Table 2 Gene-rich clusters with their significant motifs (ID, sequence, sites/occurrences, logo), p-value < 0.05, identified from the Pl. halstedii reference genome using STREME. The remaining 9 STREME motifs are listed in Additional file 4. Motifs retrieved from MEME for each cluster are tabulated in Additional file 5
Motif (ID, sequence, sites) | Motif logo | P-value (<0.05) | Cluster IDs (No. Of clusters) | Highly abundant cluster(s) ID (No. of genes) |
|---|---|---|---|---|
STREME-1, DRTGTGGWCCACAYH, 379 |
| 1.20E-07 | 11, 12, 13, 14, 23, 25, 31, 33, 41, 46, 58, 59, 63, 67, 92, 99,100,105, 114, 126, 131; (21) | 11(62), 12(68) |
STREME-3, GATTGGHTRAAAWDW, 484 |
| 9.20E-06 | 3, 5, 6, 11, 12, 13, 14, 18, 23, 24, 26, 33, 34, 41, 46, 51, 56, 59, 61, 65, 67, 69, 79, 86, 90, 91, 100,102,104, 105, 108, 111, 123, 126; (34) | 11(55), 12(59), 41 (47) |
STREME-4, TCATTYTYMAATTTK, 990 |
| 3.70E-05 | 1, 2, 3, 6, 7, 8, 11, 12, 13, 14, 18, 20, 21, 26, 27, 28, 29, 34, 35, 36, 41, 43, 59, 65, 66, 68, 70, 76, 78, 84, 86, 87, 90; (33) | 11(76), 14(48) |
STREME-6, ATGGCTACA, 49 |
| 1.90E-03 | 2, 11, 41, 66, 68; (5) | 11(30), 2(16) |
STREME-10, GCCAAYCA, 209 |
| 2.80E-02 | 8, 11, 12, 14,34, 41, 59, 63, 65, 68, 102, 105, 108; (9) | 11(3), 14(13) |
STREME-11, ARCCCCGYTRCA , 60 |
| 3.10E-02 | 17, 67, 131; (3) | 67(3) |
STREME-12, AACTTCAAC, 183 |
| 3.20E-02 | 3, 15, 23, 34, 54, 130; (6) | 3(24), 54(11) |
STREME-13, CAGCAACATC, 3114 |
| 3.20E-02 | 11; (1) | 11(55) |
