Markers + reference

Cuscuta

19 species · Convolvulaceae · Solanales

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Species 19
Genome length 61–87 kb
Candidate markers 191
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 191 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnQ-UUG LSC 667 0.2869 0.73 73.8 yes View details
rps2-trnC-GCA LSC 1228 0.2734 0.69 73.2 yes View details
trnT-GGU-psbD LSC 670 0.2580 0.93 77.6 yes View details
rbcL-accD LSC 1085 0.2319 0.88 77.5 yes View details
petD-rps11 LSC 1015 0.3118 0.65 72.4 yes View details
accD LSC 1479 0.1364 0.99 83.8 yes View details
rpl2 LSC 813 0.1128 1.00 82.9 yes View details
rps2 LSC 711 0.0901 1.00 81.5 yes View details
psbB LSC 1527 0.0784 1.00 81.5 yes View details
rpl16 LSC 1228 0.1623 0.98 81.1 yes View details
psbD LSC 1062 0.0554 1.00 80.9 yes View details
psbC LSC 1422 0.0673 1.00 80.9 yes View details
psbA LSC 1062 0.0637 1.00 80.4 yes View details
rpl20-rps12 LSC 746 0.1425 0.94 80.4 yes View details
rbcL LSC 1467 0.0660 1.00 80.3 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA CAATCCACTGCCTTCATCCA TCCTTCCGTCCCAGATCTTT 1446–1877 0.263 61.1
psbA_p2 psbA AATCCACTGCCTTCATCCAC TCCTTCCGTCCCAGATCTTT 1445–1876 0.263 61.1
psbA_p3 psbA ACAATCCACTGCCTTCATCC TCCTTCCGTCCCAGATCTTT 1447–1878 0.263 61.1
psbA_p4 psbA CAATCCACTGCCTTCATCCA TTTTGGATGGGAAAACGGGT 1717–1722 0.158 47.7
psbA_p5 psbA AATCCACTGCCTTCATCCAC TTTTGGATGGGAAAACGGGT 1716–1721 0.158 47.7
psbA-trnQ-UUG_p1 psbA-trnQ-UUG GGAGCCTCCAAATACACCAG CTTCGGGCAATTTGCTGAAG 1347–1787 0.316 64.2
psbA-trnQ-UUG_p2 psbA-trnQ-UUG CAGAGATTCCCAAGGGCATC CTTCGGGCAATTTGCTGAAG 1682–1712 0.263 62.2
psbA-trnQ-UUG_p3 psbA-trnQ-UUG GCATACCCAAGCGGAAACTA CTTCGGGCAATTTGCTGAAG 1138–1578 0.263 62.2
psbA-trnQ-UUG_p4 psbA-trnQ-UUG AAGTGCAACCCTATAGCTGC CTTCGGGCAATTTGCTGAAG 998–1438 0.211 60.0
psbA-trnQ-UUG_p5 psbA-trnQ-UUG CTCCAAATACACCAGCGACA CTTCGGGCAATTTGCTGAAG 1772–1782 0.211 59.6
rps2_p1 rps2 CCCAAGACGCCATAAGTACC TTGGCTAAGTCCTGTCAGGA 1523 0.105 43.6
rps2_p2 rps2 TCGACACTCGCTAGCTCATA TTGGCTAAGTCCTGTCAGGA 1452 0.105 43.6
rps2_p3 rps2 AGGGACCATAACCTTCACCA TTGGCTAAGTCCTGTCAGGA 1670 0.105 43.6
rps2_p4 rps2 AAAGGAACCCAGGGACCATA TTGGCTAAGTCCTGTCAGGA 1680 0.105 43.5
rps2_p5 rps2 AAGGAACCCAGGGACCATAA TTGGCTAAGTCCTGTCAGGA 1679 0.105 43.5
rps2-trnC-GCA_p1 rps2-trnC-GCA CTTGTTTCTGTGGTGGACCA GCAGCACTTCTAGAGTCCAC 1348–2185 0.579 74.7
rps2-trnC-GCA_p2 rps2-trnC-GCA CCCTGACAAATCGCGAAAAC GCAGCACTTCTAGAGTCCAC 2434–2468 0.158 51.7
rps2-trnC-GCA_p3 rps2-trnC-GCA CCTGACAAATCGCGAAAACC GCAGCACTTCTAGAGTCCAC 2433–2467 0.158 51.7
rps2-trnC-GCA_p4 rps2-trnC-GCA CCCTGACAAATCGCGAAAAC AGAATTGATCAGGCGACACC 1993 0.105 43.7
rps2-trnC-GCA_p5 rps2-trnC-GCA CCTGACAAATCGCGAAAACC AGAATTGATCAGGCGACACC 1992 0.105 43.7
trnT-GGU-psbD_p1 trnT-GGU-psbD GTAACACCATGGTAAGGCGT TTGACCAAGGGTTATAGTCA 553–786 0.789 44.7
trnT-GGU-psbD_p2 trnT-GGU-psbD GTAACACCATGGTAAGGCGT TGACCAAGGGTTATAGTCAT 552–785 0.789 43.6
trnT-GGU-psbD_p3 trnT-GGU-psbD GTAACACCATGGTAAGGCGT GATTGACCAAGGGTTATAGTCA 555–743 0.737 42.6
trnT-GGU-psbD_p4 trnT-GGU-psbD ACACCATGGTAAGGCGTAAG GATTGACCAAGGGTTATAGTCA 552–740 0.684 39.4
trnT-GGU-psbD_p5 trnT-GGU-psbD CACCATGGTAAGGCGTAAGT GATTGACCAAGGGTTATAGTCA 551–739 0.684 39.4
psbD_p1 psbD GCGGTAGAGTAACACCATGG GACAATCCATCCGTCTCCAC 2235–2457 0.579 74.2
psbD_p2 psbD GCGGTAGAGTAACACCATGG CTAGAGTCGCTAAGTGGGGA 1846–2023 0.368 65.8
psbD_p3 psbD GCGGTAGAGTAACACCATGG CACCCCCAAAATAAAGGGCT 2290 0.105 43.3
psbD_p4 psbD TCAGCGGTAGAGTAACACCA CACCCCCAAAATAAAGGGCT 2293 0.105 43.1
psbD_p5 psbD GCGTCAAGCGACTATTCTCA CACCCCCAAAATAAAGGGCT 2034 0.105 43.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (19)

