本篇主要討論古細菌的胺基酸和內部密碼子的使用情況。一開始，我們先就單一細菌，了解內部密碼子的分布情況，我們發現胺基酸對於密碼子的使用，呈現一個不規則的分布，有些密碼子的含量極高，但是有些密碼子的含量卻是極少。在含量極高的部分，有些古細菌有一致性，即可能一致偏好CG或是偏好AT。有些則沒有一致性，即密碼子並沒有一致偏好某特定核苷酸而是呈現一個多元化的偏好。

　　接下來，我們討論整體古細菌CG含量百分比，我們可以從第三章第三節關於密碼子在三個位置的含量分布圖，約略看出一些現象。由於，古細菌的偏好，往往會出現於密碼子的第三位置上。因此在第三位置的分布圖，將呈現一個平均且均勻的分布。

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