Markers + reference

Apios

2 species · Fabaceae · Fabales

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Species 2
Genome length 149–153 kb
Candidate markers 257
Primer pairs 90

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 489 0.1011 0.95 81.2 yes View details
ndhF SSC 2256 0.4351 0.83 78.7 yes View details
ccsA SSC 978 0.4680 0.91 82.6 yes View details
ndhD SSC 1500 0.4431 0.87 81.5 yes View details
ndhE SSC 306 0.4664 0.78 72.8 yes View details
ndhG-ndhI SSC 461 0.4491 0.98 77.7 yes View details
ndhI SSC 486 0.4743 0.84 78.2 yes View details
ndhA SSC 2324 0.4576 0.85 79.0 yes View details
ndhH SSC 1182 0.4617 0.80 79.3 yes View details
ycf1 SSC 5406 0.3940 0.82 73.7 yes View details
rpl32-trnL-UAG SSC 456 0.4081 0.92 79.7 yes View details
ndhF-rpl32 SSC 516 0.4214 0.85 79.1 yes View details
ndhG SSC 531 0.4765 0.80 78.0 yes View details
rps15-ycf1 SSC 396 0.3761 0.87 77.0 yes View details
trnR-UCU-trnG-GCC LSC 264 0.0440 0.95 76.9 yes View details
psbK-trnQ-UUG LSC 447 0.0427 1.00 76.8 yes View details
psaC SSC 246 0.4956 0.93 76.7 yes View details
ndhI-ndhA SSC 81 0.4521 0.90 76.0 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnR-UCU-trnG-GCC_p1 trnR-UCU-trnG-GCC AGAAGACCTCTGTCCTATCCA AGCCTTCCAAGCTAACGATG 338–344 1.000 69.2
trnR-UCU-trnG-GCC_p2 trnR-UCU-trnG-GCC AGAAGACCTCTGTCCTATCCA CCTAGCCTTCCAAGCTAACG 341–347 1.000 68.9
trnR-UCU-trnG-GCC_p3 trnR-UCU-trnG-GCC AGGTTTAGAAGACCTCTGTCCT AGCCTTCCAAGCTAACGATG 344–350 1.000 68.4
trnR-UCU-trnG-GCC_p4 trnR-UCU-trnG-GCC AGGTTTAGAAGACCTCTGTCCT CCTAGCCTTCCAAGCTAACG 347–353 1.000 68.2
trnR-UCU-trnG-GCC_p5 trnR-UCU-trnG-GCC AGAAGACCTCTGTCCTATCCA CCCTAGCCTTCCAAGCTAAC 342–348 1.000 66.7
psbK-trnQ-UUG_p1 psbK-trnQ-UUG TAGGCTTCGGGCAATTTAGC GACCAAAACCCGTTGCCTTA 574–583 1.000 74.9
psbK-trnQ-UUG_p2 psbK-trnQ-UUG CGTAGGCTTCGGGCAATTTA GACCAAAACCCGTTGCCTTA 576–585 1.000 74.7
psbK-trnQ-UUG_p3 psbK-trnQ-UUG TAGGCTTCGGGCAATTTAGC GAATAGCGGGACCAAAACCC 583–592 1.000 73.1
psbK-trnQ-UUG_p4 psbK-trnQ-UUG CGTAGGCTTCGGGCAATTTA GAATAGCGGGACCAAAACCC 585–594 1.000 72.9
psbK-trnQ-UUG_p5 psbK-trnQ-UUG TAGGCTTCGGGCAATTTAGC ACCAAAACCCGTTGCCTTAC 573–582 1.000 72.6
ycf1_p1 ycf1 GAGCTACTGAGGAACAACGG CTTTATTCGTTGGGGCCGTA 1389 0.500 59.8
ycf1_p2 ycf1 GAGCTACTGAGGAACAACGG TACTTTATTCGTTGGGGCCG 1391 0.500 59.8
ycf1_p3 ycf1 GAGCTACTGAGGAACAACGG TTTATTCGTTGGGGCCGTAG 1388 0.500 59.8
ycf1_p4 ycf1 GGTTAAATAGCCCCGGACTG CTTTATTCGTTGGGGCCGTA 1654 0.500 59.5
ycf1_p5 ycf1 GGTTAAATAGCCCCGGACTG TTTATTCGTTGGGGCCGTAG 1653 0.500 59.5
ndhF_p1 ndhF TCGGCAATAATCACAAAAACGT GTACGCTTTTTGGGAACTGC 2941 0.500 39.7
ndhF_p2 ndhF CGGCAATAATCACAAAAACGT GTACGCTTTTTGGGAACTGC 2940 0.500 36.2
ndhF_p3 ndhF CAGTTCTTCGGCAATAATCACA GTACGCTTTTTGGGAACTGC 2948 0.500 36.1
ndhF_p4 ndhF AACTGTCATAGCTCTACCCT GTACGCTTTTTGGGAACTGC 2979 0.500 35.2
ndhF_p5 ndhF TTCGGCAATAATCACAAAAACGT GTACGCTTTTTGGGAACTGC 2942 0.500 34.5
ndhF-rpl32_p1 ndhF-rpl32 GATTTAGCGACTGAGCCACA GTACGCTTTTTGGGAACTGC 1261 0.500 59.5
ndhF-rpl32_p2 ndhF-rpl32 GATTTAGCGACTGAGCCACA TCCTAAGAGCAGCGTGTCTA 1895 0.500 58.9
ndhF-rpl32_p3 ndhF-rpl32 GATTTAGCGACTGAGCCACA AGCAGCGTGTCTACCAATTT 1888 0.500 58.4
ndhF-rpl32_p4 ndhF-rpl32 ACATGAAGAGGGAATTGGGC GTACGCTTTTTGGGAACTGC 1282 0.500 58.4
ndhF-rpl32_p5 ndhF-rpl32 GATTTAGCGACTGAGCCACA CTAAGAGCAGCGTGTCTACC 1893 0.500 58.3
rpl32-trnL-UAG_p1 rpl32-trnL-UAG GCAGTTCCCAAAAAGCGTAC GAAGTAGCAAAGCCTTGGGT 1135 0.500 58.9
rpl32-trnL-UAG_p2 rpl32-trnL-UAG GCAGTTCCCAAAAAGCGTAC TCCTAAGAGCAGCGTGTCTA 654 0.500 58.6
rpl32-trnL-UAG_p3 rpl32-trnL-UAG GCAGTTCCCAAAAAGCGTAC AGCAGCGTGTCTACCAATTT 647 0.500 58.1
rpl32-trnL-UAG_p4 rpl32-trnL-UAG GCAGTTCCCAAAAAGCGTAC AAGACCCGAAGTAGCAAAGC 1142 0.500 58.1
rpl32-trnL-UAG_p5 rpl32-trnL-UAG GCAGTTCCCAAAAAGCGTAC CTAAGAGCAGCGTGTCTACC 652 0.500 58.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Apios americana NC_025909.1 148772 View on NCBI ↗
Apios chendezhaoana PV870761.1 152730 View on NCBI ↗