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Reversely, embryonic lethality correlated with a higher transgene copy number, strongly suggesting that when the Cre is partly efficient, the GFP cassette is excised from multiple transgene copies, resulting in a tiar transgene expression above the threshold level compatible with embryonic survival.
When a loop of contigs is detected along a contig path, the best number of loop copies resulting in a length closest to the gap size is calculated.
The phylogeny predicted for the sd1 data set suggests both duplication and subsequent loss of gene copies, resulting in a complex phylogenetic pattern.
The bioinformatics pipeline QDD [ 37] was used to filter for redundancy and to check for multiple copies, resulting in a final set of sequences for which we were able to design primers.
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An average coverage of 7.5 instead of 7 would reduce an estimate of 50 to 47 and an average coverage of 6.5 would add four copies, resulting in an estimate of 54.
A few years later, with the development of PCR (polymerase chain reaction) it became possible to routinely amplify and study surviving ancient DNA molecules even if only in a single copy, resulting in a rapid increase and diversification of ancient DNA research [ 3- 5].
However, other TEs (such as class I elements) are known to generate a high proportion of "dead on arrival" copies after transposition (i.e., most transposition events are asymmetric and generate a nonfunctional copy), resulting in an extremely imbalanced tree.
The contrasting transposon model postulates that all element members can be active in producing new copies, resulting in the lack of a radiation structure from the α central node.
The other copy resulted in a tandem gene duplicate in which the new copy was placed at the 5' site of the original gene (2A).
Subsequently, intermediate cells acquire a second mutational hit (point mutation in the remaining Sfpi1 copy), resulting in the formation of a malignant cell which undergoes further clonal expansion and eventually develops into cancer (23).
Thus, it appears that in this case a composite transposition event occurred using the 5′-end of one Helitron copy and the 3′-end of the other copy resulting in the creation of a compound transposon HelibatN539 (supplementary fig. S2 and table S2, Supplementary Material online).
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