty-One: GAAACGACCGAGACGCAAAGCGAGTTCACACAACTC | ||
| Line 276: | Line 373: | ||
No significant hits . . . lowest E-value is 5.6 | No significant hits . . . lowest E-value is 5.6 | ||
| − | + | Spacer Thirty-Two: TTAGATGATCAGGTAGCCTGCTACCAGTGCAGCTGC | |
[[Image:crispr2spacer32.jpg]] | [[Image:crispr2spacer32.jpg]] | ||
| − | + | Poor e-values | |
| + | |||
| + | Spacer Thirty-Three: GAGACCCAGCTTTGCCTTCCAGGTGATCAGCTCGTA | ||
[[Image:crispr2spacer33.jpg]] | [[Image:crispr2spacer33.jpg]] | ||
| + | |||
| + | Hits from prokaryotes in gene segment | ||
'''Spacer Thirty-Four:''' TCGAAGCGCTCGGTCGCGACGGAGACCAGCGACCAGCTG | '''Spacer Thirty-Four:''' TCGAAGCGCTCGGTCGCGACGGAGACCAGCGACCAGCTG | ||
| + | |||
| + | [[Image:crispr2spacer34.jpg]] | ||
| + | |||
| + | weird because two hits from our species and these 2 hits are in a conserved protein sequence and not the spacer?????????? | ||
| + | |||
| + | [[Image:crispr2spacer34more.jpg]] | ||
| − | + | Spacer Thirty-Five: TGACGACCACACACACGAGGCCGTGCGTGTGCTTGTA | |
| − | + | [[Image:crispr2spacer35.jpg]] | |
| − | + | Hits from prokaryotes in gene segment | |
| − | + | Spacer Thirty-Six: CCACGTCCCGGTGACACGCAGCTCGGTGAGATCGC | |
[[Image:crispr2spacer36.jpg]] | [[Image:crispr2spacer36.jpg]] | ||
| + | |||
| + | Hits from prokaryotes in gene segment | ||
Spacer Thirty-Seven: CATGGAGTCTTCAACATTTCATGGGCTGGGCTTGGCC | Spacer Thirty-Seven: CATGGAGTCTTCAACATTTCATGGGCTGGGCTTGGCC | ||
| Line 300: | Line 409: | ||
No significant hits . . . lowest E-value is 5.9 | No significant hits . . . lowest E-value is 5.9 | ||
| − | + | Spacer Thirty-Eight: CGCAACCCGACGATCGAGGACGGGCCGTCCCTGGA | |
[[Image:crispr2spacer38.jpg]] | [[Image:crispr2spacer38.jpg]] | ||
| + | |||
| + | Bad e-values | ||
Spacer Thirty-Nine: GCGTCGGACTGCGTCGATAGTGTTCGTGCTCATGTT | Spacer Thirty-Nine: GCGTCGGACTGCGTCGATAGTGTTCGTGCTCATGTT | ||
| Line 312: | Line 423: | ||
No significant hits . . . lowest E-value is 5.2 | No significant hits . . . lowest E-value is 5.2 | ||
| − | + | Spacer Forty-One: TACGCTCGACGACCTCCGTCGTGCGCTCCAGAAGTCA | |
[[Image:crispr2spacer41.jpg]] | [[Image:crispr2spacer41.jpg]] | ||
| + | |||
| + | hit from prokaryote in gene segment | ||
Spacer Forty-Two: GCGCTGCGGACGTGGTGTCAGAGGGGTTACCAGTAACT | Spacer Forty-Two: GCGCTGCGGACGTGGTGTCAGAGGGGTTACCAGTAACT | ||
| Line 327: | Line 440: | ||
No significant hits . . . lowest E-value is 1.3 | No significant hits . . . lowest E-value is 1.3 | ||
| − | |||
| − | |||
| Line 347: | Line 458: | ||
look at spacer length and number between our species and others?? | look at spacer length and number between our species and others?? | ||
any known viruses that infect halophiles?? | any known viruses that infect halophiles?? | ||
| + | |||
| + | blast the known viral genome against the nr/nt database and it comes up with matches: | ||
Latest revision as of 01:56, 14 November 2009
Blasting Spacers
EXPLORATION OF THE IMPORTANT FINDINGS
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 5.9
Spacer Two: TCCTACGACCTCGTCGGCGTCAACGGCTGGCCCGA
Archaeal BJ1 virus complete genome: Good Article
This is the protein sequence location that this match comes from in the virus:
Blasted this little sequence alignment section. . . did not get any significant viral alignments except its own Did blastp to determine if hypothetical protein in archaeal BJ1 virus had hits in other viruses:
The rest of the hits are bacteria and are in coding protein sequences such as ABC transporter and ATP-binding protein.
