Markers + reference

Crowea

3 species · Rutaceae · Sapindales

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Species 3
Genome length 156–156 kb
Candidate markers 273
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 383 0.0157 1.00 57.5 yes View details
psbA-trnK-UUU LSC 264 0.0126 1.00 58.6 yes View details
rps16 LSC 1168 0.0023 1.00 48.4 yes View details
rps16-trnQ-UUG LSC 798 0.0043 0.98 63.3 yes View details
rpoB-trnC-GCA LSC 1242 0.0027 1.00 60.6 yes View details
psbZ-trnG-GCC LSC 543 0.0184 1.00 61.4 yes View details
ndhC-trnV-UAC LSC 453 0.0059 1.00 42.7 yes View details
accD-psaI LSC 808 0.0034 0.97 64.0 yes View details
psaI-ycf4 LSC 444 0.0060 1.00 59.8 yes View details
rps3-rpl22 LSC 367 0.0056 0.65 49.8 yes View details
rpl32-trnL-UAG SSC 631 0.0074 1.00 63.4 yes View details
ycf1 SSC 5490 0.0019 1.00 53.7 yes View details
psaA-ycf3 LSC 739 0.0036 1.00 62.3 yes View details
trnT-GGU-psbD LSC 1218 0.0017 0.98 61.6 yes View details
trnT-UGU-trnL-UAA LSC 1033 0.0032 1.00 60.8 yes View details
atpB-rbcL LSC 780 0.0026 1.00 60.5 yes View details
atpH-atpI LSC 1173 0.0023 1.00 60.4 yes View details
petA-psbJ LSC 928 0.0022 1.00 60.3 yes View details
psbE-petL LSC 1372 0.0015 1.00 60.0 yes View details
matK-trnK-UUU LSC 734 0.0018 1.00 59.7 yes View details
trnD-GUC-trnY-GUA LSC 472 0.0042 1.00 59.2 yes View details
rbcL-accD LSC 571 0.0012 1.00 58.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTTGATCCACTTGGCCACAT CGTGCTAACCTTGGTATGGA 504–505 1.000 74.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CTTGATCCACTTGGCCACAT TCGTGCTAACCTTGGTATGG 505–506 1.000 74.7
trnH-GUG-psbA_p3 trnH-GUG-psbA TTGATCCACTTGGCCACATC CGTGCTAACCTTGGTATGGA 503–504 1.000 74.7
trnH-GUG-psbA_p4 trnH-GUG-psbA TTGATCCACTTGGCCACATC TCGTGCTAACCTTGGTATGG 504–505 1.000 74.7
trnH-GUG-psbA_p5 trnH-GUG-psbA CTTGATCCACTTGGCCACAT CGTGCTAACCTTGGTATGGAA 504–505 1.000 72.0
psbA-trnK-UUU_p1 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT GAAAAATGCATGCACGGCTT 454–456 1.000 75.5
psbA-trnK-UUU_p2 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT ACTCCATCCGACTAGTTCCG 395–397 1.000 75.3
psbA-trnK-UUU_p3 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT ATGAAAAATGCATGCACGGC 456–458 1.000 75.0
psbA-trnK-UUU_p4 psbA-trnK-UUU ACCATCCAATGTAAAGGCGG GAAAAATGCATGCACGGCTT 462–464 1.000 74.4
psbA-trnK-UUU_p5 psbA-trnK-UUU CCATCCAATGTAAAGGCGGT GAAAAATGCATGCACGGCTT 461–463 1.000 74.4
matK-trnK-UUU_p1 matK-trnK-UUU TACTCCCGAAAAAGAAGCGG TGGGTTGCTAACTCAATGGT 851–853 1.000 71.8
matK-trnK-UUU_p2 matK-trnK-UUU TACTCCCGAAAAAGAAGCGG TCAATGGTAGAGTACTCGGCT 839–841 1.000 71.5
matK-trnK-UUU_p3 matK-trnK-UUU CGGGTATAGCAAGTCGTGTT TGGGTTGCTAACTCAATGGT 834–836 1.000 70.2
matK-trnK-UUU_p4 matK-trnK-UUU AGCAAGTCGTGTTGTTGAGA TGGGTTGCTAACTCAATGGT 827–829 1.000 70.1
matK-trnK-UUU_p5 matK-trnK-UUU CGGGTATAGCAAGTCGTGTT TCAATGGTAGAGTACTCGGCT 822–824 1.000 69.9
rps16_p1 rps16 ACTCCTCCACACCCTCTTTT GCAATGACTATTCACGATTCCA 1263–1271 1.000 54.0
rps16_p2 rps16 ACTCCTCCACACCCTCTTTT AGCAATGACTATTCACGATTCCA 1264–1272 1.000 53.3
rps16_p3 rps16 ACTCCTCCACACCCTCTTTT AGCAATGACTATTCACGATTCC 1264–1272 1.000 51.8
rps16_p4 rps16 GACTCCTCCACACCCTCTTT GCAATGACTATTCACGATTCCA 1264–1272 1.000 50.2
rps16_p5 rps16 ACTCCTCCACACCCTCTTTT GCAATGACTATTCACGATTCCAT 1263–1271 1.000 49.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 855–871 1.000 80.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CGAAATTGAAATGGGGCGTC 914–930 1.000 80.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTCG 913–929 1.000 80.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 866–882 1.000 79.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAAATTGAAATGGGGCGTCG 924–940 1.000 79.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1260–1264 1.000 79.0
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGACATC 1230–1234 1.000 78.7
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCTGCGG 1316–1320 1.000 78.4
atpH-atpI_p4 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTGCAACTTTAGCTGCGG 1298–1302 1.000 78.3
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGACATC 1286–1290 1.000 78.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Crowea exalata subsp. exalata OL591170.1 156039 View on NCBI ↗
Crowea exalata subsp. revoluta OL591171.1 155873 View on NCBI ↗
Crowea saligna NC_081870.1 155807 View on NCBI ↗