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With any given gap cost, the probability of a residue aligned with a gap can be calculated proportionally from a given gap cost and other values from the un-scaled scoring matrices by taking anti-log of the log-odd values or score matrix.
A proportionally low number of DArT sequences aligned to annotated repeats (7.7%) in the sorghum genome compared to the number of DArTs aligned to annotated genes (35.1%), given that 55% of the sorghum genome is known to be repetitive and the repetitive content of sugarcane has been demonstrated to be similar to that of sorghum [[ 25],[ 44]].
If sequences are misaligned as a clade, the increase in joint-entropy is proportionally smaller because the sequences are related and aligned together which causes a larger increase in local covariation.
"The stars are aligned".
The planets are aligned.
The stars aligned.
"Finally everything is aligned".
Our interests are aligned!
Planets and stars aligned.
The stars seem aligned.
Doors should be aligned.
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CEO of Professional Science Editing for Scientists @ prosciediting.com