Markers + reference

Chonemorpha

2 species · Apocynaceae · Gentianales

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Species 2
Genome length 156–156 kb
Candidate markers 275
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 LSC 763 0.0066 1.00 60.0 yes View details
rps16-trnQ LSC 1285 0.0071 0.98 60.0 yes View details
rpoC1 LSC 2802 0.0021 1.00 57.3 yes View details
trnE-UUC-trnT-GGU LSC 915 0.0088 1.00 64.1 yes View details
ndhC-trnV-UAC LSC 1521 0.0169 0.89 71.5 yes View details
petB LSC 1407 0.0036 1.00 61.1 yes View details
ndhF-rpl32 SSC 780 0.0066 0.98 54.9 yes View details
ccsA SSC 969 0.0010 1.00 50.3 yes View details
ccsA-ndhD SSC 248 0.0363 1.00 67.8 yes View details
ndhG-ndhI SSC 550 0.0223 0.98 72.8 yes View details
trnS-trnG LSC 653 0.0033 0.92 64.7 yes View details
trnT-UGU-trnL-UAA LSC 790 0.0026 0.97 62.9 yes View details
atpH-atpI LSC 1220 0.0050 0.99 62.5 yes View details
petN-psbM LSC 1190 0.0050 1.00 61.6 yes View details
rpl14-rpl16 LSC 144 0.0140 0.99 61.2 yes View details
rpoA LSC 1008 0.0040 1.00 61.0 yes View details
matK LSC 1530 0.0020 0.99 60.6 yes View details
petA-psbJ LSC 671 0.0030 1.00 60.5 yes View details
matK-trnK LSC 699 0.0029 1.00 60.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK ACGAGCTACTTACATGCTACA TGTTTTGACTCTATCGCGCT 1697–1709 1.000 58.4
matK_p2 matK ACGAGCTACTTACATGCTACA CTGTTTTGACTCTATCGCGC 1698–1710 1.000 55.7
matK_p3 matK ACGAGCTACTTACATGCTACAT TGTTTTGACTCTATCGCGCT 1697–1709 1.000 54.4
matK_p4 matK ACGAGCTACTTACATGCTACA ACCCTGTTTTGACTCTATCGC 1701–1713 1.000 53.1
matK_p5 matK GAGCTACTTACATGCTACATCGA TGTTTTGACTCTATCGCGCT 1695–1707 1.000 52.9
matK-trnK_p1 matK-trnK ACTATGGCCATGAGCAAGTG AACGGTAGAGTACTCGGCTT 831 1.000 78.5
matK-trnK_p2 matK-trnK ACTATGGCCATGAGCAAGTG ACGGTAGAGTACTCGGCTTT 830 1.000 78.5
matK-trnK_p3 matK-trnK ACTATGGCCATGAGCAAGTG GGGTTGCTAACTCAACGGTA 844 1.000 76.1
matK-trnK_p4 matK-trnK ACTATGGCCATGAGCAAGTG TTCGGGTTGCTAACTCAACG 847 1.000 75.8
matK-trnK_p5 matK-trnK ACTATGGCCATGAGCAAGTG CAACGGTAGAGTACTCGGCT 832 1.000 72.6
trnK-rps16_p1 trnK-rps16 CCGATGGTATGGACGAATCC GGGCTCAACCTACAGGAACT 947 1.000 71.7
trnK-rps16_p2 trnK-rps16 AAAGCCGAGTACTCTACCGT GGGCTCAACCTACAGGAACT 886 1.000 71.1
trnK-rps16_p3 trnK-rps16 AAGCCGAGTACTCTACCGTT GGGCTCAACCTACAGGAACT 885 1.000 71.1
trnK-rps16_p4 trnK-rps16 CGTAAAAGATCCTAGCCGCA GGGCTCAACCTACAGGAACT 910 1.000 70.7
trnK-rps16_p5 trnK-rps16 TGCGTAAAAGATCCTAGCCG GGGCTCAACCTACAGGAACT 912 1.000 70.7
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1339–1362 1.000 75.4
rps16-trnQ_p2 rps16-trnQ AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1365–1388 1.000 75.3
rps16-trnQ_p3 rps16-trnQ TGTACTTCAAGTCGCACGTT TTCGGAGGTTCGAATCCTTC 1347–1370 1.000 74.8
rps16-trnQ_p4 rps16-trnQ TGTACTTCAAGTCGCACGTT TAAGGCAACGGGTTTTGGTC 1373–1396 1.000 74.7
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA AAATCTAAATGGGGCGTGGC 1392–1415 1.000 73.6
trnS-trnG_p1 trnS-trnG ATTAGCAATCCGCCGCTTTA TCAAACCGAAAACAAAGACCC 723–772 1.000 69.6
trnS-trnG_p2 trnS-trnG ATTAGCAATCCGCCGCTTTA CAAACCGAAAACAAAGACCCT 722–771 1.000 69.6
trnS-trnG_p3 trnS-trnG TCAAGTCATCAAGGGAAGCG TCAAACCGAAAACAAAGACCC 789–838 1.000 69.1
trnS-trnG_p4 trnS-trnG TCAAGTCATCAAGGGAAGCG CAAACCGAAAACAAAGACCCT 788–837 1.000 69.1
trnS-trnG_p5 trnS-trnG CATCAAGGGAAGCGGAAAGA TCAAACCGAAAACAAAGACCC 783–832 1.000 69.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCCGCAG 1305–1307 1.000 79.7
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CCGCAGCTTATATCGGTGAA 1291–1293 1.000 79.6
atpH-atpI_p3 atpH-atpI TACCCTCTACAGCTTGACCC TTTTGCAACTTTAGCCGCAG 1388–1390 1.000 78.8
atpH-atpI_p4 atpH-atpI GCGATACCCTCTACAGCTTG TTTTGCAACTTTAGCCGCAG 1392–1394 1.000 78.8
atpH-atpI_p5 atpH-atpI TACCCTCTACAGCTTGACCC CCGCAGCTTATATCGGTGAA 1374–1376 1.000 78.7

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
Chonemorpha eriostylis NC_072067.1 155783 View on NCBI ↗
Chonemorpha megacalyx NC_056322.1 155694 View on NCBI ↗