Markers + reference

Nematolepis

3 species · Rutaceae · Sapindales

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Species 3
Genome length 157–157 kb
Candidate markers 266
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 385 0.0365 1.00 63.8 yes View details
trnS-GCU-trnG-UCC LSC 963 0.0380 1.00 70.5 yes View details
trnD-GUC-trnY-GUA LSC 472 0.0205 1.00 60.3 yes View details
psbC-trnS-UGA LSC 247 0.0469 0.81 79.3 yes View details
trnT-UGU-trnL-UAA LSC 986 0.0135 1.00 62.3 yes View details
ndhC-trnV-UAC LSC 453 0.0207 1.00 48.7 yes View details
rpl22 IRb 222 0.0180 1.00 37.2 yes View details
rpl32-trnL-UAG SSC 594 0.0236 1.00 63.0 yes View details
rps15-ycf1 SSC 357 0.0205 1.00 40.9 yes View details
ycf1 SSC 5484 0.0106 1.00 44.8 yes View details
psbM-trnD-GUC LSC 592 0.0135 1.00 63.7 yes View details
trnR-ACG-trnN-GUU IRb 616 0.0043 1.00 62.0 yes View details
ndhH SSC 1182 0.0051 1.00 62.0 yes View details
trnN-GUU-trnR-ACG IRa 616 0.0043 1.00 62.0 yes View details
trnR-UCU-atpA LSC 216 0.0216 1.00 61.7 yes View details
rps2-rpoC2 LSC 223 0.0150 1.00 61.3 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0339 1.00 61.1 yes View details
petD-rpoA LSC 260 0.0207 0.99 60.0 yes View details
rps12-trnV-GAC IRb 1780 0.0026 1.00 59.8 yes View details
trnV-GAC-rps12 IRa 1780 0.0026 1.00 59.8 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCAGTGCTATGCATGGTTCC 838–843 1.000 81.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCCATTCCACATGTTAGGCG 885 0.333 52.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCCATTCCACATGTTAGGCG 899 0.333 52.0
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCCATTCCACATGTTAGGCG 898 0.333 52.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCCATTCCACATGTTAGGCG 900 0.333 52.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TGAACGAATCACACTTTTACCAC 686–1065 1.000 57.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA ACGAATCACACTTTTACCACT 684–1062 1.000 56.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAACGAATCACACTTTTACCAC 744–1123 1.000 56.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA GAACGAATCACACTTTTACCACT 686–1064 1.000 55.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC TGAACGAATCACACTTTTACCAC 683–1062 1.000 55.4
trnR-UCU-atpA_p1 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT ACGCTTTCTCCTTCAAGAACA 311–1668 1.000 71.2
trnR-UCU-atpA_p2 trnR-UCU-atpA AATGCGCCAAAAATTTCGGA ACGCTTTCTCCTTCAAGAACA 337–1667 1.000 69.1
trnR-UCU-atpA_p3 trnR-UCU-atpA ATGCGCCAAAAATTTCGGAA ACGCTTTCTCCTTCAAGAACA 336–1668 1.000 69.1
trnR-UCU-atpA_p4 trnR-UCU-atpA TGCGCCAAAAATTTCGGAAT ACGCTTTCTCCTTCAAGAACA 335–1668 1.000 69.1
trnR-UCU-atpA_p5 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT GAAACCCTTTTGCAAGAAGCT 349–1706 1.000 69.0
rps2-rpoC2_p1 rps2-rpoC2 GGTGCCATTCTAGGATTCCA ACAGGGAATTTATTCGGGGG 423–424 1.000 66.9
rps2-rpoC2_p2 rps2-rpoC2 CCTGCTTCCATCATCTCTTCC ACAGGGAATTTATTCGGGGG 375–376 1.000 66.1
rps2-rpoC2_p3 rps2-rpoC2 CATTTCCGAGTACCATGACCA ACAGGGAATTTATTCGGGGG 405–406 1.000 65.1
rps2-rpoC2_p4 rps2-rpoC2 GGTGCCATTCTAGGATTCCA AACAGGGAATTTATTCGGGGG 424–425 1.000 64.7
rps2-rpoC2_p5 rps2-rpoC2 AGGTGCCATTCTAGGATTCC ACAGGGAATTTATTCGGGGG 424–425 1.000 64.5
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGCAGTAGGAACTAGAACGA TTTTACTTGCCCGGGATTGT 739–747 1.000 70.4
psbM-trnD-GUC_p2 psbM-trnD-GUC AGGCAGTAGGAACTAGAACGA TACTTGCCCGGGATTGTAGT 736–744 1.000 69.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AGCAAAAAGGCAGTAGGAACT TTTTACTTGCCCGGGATTGT 746–754 1.000 69.2
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGCAGTAGGAACTAGAACGA TTCAATTGGTCAGAGCACCG 717–725 1.000 69.0
psbM-trnD-GUC_p5 psbM-trnD-GUC AGCAAAAAGGCAGTAGGAACT TACTTGCCCGGGATTGTAGT 743–751 1.000 68.2
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 541–543 1.000 76.5
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 540–542 1.000 76.5
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 562–564 1.000 75.5
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 561–563 1.000 75.3
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 595–597 1.000 74.9

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
Nematolepis phebalioides NC_081885.1 156828 View on NCBI ↗
Nematolepis squamea NC_081886.1 156812 View on NCBI ↗
Nematolepis wilsonii NC_081887.1 157338 View on NCBI ↗