| Option |
Usage |
Value |
| -a | Auto parameters mode | True |
| -A | Not used | |
| -b | Blast database name | CP001816 |
| -B | Not used | |
| -c | Use complexity filter | True |
| -C | DNA concentration | 1e-06 |
| -d | Files used to generate the blast database | CP001816.gbk |
| -D | Search space size | 3000 |
| -e | Not used | |
| -E | Not used | |
| -f | Forward mode | True |
| -F | Not used | |
| -g | Minimum distance between probes 5' ends | 69 |
| -G | Grid-computation mode | True |
| -h | Help available | YES |
| -H | Not used | |
| -i | Input sequence file | CP001816.gbk |
| -I | Not used | |
| -j | Not used | |
| -J | Not used | |
| -k | Genbank feature annotation requested | 3 |
| -K | Genbank feature requested | 1 |
| -l | Minimum probe length | 45 |
| -L | Maximum probe length | 47 |
| -m | Prohibited sequences | GGGGG;CCCCC;TTTTT;AAAAA |
| -M | Mismatch mode | False |
| -n | Maximum number of probes requested per input sequence | 3 |
| -N | Number of process to run in parallel | 1 |
| -o | Output file | Sulfurospirillum_deleyianum_DSM_6946_oligo.txt |
| -O | Not used | |
| -p | Minimum probe %GC content | 32 |
| -P | Maximum probe %GC content | 45 |
| -q | Not used | |
| -Q | Not used | |
| -r | Rejected sequence file | Sulfurospirillum_deleyianum_DSM_6946_rejected.fas |
| -R | Log file | Sulfurospirillum_deleyianum_DSM_6946.log |
| -s | Temperature to fold a probe to detect secondary structures | 59 |
| -S | Sodium concentration | 1 |
| -t | Minimum probe Tm | 79 |
| -T | Maximum probe Tm | 86 |
| -u | Transcript specific mode | False |
| -U | Gene specific mode | False |
| -v | Not used | |
| -V | Not used | |
| -w | Not used | |
| -W | Not used | |
| -x | Temperature to start to consider cross-hybridization | 59 |
| -X | Not used | |
| -y | Requested length for the 5' linker sequence | 15 |
| -Y | Requested length for the 3' linker sequence | 15 |
| -z | Not used | |
| -Z | Not used | |