Sequencing work and NCBI blasting of new sequences and outliers

Procedure: 
1. Take the new data and work with NCBI to try to find out what was sequenced using BlastN and BlastX.
2. Align the new sequences produced on august 10th to the Renilla reniformis sequence used to create primers.
3. Check NCBI blast of sequence outliers that did not align with the majority of sequences using BlastN and BlastX.
4. Check NCBI to see if Renilla sequence matches any other luciferase sequences using BlastN and BlastX.

Results:
1. The concencous sequence did show a relationship to Renilla reniformis though it had a low e-value
2. The alignment of the new sequences to Renilla reniformis only aligned when the cost matrix of the Geneious alignment was at 51%, and when I did a muscle alignment, though it showed a lot of gaps which questions the validity of the alignment. At 51% gaps were visible but were small usually only 1 base pair long.
3. Outliers did not show a strong e-value so unlikely that it would be useable
4. The Renilla sequence used to produce the primers did relate to other Luciferase sequences but with a very low e-value.

Side note: Blogger is not allowing me to add in titles between pictures. Not sure how to work with it so I can better differentiate each area. The conflict seems to be how to images are formatted in blogger

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NCBI BLASTN SUITE: Consensus sequence produced august 10th 2015

BLASTX: Consensus sequence produced august 10th 2015

Geneious alignment of sequences produced august 10th 2015 compared to Renilla reniformis sequence used to produce primers , Cost Matrix 51%

Geneious alignment of sequences produced august 10th 2015 compared to Renilla reniformis sequence used to produce primers, Cost matrix 65%

Geneious alignment of sequences produced august 10th 2015 compared to Renilla reniformis sequence used to produce primers, Cost matrix 70%

Geneious alignment of sequences produced august 10th 2015 compared to Renilla reniformis sequence used to produce primers, Cost Matrix 93%

Muscle alignment of sequences produced august 10th 2015 compared to Renilla reniformis sequence used to produce primers 

alignment of all sequencing data (note: running blasts on oddball sequences that did not align with majority shown to the left) 

Sequences blasted

BlastN of PenF-01-luciferase_f.ab1

BlastX of PenF-01-luciferase_f.ab1

BlastN of PenF-02-luciferase_f.ab1

BlastX of PenF-02-luciferase_f.ab1

BlastN PenR-01-Luciferase_R.ab1

BlastX PenR-01-Luciferase_R.ab1

BlastN PenR-02-Luciferase_R.ab1

BlastX PenR-02-Luciferase_R.ab1

BlastN SeaPen_luciferase_R1-Rr_46_65F.1.ab1

BlastX SeaPen_luciferase_R1-Rr_46_65F.1.ab1

BlastN SeaPen_luciferase_R1-Rr_46_65F.ab1

BlastX SeaPen_luciferase_R1-Rr_46_65F.ab1

BlastN of Renilla Luciferase cDNA

BlastX of Renilla Luciferase cDNA