The phrase "alignment we could" is not correct and lacks clarity in written English.
It may be used in a context where you are discussing potential alignment or agreement, but it needs additional context to be meaningful.
Example: "In our meeting, we discussed the alignment we could achieve on the project goals."
Alternatives: "alignment we might" or "alignment we can".
Combining the results from both alignments, we could determine the position of the best matching sequence within the PA14 genome, the sequence similarity, i.e. the fraction of nucleotides that is identical in both sequences that are compared, and furthermore the exact positions of mismatches and gaps.
After a multiple sequence alignment analysis, we could find that Glycine-rich peptides in Hainan-sourced population have more diversity and also a higher abundance.
This variability precluded meaningful intron sequence alignments, so we could not use the intron sequence to establish relationships among DAM genes.
After examining the alignment in ClustalX, we could see that the middle was conserved except for an 84 bp deletion in one instance and a 67 bp insertion in another.
We tallied spliced and unspliced alignments separately, since we could be confident when directionality of a spliced alignment agreed with a gene prediction, but could not be confident about unspliced alignments.
As can be seen on the multiple sequence alignment (available in TreeBASE), we could not align the 14 blocks with enough confidence (p < 0.01) on the corresponding query sequences, the worst case being the N. capensis ω virus sequence for which only 3 blocks could be confidently aligned.
We expected phylogenomic analyses of the inhibin/activin family to have limited power given the limited alignment length [41], and we could not reject the likely species tree based upon bootstrap support (Figs. 2C and S3).
Using the ECR browser [37] to generate an alignment of the RPS13, we could observe a high GC content in the intron 1 (>65%), as well as small size (141 nt), and a high conservation among human, mouse and cow (Figure 2).
As we considered only perfectly matching reads after the initial alignment to the genome, we could easily translate from color space to base space sequence format.
As our visions for how productivity software could work came into alignment, we thought about building it inside of Facebook.
