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Average gap block length: The total number of gap characters divided by the total number of gap blocks.
These attributes are summary statistics computed from each MSA (e.g., the average gap block length and the number of gap blocks, see Materials and Methods).
Each trio consisted of either three mismatches, two mismatches and one gap block, or one mismatch and two gap blocks that were located in different sequences of a pair.
The gap cost is calculated as p = o + g(l - 1), where o is the opening gap cost, g is the extending gap cost, and l is the length of the gap block.
When a mismatch or gap block was found and the next two mismatches and/or gaps were located within a region of n - 1 consecutive sites, the conditional probability of the trio within n sites Ptrio(n) (n ≥ 3) was calculated by the equation given below, P trio (n ) = 1 - (1 - p d ) n - 1 - (n - 1 ) p d (1 - p d ) n - 2 where pd represents the average number of mismatches and gap blocks per site.
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The algorithm tracks the earliest outstanding TSN per path and updates the path's cwnd just with the information contained in gap blocks, even if the cumulative TSN is not modified.
When a SACK is received, the cumulative TSN and the list of gap blocks are used to calculate the amount of outstanding bytes, that is, the total size of chunks already sent and not yet acknowledged.
On the other hand, if the loss is detected with the inspection of gap blocks in a received SACK, both the ssthresh and the cwnd are reduced to a half of the previous value of cwnd.
Then you see the speed option, you see the read option, you see gap blocking, zone blocking, sweep blocking.
Total number of gap blocks in the MSA: Gap blocks are one or more consecutive gap characters.
The conditional probability of the two gap blocks within n sites Pduo(n) (n ≥ 2) is given as follows: P duo (n ) = 1 - (1 - p g ) n - 1 where pg is the average number of the gap blocks per site.
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