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MitoFish Reference

Reference Info

MitoFish is a fish-specific mitochondrial genome reference.

refMitoFish="MitoFish_Complete_Partial_mtDNA_v362.fa"

=> N(MitoFish): 658,022
=> N(order)   :      83
=> N(family)  :     547
=> N(genus)   :   4,607
=> N(species) :  35,924

First PCR

for E in 3 
do
  # PCR with size restriction (±10%) or expected size
  ${u} -search_pcr ${refMitoFish} \
       -db primer_fragment.fa \
       -strand both \
       -maxdiffs ${E} \
       -minamp 650 \
       -maxamp 800 \
       -pcrout MitoFish-Fragment.txt \
       -ampout MitoFish-Fragment.fa
done
CorrectOrientation.sh MitoFish-Fragment.fa MitoFish-Fragment.txt MitoFish-Fragment_FRC.fa

PCR amplicon length distribution:

# 650  3
# 660  17
# 670  4
# 680  5
# 690 * 83
# 700 ************************************************************ 4913
# 710 ************************************************* 4041
# 720 **** 320
# 730  15
# 740  29
# 750  3
# 760  0
# 770  2
# 780  0
# 790  0
# 800  1

# total hits: 9,436

MitoFish PCR Reference

echo "# N(total):$(cfa MitoFish-Fragment_FRC.fa)"
# N(total):  9,436
# N(unique): 9,434 (two PCR hits for: KM273123 and KP164983)

MitoFish: MiFish-U-F / Teleo-R Fragment