Spacer Three: CACCCTACAACAGGTGAAATCTACCAGACAAAAGA
All of these hits are bacteria and the bacteria hits are part of coding proteins such as conserved hypothetical protein; putative membrane protein, which I did a blastp for and found no viral matches
Spacer Four: TCACCCAAGCGCAAGCAACAGCTGATCGAGGACCTG
Hits come from prokaryotes and is from a coding segment
Spacer Five: GCGACGGCGGCCAGTTCCGCGAGGGCGGGAAGGTCC
The following hits are the only significant hits that come from a prokaryote but are n a coding segment of DNA
Spacer Six: TGCGAGTGTTGCGGGGAACCGACTCGGGTAGGCCAG
Aligns with something in our genome. . . NOT another spacer but a segment of DNA that flanks two genes and is non-coding. . .
Spacer Seven: ACGGTTTCGCTACCACCATCGCCACCAGCAACTGCCG
Hit from a prokaryote that is in its coding region
Spacer Eight: GACGAGTATGCCAACCGGCTCGTGAGCGGGCGC
No significant hits . . . lowest E-value is 1.2
Spacer Nine: TGGTAGGCGTCGTAGGTGTTCGTGGCGAGCGTGTC
Hit from prokaryote that is in its coding region
Spacer Ten: ACTCACTGGATTATGACCCCTACAACGAGGGCGTCA
No significant hits . . . lowest E-value is 1.4
Spacer Eleven: GGATCTCGATCGTTGTAGTATCCATAGCTGCTATACC
Hits from gene segment in prokaryote or promoter sequence because flanking two genes
Spacer Twelve: GAAGTAACGCAACTCCAGTGAGCGCTACTGAGAGCCC
No significant hits . . . lowest E-value is 1.5
Spacer Thirteen:CCGATCACGCCCTGCCGATACTGGTAGTTCGCGATA
Hit from prokaryote in gene segment
Spacer Fourteen: TCGTCGGCCGGCTCGTCGGCCGACGTGGACTTGC
first hit from prokaryote gene region 2nd hit: from virus
this virus when you blast it. . . it infects pathogens, bacteria and plant. . .maybe archaea too????
Spacer Fifteen: AGTAGGTCTAATGTCTCTCTGTCGTCTATCAGCCCCG
No significant hits . . . lowest E-value is 23
Spacer Sixteen: GCTCTCCGGTGTCACAGGTCAGGTCACGGTCTCCGC
No significant hits . . . lowest E-value is 5.6
Spacer Seventeen: ACGGACAAGTCATCCACCCGCCAGTATCTCCCGGT
Bad hit from prokaryote coding sequence
Spacer Eighteen: AAATACGATCCTGCGGTGACGCTACGTCCGGGGCAGC
No significant hits . . . lowest E-value is 1.5
Spacer Nineteen: CAGATGTGGGGTCTGTGGCCACAGTCTAACATCTCT
No significant hits . . . lowest E-value is 1.4
Spacer Twenty: CCTGATAACGGACTCTTGTAGGTCCGTTAGGTCGT
No significant hits . . . lowest E-value is 5.2
Spacer Twenty-One: AAAAATGAGTGACGTAGACATTCGGCAAAATGCCGG
No significant hits . . . lowest E-value is 1.4
Spacer Twenty-Two: CAGCAGCGAAACGAGCCGTCCGTCCTTTTGAGACA
Hit from prokaryote in gene segment
Spacer Twenty-Three: GTCTAGCCCAGTCTGGTCGGGGTGGTCGGCAGGATCGG
Bad -values= throw out
Spacer Twenty-Four: CACTCCTCATATGTCTGTTCGAGCAGCGGGACGTG
Hit from prokaryote in gene segment
Spacer Twenty-Five: ACCGTTGCCGCCGATCGGCAGCGAGCCGGTGATGTGT
Hits from prokaryotes in flanking sequence or in gene sequence. . . check to see if this is in spacer!!
