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We located the selected regions based on their locus ID and followed standard primer design guidelines, aiming for primers with a length of 22 25 bp, 40 60% GC content, melting temperature (Tm) = 55 62°C, the presence of a 3′ GC clamp, and without repeats, runs, or secondary structures such as hairpins, dimers, and cross-dimers.
For each demultiplexed sample, we computationally sorted reads based on their locus of origin and reaction type (E or G) by matching the start of read 1 to each of the 60 3' flank primers and the start of read 2 to each of the 60 5' flank primers (E reactions) or the L1-specific primer (G reactions) (Additional file 3: Figure S2).
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In addition, several genes were clearly adjacent to one another based on their loci.
Loci throughout the genome show different levels of neutral substitution between BY and RM due to ancestral recombination (see Text S1), so if cis-acting QTL are selectively neutral, we expect them to accumulate at a clock-like rate based on their locus-specific coalescence time.
Microsatellites can be assigned to estimated death rate classes based on their locus-specific probabilities for each class.
After eliminating the incomplete sequences manually, 159 sequences remained were finally identified as ZmPPs and renamed based on their loci on chromosomes.
In this study, we identified 136 WRKY proteins encoded by 119 WRKY genes from the maize B73 genome and named them from ZmWRKY1 to ZmWRKY119 based on their loci on corresponding chromosomes.
The location of soybean SWEET genes was determined based on their physical positions on chromosomes corresponding to their locus numbers in the SoyKB browser [ 91].
Therefore, the P-values for the GO categories that clearly deviate from the assumptions made by the hypergeometric test should be computed considering that the probability of a given GO category does not only depend on the number of genes assigned to it, but also on the length of their loci.
The first search mode allows users to request genes on the basis of their locus-tag, gene name, GI (GenBank Identifier) or domain possession.
A second menu, P2CS Search, provides several search modes that allow users to request genes on the basis of their locus-tag, domain possession or TCS class.
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CEO of Professional Science Editing for Scientists @ prosciediting.com