Parameter | Value | Description | |
---|---|---|---|
BLASTZ | O | 150 | Gap |
E | 100 | Gap | |
K | 500 | Maximal segment pair (MSP) score | |
L | 500 | Gapped alignment threshold | |
W | 6 | Word size | |
StemPrediction | |||
MIN_ARM_LENGTH | 16 | Minimum stem arm length (nt) | |
MAX_ENERGY | -15.0 | Minimum free energy of the stem | |
MAX_BULGE_SIZE | 5 | Maximum number of unpaired nt on a single strand in the stem | |
MAX_BULGE_BASES | 7 | Maximum number of unpaired nt on both strand in the stem | |
MAX_GLUE_DISTANCE | 10 | Maximum distance for two stems to be glued (joined) StemPrediction | |
MAX_FILTER_ENERGY | -15.0 | Minimum free energy of the glued stem |