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

Species Accession Length (bp) Link
Cuscuta campestris NC_052920.1 86727 View on NCBI ↗
Cuscuta chapalana NC_043870.1 84607 View on NCBI ↗
Cuscuta chinensis NC_073571.1 87103 View on NCBI ↗
Cuscuta corymbosa var. stylosa NC_073573.1 79684 View on NCBI ↗
Cuscuta costaricensis NC_042956.1 86691 View on NCBI ↗
Cuscuta erosa NC_042948.1 60959 View on NCBI ↗
Cuscuta gronovii NC_009765.1 86744 View on NCBI ↗
Cuscuta haughtii NC_073576.1 82941 View on NCBI ↗
Cuscuta indecora NC_073574.1 81804 View on NCBI ↗
Cuscuta macrocephala NC_073572.1 80284 View on NCBI ↗
Cuscuta micrantha NC_073579.1 85736 View on NCBI ↗
Cuscuta nevadensis NC_073580.1 83906 View on NCBI ↗
Cuscuta pacifica NC_073578.1 82539 View on NCBI ↗
Cuscuta pentagona NC_039759.1 86380 View on NCBI ↗
Cuscuta polyanthemos NC_073581.1 84968 View on NCBI ↗
Cuscuta strobilacea NC_043775.1 63787 View on NCBI ↗
Cuscuta subinclusa PX715229.1 83079 View on NCBI ↗
Cuscuta vandevenderi NC_073575.1 82777 View on NCBI ↗
Cuscuta volcanica NC_073577.1 85698 View on NCBI ↗