Spacer Twenty-Six: TCAAAGCGAGCCTCGAACGCGACGACGAAGATATG
Hits from prokaryotes in gene segment
Spacer Twenty-Seven: TCCTCCTTGTACCCACGGTCTTGCCGATCCATCCCG
No significant hits . . . lowest E-value is 1.4
Spacer Twenty-Eight: GACTGGCGTGTTGCCGTTCAGGCCGGCGTTGATCCCG
Hits from prokaryotes in gene segment
Spacer Twenty-Nine: CTCAGCAGCAGTCAACGGCATTTTATACACCTTGT
No significant hits . . . lowest E-value is 1.3
Spacer Thirty: CACCCCTTCCGGGGAGACGAGGAAACCCCGGACGA
Bad e-value and top hit is a bunch of gene from bacteria
Spacer Thirty-One: GTCACGCTGTCTGACGATATGGCTGACCAGGTGC
Hit from prokaryotes in gene segment
Spacer Thirty-Two: CACTCCTGGGCGGCCTCATCGGCGGCCATCGTC
Hit from prokaryotes in gene segment
Spacer Thirty-Three: GTTGTGTGAGGTATGCGATGGACACCACCGATCACG
No significant hits . . . lowest E-value is 1.4
CRISPR Two Spacers: CHANGED parameters to be 1.-1 match/mistatch to make it less intense. . . also excluded eukaryotes NOW
Spacer One: TCCGAGACGTGTTCCCTCTCTAGCTGTGCATCTTCC
Hits from prokaryote in gene segment
Spacer Two: CAGATCTAAAACAATGTCATACGGAAAAATCGACATC
No significant hits . . . lowest E-value is 1.5
Spacer Three: GATCCGGAATATGAAGTGACGAACGATCCGGATACGG
E-values not good and prokaryotes
Spacer Four: TCGACGAGATCGGCGCGAACTCGTTCGCTGATACT
Hits from prokaryote in gene segment
Spacer Five: TCGGGGACCGAGACGACGGGGCCGGGTGCTGTCT
Hit from a virus (same virus even though called different names):
Spacer Six: CCGGAGGGGCCGCTGCGTGGGTGATCTGGAGAGAAGA
E-values not good and from prokaryotes
Spacer Seven: GTTGCGTGAGCTAGCGAAACACCGAGTCCGTGTGAT
No significant hits . . . lowest E-value is 5.5
Spacer Eight: ACGGAAATCCAGCCGATCACCCTCCGAGAGGAGAGG
Hit from prokaryote in gene segment
Spacer Nine: CGGACATTCAGAAGCGCCTGACTAACCGCATGGCT
No significant hits . . . lowest E-value is 5.2
Spacer Ten: CGGGAAGACCACGACCGCCCGCGCCCTCCAGTTCGA
First hit from bacteria in gene segment. . . Second hit is from another archaea in a conserved hypothetical protein. . . is this a true protein. . .??
