Markers + reference

Melodinus

2 species · Apocynaceae · Gentianales

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Species 2
Genome length 155–155 kb
Candidate markers 266
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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1211 0.0025 1.00 60.2 yes View details
atpF LSC 1259 0.0032 1.00 60.7 yes View details
ndhC-trnV-UAC LSC 1269 0.0024 1.00 60.1 yes View details
psbE-petL LSC 1182 0.0009 0.99 60.2 yes View details
trnR-ACG-trnN-GUU IRb 570 0.0070 1.00 62.2 yes View details
trnN-GUU-ndhF IRb 1442 0.0014 1.00 51.8 yes View details
ndhF SSC 2235 0.0009 1.00 44.5 yes View details
ycf1 SSC 5415 0.0015 1.00 42.8 yes View details
ycf1-trnN-GUU IRa 328 0.0030 1.00 46.7 yes View details
trnN-GUU-trnR-ACG IRa 570 0.0070 1.00 62.2 yes View details
accD-psaI LSC 625 0.0000 0.99 59.7 yes View details
ycf4-cemA LSC 688 0.0015 1.00 59.6 yes View details
trnK-UUU-rps16 LSC 741 0.0014 1.00 59.5 yes View details
rpl32-trnL-UAG SSC 947 0.0011 1.00 59.5 yes View details
trnC-GCA-petN LSC 875 0.0011 1.00 59.4 yes View details
rpoA LSC 1008 0.0010 1.00 59.3 yes View details
ndhF-rpl32 SSC 729 0.0000 0.99 59.3 yes View details
trnT-GGU-psbD LSC 1192 0.0008 1.00 59.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC GGTGCTCAACCTACAGGAAC 926–928 1.000 77.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 865–867 1.000 77.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 864–866 1.000 77.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC GGTGCTCAACCTACAGGAAC 950–952 1.000 76.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT GGTGCTCAACCTACAGGAAC 949–951 1.000 76.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATCAAAATGGGGCGTGG 1342 1.000 79.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATCAAAATGGGGCGTGG 1353 1.000 78.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1284 1.000 78.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1295 1.000 77.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAAATCAAAATGGGGCGTGG 1354 1.000 74.0
atpF_p1 atpF TTTCGTCAGCTCGAATGGTT GAGGGGCGAAGTGATACAAA 1417–1418 1.000 75.8
atpF_p2 atpF TTTCGTCAGCTCGAATGGTT AAGAGGGGCGAAGTGATACA 1419–1420 1.000 75.5
atpF_p3 atpF TTTCGTCAGCTCGAATGGTT AGAGGGGCGAAGTGATACAA 1418–1419 1.000 75.5
atpF_p4 atpF TCGTCAGCTCGAATGGTTAC GAGGGGCGAAGTGATACAAA 1415–1416 1.000 74.9
atpF_p5 atpF TCGTCAGCTCGAATGGTTAC AGAGGGGCGAAGTGATACAA 1416–1417 1.000 74.6
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 985 1.000 79.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 983 1.000 79.4
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 986 1.000 78.8
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 931 1.000 78.2
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTCTTCCCCACACTACGAGT 1001 1.000 77.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GAAACGGTCCCTACGTAACC 1348 1.000 79.2
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GGACCAGCCTACAAAAACGA 1366 1.000 78.3
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GAAACGGTCCCTACGTAACC 1311 1.000 77.8
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1356 1.000 77.3
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1329 1.000 76.9
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT AGAAGGTCTACGGTTCGAGT 1400 1.000 77.5
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CTGGTCCTTTGCTAATCGGG AGAAGGTCTACGGTTCGAGT 1417 1.000 75.9
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CCTTTGCTAATCGGGGCTAA AGAAGGTCTACGGTTCGAGT 1412 1.000 75.9
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT GAAGGTCTACGGTTCGAGTC 1399 1.000 74.7
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TCCTTTGCTAATCGGGGCTA AGAAGGTCTACGGTTCGAGT 1413 1.000 74.6

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
Melodinus fusiformis PV751239.1 154913 View on NCBI ↗
Melodinus tenuicaudatus NC_079613.1 154916 View on NCBI ↗