Markers + reference

Inga

2 species · Fabaceae · Fabales

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Species 2
Genome length 175–176 kb
Candidate markers 284
Primer pairs 55

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 284 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF SSC 2238 0.4487 0.77 77.6 yes View details
ndhF-rpl32 SSC 946 0.4399 0.87 81.4 yes View details
rpl32-trnL-UAG SSC 462 0.4450 0.89 79.0 yes View details
ccsA SSC 972 0.4605 0.88 81.8 yes View details
rpl32 SSC 168 0.5192 0.93 77.8 yes View details
psbC-trnS-UGA LSC 242 0.0413 1.00 76.3 yes View details
trnL-UAG-ccsA SSC 92 0.4321 0.88 75.4 yes View details
trnL-UAG SSC 80 0.5256 0.97 75.1 yes View details
psaJ-rpl33 LSC 550 0.0168 0.97 69.8 yes View details
psaA-ycf3 LSC 825 0.0297 0.90 67.9 yes View details
trnM-CAU-atpE LSC 276 0.0217 1.00 65.0 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 55 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbC-trnS-UGA_p1 psbC-trnS-UGA CAGCGGGATTTGAAAAAGGC GAGAGATGGCTGAGTGGTTG 402 1.000 79.5
psbC-trnS-UGA_p2 psbC-trnS-UGA GCAGCGGGATTTGAAAAAGG GAGAGATGGCTGAGTGGTTG 403 1.000 79.5
psbC-trnS-UGA_p3 psbC-trnS-UGA CAGCGGGATTTGAAAAAGGC GCTGAGTGGTTGATAGCTCC 394 1.000 79.3
psbC-trnS-UGA_p4 psbC-trnS-UGA CAGCGGGATTTGAAAAAGGC GGCTGAGTGGTTGATAGCTC 395 1.000 79.3
psbC-trnS-UGA_p5 psbC-trnS-UGA GCAGCGGGATTTGAAAAAGG GCTGAGTGGTTGATAGCTCC 395 1.000 79.3
psaA-ycf3_p1 psaA-ycf3 CCCATTCCTCGAAAGACGTT TTGGTTGAAGATCACAGGGC 908–935 1.000 84.4
psaA-ycf3_p2 psaA-ycf3 AGAAATGACCGGGTTTAGCC TTGGTTGAAGATCACAGGGC 926–953 1.000 84.2
psaA-ycf3_p3 psaA-ycf3 CCCATTCCTCGAAAGACGTT AAGATCACAGGGCGTTTTGA 901–928 1.000 83.0
psaA-ycf3_p4 psaA-ycf3 CCCATTCCTCGAAAGACGTT AGATCACAGGGCGTTTTGAA 900–927 1.000 83.0
psaA-ycf3_p5 psaA-ycf3 CCCATTCCTCGAAAGACGTT TGAAGATCACAGGGCGTTTT 903–930 1.000 83.0
trnM-CAU-atpE_p1 trnM-CAU-atpE TATTGCTTTCATACGGCGGG CTCTCAGACGAGCTAGGACA 375 1.000 77.7
trnM-CAU-atpE_p2 trnM-CAU-atpE TATTGCTTTCATACGGCGGG CGAGCTAGGACACGAGTAGA 367 1.000 77.5
trnM-CAU-atpE_p3 trnM-CAU-atpE TATTGCTTTCATACGGCGGG TCTCAGACGAGCTAGGACAC 374 1.000 75.9
trnM-CAU-atpE_p4 trnM-CAU-atpE GTATTGCTTTCATACGGCGG CTCTCAGACGAGCTAGGACA 376 1.000 75.7
trnM-CAU-atpE_p5 trnM-CAU-atpE GTATTGCTTTCATACGGCGG CGAGCTAGGACACGAGTAGA 368 1.000 75.5
psaJ-rpl33_p1 psaJ-rpl33 GTGGCACCAGTGGTAAGTAC ACACTGTTTCGAACACAATTGG 726 1.000 64.8
psaJ-rpl33_p2 psaJ-rpl33 GTGGCACCAGTGGTAAGTAC CACTGTTTCGAACACAATTGGT 725 1.000 64.8
psaJ-rpl33_p3 psaJ-rpl33 GTGGCACCAGTGGTAAGTAC TCGGATATCTTTACCTTTGGCC 682 1.000 64.5
psaJ-rpl33_p4 psaJ-rpl33 TGGCACCAGTGGTAAGTACT ACACTGTTTCGAACACAATTGG 725 1.000 64.1
psaJ-rpl33_p5 psaJ-rpl33 TGGCACCAGTGGTAAGTACT CACTGTTTCGAACACAATTGGT 724 1.000 64.1
ndhF_p1 ndhF AAAGGGTTCTCGACGGTTTG CCCGCTTACTTGGTCGTTAA 2966 0.500 56.1
ndhF_p2 ndhF CTCGACGGTTTGGTTTATGC CCCGCTTACTTGGTCGTTAA 2958 0.500 55.2
ndhF_p3 ndhF GGTTCTCGACGGTTTGGTTT CCCGCTTACTTGGTCGTTAA 2962 0.500 53.8
ndhF_p4 ndhF AAAGGGTTCTCGACGGTTTG TATCCCGCTTACTTGGTCGT 2969 0.500 52.5
ndhF_p5 ndhF AAAGGGTTCTCGACGGTTTG TTATCCCGCTTACTTGGTCG 2970 0.500 52.0
ndhF-rpl32_p1 ndhF-rpl32 GGGGAATTGGGCAGACTTAG AGCGTGTCTACCGATTTCAC 2340 0.500 59.5
ndhF-rpl32_p2 ndhF-rpl32 GGGGAATTGGGCAGACTTAG CAGCGTGTCTACCGATTTCA 2341 0.500 59.5
ndhF-rpl32_p3 ndhF-rpl32 AAATAACAGGAAGGCGCACA AGCGTGTCTACCGATTTCAC 2307 0.500 59.2
ndhF-rpl32_p4 ndhF-rpl32 AATAACAGGAAGGCGCACAA AGCGTGTCTACCGATTTCAC 2306 0.500 59.2
ndhF-rpl32_p5 ndhF-rpl32 ATAACAGGAAGGCGCACAAA AGCGTGTCTACCGATTTCAC 2305 0.500 59.2

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
Inga edulis NC_047315.1 175674 View on NCBI ↗
Inga leiocalycina NC_028732.1 175489 View on NCBI ↗