Table 1.
Arrays used by enhanced suffix arrays (columns 2–5), compressed suffix arrays (columns 2, 6 and 7) and FM-indexes (columns 8 – 14) for string S = ACATACAGATG$
| ESA |
CSA |
FM-index ‘rank’ |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| i | SA | LCP | child | sl | SA−1 | Ψ | BWT | $ | A | C | G | T | LF | S[SA[i]..] |
| 0 | 11 | −1 | 2 | 2 | G | 0 | 0 | 0 | 1 | 0 | 8 | $ | ||
| 1 | 4 | 0 | 6 | [0..11] | 7 | 6 | T | 0 | 0 | 0 | 1 | 1 | 10 | ACAGATG$ |
| 2 | 0 | 3 | 2 | [6..7] | 4 | 7 | $ | 1 | 0 | 0 | 1 | 1 | 0 | ACATACAGATG$ |
| 3 | 6 | 1 | 4 | [0..11] | 10 | 9 | C | 1 | 0 | 1 | 1 | 1 | 6 | AGATG$ |
| 4 | 2 | 1 | 5 | 1 | 10 | C | 1 | 0 | 2 | 1 | 1 | 7 | ATACAGATG$ | |
| 5 | 8 | 2 | 3 | [10..11] | 6 | 11 | G | 1 | 0 | 2 | 2 | 1 | 9 | ATG$ |
| 6 | 5 | 0 | 8 | 3 | 3 | A | 1 | 1 | 2 | 2 | 1 | 1 | CAGATG$ | |
| 7 | 1 | 2 | 7 | [1..5] | 9 | 4 | A | 1 | 2 | 2 | 2 | 1 | 2 | CATACAGATG$ |
| 8 | 10 | 0 | 10 | 5 | 0 | T | 1 | 2 | 2 | 2 | 2 | 11 | G$ | |
| 9 | 7 | 1 | 9 | [0..11] | 11 | 5 | A | 1 | 3 | 2 | 2 | 2 | 3 | GATG$ |
| 10 | 3 | 0 | 8 | 1 | A | 1 | 4 | 2 | 2 | 2 | 4 | TACAGATG$ | ||
| 11 | 9 | 1 | 11 | [0..11] | 0 | 8 | A | 1 | 5 | 2 | 2 | 2 | 5 | TG$ |
From left to right: index position, suffix array, LCP array, child array, suffix link array, inverse suffix array, Ψ-array, BWT text, ‘rank’ array, LF-mapping array and suffixes of string S. FM-indexes also require an array C(S).