Table 2 Cluster ranking. AptaCluster (Freq.), AptaCluster (Div.), and APTANI (Freq.), APTANI (Div.) represent the cluster ranking of frequency and diversity (the number of non-redundant sequences) of AptaCluster and APTANI, respectively. Sequences with a frequency of less than 10 were excluded before the clustering analysis. Because FASTAptamer and APTANI did not finish with all sequence data. *: This sequence is filtered as the frequency is less than 10. **: The ranking of clusters is tied; however, the sequences are not grouped in the same cluster. ***: These sequences did not include any motifs estimated by AptaTRACE, thus the sequences are not grouped into any clusters
Sequence information | Cluster ranking | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Sequence | ID | Ranking | Frequency | Binding | FASTAptamer | AptaCluster | AptaCluster | APTANI | APTANI | AptaTRACE | FSBC |
(Freq.) | (Div.) | (Freq.) | (Div.) | (lmin=5) | |||||||
aggaggggGACTTaggactgggtttaggg | seq1 | 6 | 92237 | Yes | 6 | 7 | 5 | 7 | 870 | 1 | 5 |
agggTATGGACTTCgacgtctcggctgaa | seq2 | 24 | 20057 | Yes | 15 | 17 | 15 | 15 | 699 | 1 | 1 |
cgcacaggaaggTATGGACTTCgacgttt | seq3 | 63 | 8750 | Yes | 24 | 64 | 65 | 58 | 290 | 1 | 1 |
ggTATGGACTTCgacgtcttctgacctaa | seq4 | 82 | 6753 | Yes | 15 | 81 | 72 | 68 | 2188 | 1 | 1 |
gaaaTATGGACTTCgatacgccggctgag | seq5 | 255 | 1483 | Yes | 60 | 229 | 112740 | 102 | 626 ∗∗ | 1 | 1 |
agtatctatccGACTTggatttacgttcg | seq6 | 8459 | 84 | Yes | 546 | 9921 | 28056 | 1993 | 626 ∗∗ | NA*** | 5 |
tatccGACTTggatggctgagcaaggcta | seq7 | 100914 | 15 | Yes | 731 | 94490 | 125262 | 2038 | 626 ∗∗ | 5 | 5 |
aggaggggGACTTaggactgggtttatga∗ | seq8 | 281478 | 4 | Yes | NA | NA | NA | NA | NA | NA | NA |
gcaggtgtggtttgctgaggTGGGCCctg | seq9 | 1 | 583447 | No | 1 | 1 | 2 | 1 | 125 | 4 | 26 |
tttggtttgctgTATGGtgggctctgtta | seq10 | 8 | 70095 | No | 7 | 8 | 10 | 8 | 916 ∗∗ | 4 | 16 |
gtgagggtgAGGACaggttagcgtggtgg | seq11 | 10 | 51669 | No | 9 | 11 | 9 | 16 | 916 ∗∗ | 7 | 54 |
ggtgaggcgGACGTatcttttagcaaatc | seq12 | 12 | 45038 | No | 10 | 12 | 13 | 13 | 520 | 11 | 41 |
tcgcttgaacggggaactactccaGACGT | seq13 | 23 | 20380 | No | 14 | 21 | 23 | 45 | 2270 | NA*** | 41 |
gTGGGCgcacttagacggggtgatcgtaa | seq14 | 375 | 831 | No | 75 | 335 | 76783 | 387 | 1739 | NA*** | 37 |
ACTTAtttgtcttaagtggcgggtcaatg | seq15 | 398 | 771 | No | 78 | 238 | 556 | 460 | 2188 | 8 | 47 |
gggtccCTTCGgggtgacgatggtatcta | seq16 | 520 | 504 | No | 107 | 466 | 120874 | 1758 | 2253 | NA*** | 11 |
ggtGTGGGgagggtcgtattgtgtcctgt | seq17 | 3847 | 126 | No | 388 | 4568 | 59849 | 92 | 1 | 5 | 66 |
cttatttgtgtttagtggcgggcGTTTGt | seq18 | 29324 | 41 | No | 50 | 539 | 110 | 44 | 323 | NA*** | 92 |
ctatttgTTCTAgtggcggtcatctaagg | seq19 | 44000 | 31 | No | 50 | 9134 | 4859 | 2043 | 2253 | NA*** | 88 |