Markers + reference

Carallia

2 species · Rhizophoraceae · Malpighiales

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Species 2
Genome length 162–162 kb
Candidate markers 267
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl32-trnL-UAG SSC 1386 0.4494 0.83 80.4 yes View details
ccsA SSC 1032 0.4738 0.78 79.0 yes View details
ccsA-ndhD SSC 269 0.4940 0.93 76.8 yes View details
ndhD SSC 1485 0.4685 0.91 82.5 yes View details
ndhG SSC 579 0.4871 0.80 79.1 yes View details
ndhA SSC 2149 0.4853 0.82 78.7 yes View details
ndhH SSC 1182 0.4809 0.84 80.6 yes View details
rpl22-rps19 LSC 87 0.0575 1.00 82.2 yes View details
ndhF-rpl32 SSC 776 0.4215 0.98 80.2 yes View details
rps15-ycf1 SSC 450 0.4767 0.96 80.0 yes View details
ndhF SSC 2265 0.4366 0.84 78.9 yes View details
ndhG-ndhI SSC 402 0.4326 0.96 78.6 yes View details
ndhD-psaC SSC 145 0.5333 0.93 76.9 yes View details
ndhH-rps15 SSC 111 0.4118 0.92 76.5 yes View details
ndhE-ndhG SSC 200 0.4451 0.91 76.2 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpl22-rps19_p1 rpl22-rps19 CGTGCTTTGTAGGCGGATAT GTGGGCCATAAATTGGGAGA 251–290 1.000 76.8
rpl22-rps19_p2 rpl22-rps19 GCCCGCGAATTTGATCAATT GTGGGCCATAAATTGGGAGA 277–316 1.000 76.1
rpl22-rps19_p3 rpl22-rps19 CGTGCTTTGTAGGCGGATAT GGTGGGCCATAAATTGGGAG 252–291 1.000 75.7
rpl22-rps19_p4 rpl22-rps19 GCCCGCGAATTTGATCAATT GGTGGGCCATAAATTGGGAG 278–317 1.000 75.0
rpl22-rps19_p5 rpl22-rps19 CGTGCTTTGTAGGCGGATAT TAACAGATCGTATGGTGGGC 265–304 1.000 73.1
ndhF_p1 ndhF ACGAAGGGGACTAAACAGGA AACCACTTCCGACTTCTTGA 2885 0.500 49.5
ndhF_p2 ndhF ACGGAAGAAAGGGAGGAAGA AACCACTTCCGACTTCTTGA 2936 0.500 49.4
ndhF_p3 ndhF GCAGAATACCGTCACCCATT AACCACTTCCGACTTCTTGA 2986 0.500 49.3
ndhF_p4 ndhF GATCCGGACAAAATCGACGA AACCACTTCCGACTTCTTGA 2807 0.500 49.0
ndhF_p5 ndhF AGGGGACTAAACAGGAACCA AACCACTTCCGACTTCTTGA 2881 0.500 48.6
ndhF-rpl32_p1 ndhF-rpl32 AGGCAATAGGTCGTGTGAAC CGACAAAGCTTTCAAGGCTG 1476 0.500 58.9
ndhF-rpl32_p2 ndhF-rpl32 AGGCAATAGGTCGTGTGAAC TTCAAGGCTGCCCAATATCC 1466 0.500 58.7
ndhF-rpl32_p3 ndhF-rpl32 AGGCAATAGGTCGTGTGAAC TTGTGACAAGTAGGCCGATG 2003 0.500 58.5
ndhF-rpl32_p4 ndhF-rpl32 TGACAAGCATTCGAGGCAAT CGACAAAGCTTTCAAGGCTG 1489 0.500 58.3
ndhF-rpl32_p5 ndhF-rpl32 GGGTCGATCAAGTGTCCAAA CGACAAAGCTTTCAAGGCTG 1234 0.500 58.2
rpl32-trnL-UAG_p1 rpl32-trnL-UAG CAGCCTTGAAAGCTTTGTCG AGCGTGTCTACCGATTTCAC 1510 0.500 59.6
rpl32-trnL-UAG_p2 rpl32-trnL-UAG CAGCCTTGAAAGCTTTGTCG CAGCGTGTCTACCGATTTCA 1511 0.500 59.6
rpl32-trnL-UAG_p3 rpl32-trnL-UAG CAGCCTTGAAAGCTTTGTCG AAAAGCCCCGAAGTAGCAAA 2027 0.500 59.6
rpl32-trnL-UAG_p4 rpl32-trnL-UAG CAGCCTTGAAAGCTTTGTCG AAAGCCCCGAAGTAGCAAAA 2026 0.500 59.6
rpl32-trnL-UAG_p5 rpl32-trnL-UAG GGATATTGGGCAGCCTTGAA AGCGTGTCTACCGATTTCAC 1520 0.500 59.4
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT TTACGCCAGATGTTCCATGG 1620 0.500 59.6
ccsA_p2 ccsA TGAAATCGGTAGACACGCTG TTACGCCAGATGTTCCATGG 1619 0.500 59.6
ccsA_p3 ccsA GTGAAATCGGTAGACACGCT TTGGCAGGAACGAGTTTTGA 1887 0.500 59.6
ccsA_p4 ccsA TGAAATCGGTAGACACGCTG TTGGCAGGAACGAGTTTTGA 1886 0.500 59.6
ccsA_p5 ccsA GTGAAATCGGTAGACACGCT TATCTTGACGAAATGGGCGG 1851 0.500 59.5
ccsA-ndhD_p1 ccsA-ndhD TTTGCTACTTCGGGGCTTTT TTACGCCAGATGTTCCATGG 1103 0.500 59.6
ccsA-ndhD_p2 ccsA-ndhD TTTTGCTACTTCGGGGCTTT TTACGCCAGATGTTCCATGG 1104 0.500 59.6
ccsA-ndhD_p3 ccsA-ndhD TTTGCTACTTCGGGGCTTTT TTGGCAGGAACGAGTTTTGA 1370 0.500 59.6
ccsA-ndhD_p4 ccsA-ndhD TTTTGCTACTTCGGGGCTTT TTGGCAGGAACGAGTTTTGA 1371 0.500 59.6
ccsA-ndhD_p5 ccsA-ndhD TTTGCTACTTCGGGGCTTTT TATCTTGACGAAATGGGCGG 1334 0.500 59.5

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
Carallia brachiata NC_061056.1 162460 View on NCBI ↗
Carallia diplopetala NC_062600.1 162052 View on NCBI ↗