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The amount of gap in an alignment was determined as a percentage, in the following manner.
Results indicate that increasing GAP concentration with a constant amount of GTPases causes more GTP consumption resulting in a lower light output (Fig. 6A, B ), thus demonstrating activation of GTPase activity by increasing the amount of GAP in the reaction.
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Data used in the study have only a small amount of gaps in coverage, and the array is spatially fairly dense with station spacing of the order 100 km in the central and northern parts of the array.
In particular, varying the amount of gaps in the alignment had an impact.
Pairwise or complete deletion of gap positions does not yield significant differences in the results because of the small amount of gaps in the MSA (only positions with less than 2% gaps were considered).
Sequence-repeats resulted in a large amount of gaps in the assembly as they could not be resolved with reads shorter than the repeat itself, even if paired-end tags were used to scaffold the assembled contigs.
This indicates that either the sequencing of Bouvet et al. (2007) inadvertently contained errors or there is yet another stand-alone copy of OPHIO3 somewhere else in the H327 genome within the small amount of gaps (∼84 kb) in our assembly.
First, changes in relative amounts of gap gene expression may impact early eve and ftz expression differently.
The study's author adds that these figures probably understate the amount universities are spending because of gaps in reporting.
While linkage mapping provides little help with determining the sizes of gaps in sequencing and/or assembly between scaffolds, FISH permits estimates of the amounts of DNA in gaps based on gap lengths and linear DNA densities of 3.3 Mb/µm for kinetochores, 1.5 Mb/µm for euchromatin, and 8.8 Mb/µm for heterochromatin (Table S6).
However, the gap sizes estimated by FISH were almost always larger than those estimated by optical mapping (Table S8), so if optical mapping is more accurate for estimating gap sizes, then the true amount of DNA in gaps may be less than our estimate based on FISH.
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