Markers + reference

Scurrula

7 species · Loranthaceae · Santalales

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Species 7
Genome length 120–124 kb
Candidate markers 232
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 232 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 428 0.0990 0.97 79.6 yes View details
trnS-GCU-trnR-UCU LSC 393 0.0915 0.98 77.9 yes View details
trnC-GCA-petN LSC 277 0.0887 0.97 77.5 yes View details
petN-psbM LSC 752 0.0526 1.00 85.2 yes View details
trnT-GGU-psbD LSC 940 0.0592 1.00 83.6 yes View details
trnS-UGA-psbZ LSC 335 0.0980 0.94 78.3 yes View details
rps4-trnT-UGU LSC 359 0.0569 0.99 79.4 yes View details
trnT-UGU-trnL-UAA LSC 556 0.0780 0.99 88.7 yes View details
accD-psaI LSC 476 0.0774 1.00 81.1 yes View details
rpl16 LSC 1187 0.0656 0.99 83.1 yes View details
ycf1 IRb 942 0.0139 1.00 63.3 no View details
ycf1 SSC 5061 0.0422 1.00 75.2 yes View details
rpoB-trnC-GCA LSC 835 0.0525 0.98 88.3 yes View details
trnR-ACG-trnN-GUU IRb 548 0.0444 1.00 87.4 yes View details
trnN-GUU-trnR-ACG IRa 548 0.0387 1.00 84.8 yes View details
atpB-rbcL LSC 730 0.0488 0.99 84.3 yes View details
rbcL-accD LSC 547 0.0569 0.99 84.2 yes View details
trnW-CCA-trnP-UGG LSC 114 0.0498 0.96 82.6 yes View details
psaA-ycf3 LSC 671 0.0451 0.98 82.2 yes View details
psbA-matK LSC 564 0.0475 1.00 81.9 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
psbA-matK_p1 psbA-matK TAAAGGCGGTTTTCAGTGCT TGGCGCGAAGTCAAATGATA 1080–1177 1.000 91.7
psbA-matK_p2 psbA-matK GTAAAGGCGGTTTTCAGTGC TGGCGCGAAGTCAAATGATA 1081–1178 1.000 91.5
psbA-matK_p3 psbA-matK CAAGAAAACAGCAGTCGCAG TGGCGCGAAGTCAAATGATA 1471–1568 1.000 89.7
psbA-matK_p4 psbA-matK TAAAGGCGGTTTTCAGTGCT ATGGAGGAGGAGCAAGTTCT 718–812 0.857 85.5
psbA-matK_p5 psbA-matK CAAGAAAACAGCAGTCGCAG ATGGAGGAGGAGCAAGTTCT 1109–1203 0.857 83.0
psbK-psbI_p1 psbK-psbI CCTTACCACTTGACTACGCC TAAAGCGGCGGATTGCTAAT 1045–1211 1.000 91.6
psbK-psbI_p2 psbK-psbI CTTACCACTTGACTACGCCC TAAAGCGGCGGATTGCTAAT 1044–1210 1.000 91.6
psbK-psbI_p3 psbK-psbI TGTTTGGCAAGCTGCTCTAA TAAAGCGGCGGATTGCTAAT 602–728 1.000 91.5
psbK-psbI_p4 psbK-psbI TTGTTTGGCAAGCTGCTCTA TAAAGCGGCGGATTGCTAAT 603–729 1.000 91.5
psbK-psbI_p5 psbK-psbI CTTACCACTTGACTACGCCC CCATACCTATCCGGGCTGTA 1194–1361 1.000 91.4
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU TGTTTGGCAAGCTGCTCTAA GTTTCGAGAGTAGGATCCGC 1793–1919 1.000 90.9
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU TTGTTTGGCAAGCTGCTCTA GTTTCGAGAGTAGGATCCGC 1794–1920 1.000 90.9
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA GTTTCGAGAGTAGGATCCGC 1129–1241 1.000 90.7
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU GCATCACTCGTACAACGGAT GTTTCGAGAGTAGGATCCGC 1147–1259 1.000 90.4
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU TACGCATCACTCGTACAACG GTTTCGAGAGTAGGATCCGC 1150–1262 1.000 90.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC CCGGATTTGAACTGGGGAAA 746–919 1.000 91.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC AACTGGGGAAAGGGGATTTG 737–910 1.000 89.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC ATTTGAACTGGGGAAAGGGG 742–915 1.000 89.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCTCATTTCCATCCCAGA CCGGATTTGAACTGGGGAAA 748–921 1.000 89.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCTCATTTCCATCCCAGAGC TGAACTGGGGAAAGGGGATT 739–912 1.000 87.6
trnC-GCA-petN_p1 trnC-GCA-petN TCAGCCCCAGTAACGTTCTA GCCACTGTGAACTCTCGAAT 1100–1155 1.000 90.7
trnC-GCA-petN_p2 trnC-GCA-petN TCAGCCCCAGTAACGTTCTA GATTGGGCTGTTGACAAACG 1162–1208 0.857 85.3
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GATTGGGCTGTTGACAAACG 842–894 0.857 85.2
trnC-GCA-petN_p4 trnC-GCA-petN TCAGCCCCAGTAACGTTCTA AGGACTTGATTGGGCTGTTG 1169–1215 0.714 77.5
trnC-GCA-petN_p5 trnC-GCA-petN TCAGCCCCAGTAACGTTCTA GGACTTGATTGGGCTGTTGA 1168–1214 0.714 77.4
petN-psbM_p1 petN-psbM TCAGCCCCAGTAACGTTCTA AGTTCAACGGGTTAGAGCAC 1918–2174 1.000 90.1
petN-psbM_p2 petN-psbM TCAGCCCCAGTAACGTTCTA CAATCCCGACGAAGCCAATA 1860–2116 0.714 79.6
petN-psbM_p3 petN-psbM TTTCCCCAGTTCAAATCCGG CAATCCCGACGAAGCCAATA 1540–1806 0.714 79.5
petN-psbM_p4 petN-psbM TTTCAGCCCCAGTAACGTTC CAATCCCGACGAAGCCAATA 1862–2118 0.714 79.3
petN-psbM_p5 petN-psbM GTATCATTTTGGCGGCATGG CAATCCCGACGAAGCCAATA 1592–1858 0.714 79.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Scurrula atropurpurea NC_088739.1 122457 View on NCBI ↗
Scurrula balansae NC_088729.1 122438 View on NCBI ↗
Scurrula buddleioides NC_088738.1 122292 View on NCBI ↗
Scurrula chingii NC_053563.1 122764 View on NCBI ↗
Scurrula notothixoides NC_041305.1 123810 View on NCBI ↗
Scurrula parasitica NC_040862.1 121750 View on NCBI ↗
Scurrula pulverulenta NC_088735.1 119811 View on NCBI ↗