The phrase "all alignments with" is correct and usable in written English.
It can be used when discussing agreements, relationships, or connections between different entities or concepts.
Example: "We need to review all alignments with our partners to ensure we are on the same page."
Alternatives: "all agreements with" or "all connections with".
To determine which variables to consider, we align the reads to the isoform sequences and keep all alignments with at most x mismatches.
All alignments with RNAz classification score P > 0.5 were considered.
Looking at all alignments with >36% identity, 16 411 alignment boundaries changed accuracy bins.
All alignments with classification score p > 0.5 were stored as conserved secondary RNA structures.
Since highly repetitive/low complexity genomic regions may result in ambiguous or low confidence alignments, we conservatively filtered out all alignments with mapping quality (MAPQ) < 35.
We further removed all alignments with more than five mismatches in the first 40 colors and a mapping quality below 20.
So I invite you to inquire when you are scheming, dreaming, pondering, planning, creating goals and visions: "What is my true Sankapla?, How can I connect with my Highest Self?" I wish you all Alignment with your Inner Divinity, your Big Love, and your Truth.
For remaining sequences, all-versus-all alignments with BLASTN were carried out to ensure that these sequences had no redundancy.
We used the MosaikAligner in the "all" alignment mode with a hash size of 13 and 20 bp as alignment candidate threshold, allowing a maximum of 4 mismatches.
The Illumina FASTQ sequencing files from three independent replicates were aligned to hg19 with bowtie [ 30] with the following parameters: m = 1 (i.e. removes all those alignments with more than one match).
All the resulting alignments with at least 50% identities and an alignment length of at least 50% of the size of the PAO1 protein were considered as orthologs.
