Markers + reference

Parrotia

2 species · Hamamelidaceae · Saxifragales

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Species 2
Genome length 159–159 kb
Candidate markers 270
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnT-GGU-psbD LSC 1364 0.0037 1.00 53.6 yes View details
trnT-UGU-trnL-UAA LSC 1031 0.0058 1.00 55.6 yes View details
trnF-GAA-ndhJ LSC 706 0.0086 0.98 65.2 yes View details
atpB-rbcL LSC 741 0.0067 1.00 62.6 yes View details
accD LSC 1530 0.0026 1.00 57.1 yes View details
accD-psaI LSC 687 0.0058 1.00 55.3 yes View details
ndhF-rpl32 SSC 1082 0.0075 0.98 54.8 yes View details
ndhD SSC 1521 0.0046 1.00 48.6 yes View details
ndhA SSC 2176 0.0037 0.99 60.5 yes View details
rps15-ycf1 SSC 377 0.0135 0.98 63.4 yes View details
ycf1 SSC 5577 0.0030 1.00 40.2 yes View details
rps19-rpl2 IRb 72 0.0317 0.88 73.0 yes View details
trnL-UAG-ccsA SSC 99 0.0206 0.98 66.3 yes View details
ycf4-cemA LSC 910 0.0045 0.98 63.1 yes View details
psbT-psbN LSC 59 0.0169 1.00 62.2 yes View details
ndhC-trnV-UAC LSC 1152 0.0026 0.99 61.6 yes View details
trnC-GCA-petN LSC 842 0.0048 1.00 61.5 yes View details
trnE-UUC-trnT-GGU LSC 877 0.0046 1.00 61.5 yes View details
petA-psbJ LSC 1053 0.0038 1.00 61.2 yes View details
rpl16 LSC 1414 0.0028 1.00 60.5 yes View details
rpl2-trnH-GUG IRa 88 0.0263 0.86 60.5 no 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACGAGCGAAAGGGAAAATGT 946 1.000 78.8
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CCATACTACGAGCGAAAGGG 953 1.000 78.6
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CCCATACTACGAGCGAAAGG 954 1.000 78.6
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CCCCATACTACGAGCGAAAG 955 1.000 78.6
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 908 1.000 78.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 1017–1018 1.000 79.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TACCGCTGAGTTAAAAGGGC 982–983 1.000 78.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 979–980 1.000 78.3
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 1014–1015 1.000 77.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TACCGCTGAGTTAAAAGGGC 944–945 1.000 77.5
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1528–1530 1.000 77.6
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CAAAAACGAAACGGTCCCTC 1527–1529 1.000 76.4
trnT-GGU-psbD_p3 trnT-GGU-psbD AGGAATTGAATCAAACGCGC ACAAAAACGAAACGGTCCCT 1546–1548 1.000 76.3
trnT-GGU-psbD_p4 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA ACAAAAACGAAACGGTCCCT 1491–1493 1.000 76.2
trnT-GGU-psbD_p5 trnT-GGU-psbD CAAACGCGCCCTTTTAACTC ACAAAAACGAAACGGTCCCT 1535–1537 1.000 75.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA AAAGCCAGCTATCGGAATCG ACCAATTTCGCCATATCCCC 1123–1126 1.000 79.6
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 1078–1081 1.000 79.6
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA AAAGCCAGCTATCGGAATCG TAGCGTCTACCAATTTCGCC 1131–1134 1.000 79.0
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 1086–1089 1.000 79.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1110–1113 1.000 78.7
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA AGTTGGATAGGATGGCCCTT 838–848 1.000 80.9
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA AGTTGGATAGGATGGCCCTT 802–812 1.000 80.6
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ TGAGGATGATACGTCGGGAA AGTTGGATAGGATGGCCCTT 863–873 1.000 80.4
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ GGATGATACGTCGGGAATGG AGTTGGATAGGATGGCCCTT 860–870 1.000 80.2
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA ACGCCTGAAACGCATCTTAA 866–876 1.000 80.0
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GTCCTTTGCTAATCGGAGCT AGAAGGTCTACGGTTCGAGT 1281–1297 1.000 77.1
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CGGTCCTTTGCTAATCGGAG AGAAGGTCTACGGTTCGAGT 1283–1299 1.000 76.2
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CTCCGGTCCTTTGCTAATCG AGAAGGTCTACGGTTCGAGT 1286–1302 1.000 76.2
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GTCCTTTGCTAATCGGAGCT GAAGGTCTACGGTTCGAGTC 1280–1296 1.000 74.3
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GGTCCTTTGCTAATCGGAGC AGAAGGTCTACGGTTCGAGT 1282–1298 1.000 74.0

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
Parrotia persica NC_071840.1 159169 View on NCBI ↗
Parrotia subaequalis NC_037243.1 159280 View on NCBI ↗