Spacer Eleven: GGCTTCTACGTCGGCAACCGGACCGAGGACGGCGATG
Hit with significant e-value is from a bacteria in a gene segment
Spacer Twelve: AAGTACGCCTCGATCATCAACGGCGTCCGGGCTGT
E-values no good and from a prokaryote in a gene
Spacer Thirteen: GATGCTGTTGAGCTCGTAGCGATCCCACTCGGCGT
No significant hits . . . lowest E-value is 1.3
Spacer Fourteen: AGCCCTTGTGCAATGATCGGGAGTGCAATCCGACC
No significant hits . . . lowest E-value is 5.2
Spacer Fifteen: TCAGGCGAGTTGTCGGACGAACAGCTTGAAGCGTGT
No significant hits . . . lowest E-value is 1.4
Spacer Sixteen: TCGTCGAGCGGCAGGCCGCCGACCGCTACGGGCTG
Hits from prokaryotes in gene segment
Spacer Seventeen: CGACACGGTCGAAGATGCTGGCAGCTCGCGAATCGC
Bad e-value
Spacer Eighteen: GGATCTCGACGGCCGCGTGGCCGTGCATCTCGGGGTC
Hit from prokaryote in gene segment
Spacer Nineteen: AACGCTTCAACGCGCTCTATTGACCGAGCGTATCG
No significant hits . . . lowest E-value is 1.3
Spacer Twenty: AGATCTCGCGGATAAGCTGCCCCCGCCCTCCCATGAG
No significant hits . . . lowest E-value is 5.9
Spacer Twenty-One: CACTTCGAGCGGACTTTGGGCCACCCCGGAAAGTCAG
No significant hits . . . lowest E-value is 1.5
Spacer Twenty-Two: CGATACGTCCGGGACGCCCGTGACGACCACCACTGC
Bad e-value
Spacer Twenty-Three: GGAGGAGCGGATGGACATGAGCGACACGACGATCCG
No significant hits . . . lowest E-value is 1.4
Spacer Twenty-Four: GAGCATCTCTCCAATCAGCGGTCATCAACCGCGA
Hits from prokaryotes in gene segment
Spacer Twenty-Five: AGTATCTGTCTACGCGATACCGCACCGTCAGAGTG
No significant hits . . . lowest E-value is 1.3
Spacer Twenty-Six: TACGACCTTCCCACTGAGGGTCTTGAGCTAACGATT
No significant hits . . . lowest E-value is 5.6
Spacer Twenty-Seven: GCGACGTGCTTACCTCTGACGCCAATATTGACCTT
No significant hits . . . lowest E-value is 5.2
Spacer Twenty-Eight: TTCATCAAGAGGCACACAAGCATGGTGCGTCCAAA
No significant hits . . . lowest E-value is 5.2
Spacer Twenty-Nine: CTGGCCTACCCGAGTCGGTTCCCCGCAGCACTCGCA
Spacer Thirty: ACGATCGTCACCGACACCCTCGGGGCCGGCGGCGC
Hits from prokaryotes in gene segment
Spacer Thirty-One: GAAACGACCGAGACGCAAAGCGAGTTCACACAACTC
No significant hits . . . lowest E-value is 5.6
Spacer Thirty-Two: TTAGATGATCAGGTAGCCTGCTACCAGTGCAGCTGC
Poor e-values
Spacer Thirty-Three: GAGACCCAGCTTTGCCTTCCAGGTGATCAGCTCGTA
Hits from prokaryotes in gene segment
Spacer Thirty-Four: TCGAAGCGCTCGGTCGCGACGGAGACCAGCGACCAGCTG
weird because two hits from our species and these 2 hits are in a conserved protein sequence and not the spacer??????????
Spacer Thirty-Five: TGACGACCACACACACGAGGCCGTGCGTGTGCTTGTA
Hits from prokaryotes in gene segment
Spacer Thirty-Six: CCACGTCCCGGTGACACGCAGCTCGGTGAGATCGC
Hits from prokaryotes in gene segment
Spacer Thirty-Seven: CATGGAGTCTTCAACATTTCATGGGCTGGGCTTGGCC
No significant hits . . . lowest E-value is 5.9
Spacer Thirty-Eight: CGCAACCCGACGATCGAGGACGGGCCGTCCCTGGA
Bad e-values
Spacer Thirty-Nine: GCGTCGGACTGCGTCGATAGTGTTCGTGCTCATGTT
No significant hits . . . lowest E-value is 1.4
Spacer Forty: CAGACTTCTACTGGAAGGCGAAAACTGAGAAGGCA
No significant hits . . . lowest E-value is 5.2
Spacer Forty-One: TACGCTCGACGACCTCCGTCGTGCGCTCCAGAAGTCA
hit from prokaryote in gene segment
Spacer Forty-Two: GCGCTGCGGACGTGGTGTCAGAGGGGTTACCAGTAACT
No significant hits . . . lowest E-value is 1.6
Spacer Forty-Three: ACTCCGGGTACACTGGTGGCGATGCTCTACTCGCC
No significant hits . . . lowest E-value is 1.3
Spacer Forty-Four: ACACGTTTCTTTTTTTCAGGAGCCATCACTCACTC
No significant hits . . . lowest E-value is 1.3
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??
blast the known viral genome against the nr/nt database and it comes up with matches:
