Markers + reference

Cytisus

3 species · Fabaceae · Fabales

Back to catalogue

Species 3
Genome length 151–153 kb
Candidate markers 250
Primer pairs 110

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 250 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl16 LSC 1547 0.0155 1.00 57.1 yes View details
rpoA LSC 996 0.0100 1.00 50.5 yes View details
rpl33-psaJ LSC 485 0.0330 1.00 64.8 yes View details
psbM-petN LSC 1148 0.0215 1.00 64.3 yes View details
trnG-trnS LSC 822 0.0294 0.98 76.8 yes View details
trnF-ndhJ LSC 604 0.0304 1.00 69.0 yes View details
atpB-rbcL LSC 789 0.0221 1.00 63.6 yes View details
psbA-trnH LSC 271 0.0531 1.00 75.0 yes View details
ycf1-rps15 SSC 424 0.0339 1.00 66.3 yes View details
ndhI-ndhG SSC 352 0.0421 0.99 70.9 yes View details
rpoA-petD LSC 222 0.0581 0.98 76.3 yes View details
trnM-atpE LSC 134 0.0697 1.00 75.5 yes View details
trnR-trnG LSC 150 0.0578 1.00 74.1 yes View details
trnH-rpl2 LSC 109 0.0412 0.89 70.5 yes View details
trnfM-trnG LSC 127 0.0394 1.00 69.8 yes View details
atpI-atpH LSC 1337 0.0200 0.99 68.6 yes View details
cemA-ycf4 LSC 342 0.0343 0.99 68.0 yes View details
rpl36-rps11 LSC 321 0.0304 0.99 67.8 yes View details
rpl16-rpl14 LSC 133 0.0365 0.96 66.8 yes View details
petG-petL LSC 163 0.0327 1.00 66.5 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
rpl16_p1 rpl16 TCATTTGATATTGATAGAATTGCT TCCCAAAGACCTCTTTCCTT 1603 0.333 13.3
rpl16_p2 rpl16 TCATTTGATATTGATAGAATTGCT TCCCAAAGACCTCTTTCCTTTG 1603 0.333 13.3
rpl16_p3 rpl16 TCATTTGATATTGATAGAATTGCT TCCCAAAGACCTCTTTCCTTT 1603 0.333 13.3
rpl16_p4 rpl16 TCATTTGATATTGATAGAATTGCT CCCAAAGACCTCTTTCCTTTG 1602 0.333 13.3
rpl16_p5 rpl16 TCATTTGATATTGATAGAATTGCT AGACCTCTTTCCTTTGGTTCT 1597 0.333 13.3
rpl16-rpl14_p1 rpl16-rpl14 ACTCAATTCATTATTTCGGGA CCGCTGTTATCGGCTACATT 188–201 1.000 46.9
rpl16-rpl14_p2 rpl16-rpl14 AACTCAATTCATTATTTCGGGA CCGCTGTTATCGGCTACATT 189–202 1.000 46.9
rpl16-rpl14_p3 rpl16-rpl14 ACTCAATTCATTATTTCGGGAT CCGCTGTTATCGGCTACATT 188–201 1.000 46.9
rpl16-rpl14_p4 rpl16-rpl14 GAACTCAATTCATTATTTCGGGA CCGCTGTTATCGGCTACATT 190–203 1.000 46.8
rpl16-rpl14_p5 rpl16-rpl14 GAACTCAATTCATTATTTCGGG CCGCTGTTATCGGCTACATT 190–203 1.000 46.8
rpl36-rps11_p1 rpl36-rps11 AAAATAAGGGCCTCTGCTCG TCCATTTTTACGCGAACCCA 458–476 1.000 84.6
rpl36-rps11_p2 rpl36-rps11 AAAATAAGGGCCTCTGCTCG CGTCCATTTTTACGCGAACC 460–478 1.000 84.4
rpl36-rps11_p3 rpl36-rps11 AAAATAAGGGCCTCTGCTCG TACGCGAACCCATTTTGAGT 450–468 1.000 84.2
rpl36-rps11_p4 rpl36-rps11 AAAATAAGGGCCTCTGCTCG GTCCATTTTTACGCGAACCC 459–477 1.000 83.4
rpl36-rps11_p5 rpl36-rps11 ATAAGGGCCTCTGCTCGTAA TCCATTTTTACGCGAACCCA 455–473 1.000 83.3
rpoA_p1 rpoA CGGGCGGAAGTCATGATAAA TAATGGTTTCGGTACCTGCG 1622–1628 1.000 82.1
rpoA_p2 rpoA CGGGCGGAAGTCATGATAAA GGTTGGGTATTGGAGCAACA 1496–1502 1.000 81.6
rpoA_p3 rpoA CGGGCGGAAGTCATGATAAA GTGGTTGGGTATTGGAGCAA 1498–1504 1.000 81.6
rpoA_p4 rpoA CGGGCGGAAGTCATGATAAA TGGTTGGGTATTGGAGCAAC 1497–1503 1.000 81.6
rpoA_p5 rpoA TGGGTTCGCGTAAAAATGGA TAATGGTTTCGGTACCTGCG 1867–1873 1.000 81.4
rpoA-petD_p1 rpoA-petD GAAGCCTCCCGGAATTTGAT TAATGGTTTCGGTACCTGCG 750–755 1.000 83.7
rpoA-petD_p2 rpoA-petD GAAGCCTCCCGGAATTTGAT GGTTGGGTATTGGAGCAACA 624–629 1.000 83.7
rpoA-petD_p3 rpoA-petD GAAGCCTCCCGGAATTTGAT TGGTTGGGTATTGGAGCAAC 625–630 1.000 83.7
rpoA-petD_p4 rpoA-petD GAAGCCTCCCGGAATTTGAT GTTTGATTCGTGCTTGAGCC 1128–1133 1.000 82.3
rpoA-petD_p5 rpoA-petD GAAGCCTCCCGGAATTTGAT GTGCTTGAGCCGTATGATGA 1119–1124 1.000 82.0
rpl33-psaJ_p1 rpl33-psaJ TATCTTTACCCTTGGCCAT GATGCATTGATATTCCCGTT 537–554 1.000 44.1
rpl33-psaJ_p2 rpl33-psaJ TATCTTTACCCTTGGCCAT GATGCATTGATATTCCCGTTT 537–554 1.000 44.1
rpl33-psaJ_p3 rpl33-psaJ TATCTTTACCCTTGGCCAT TGCATTGATATTCCCGTTTT 535–552 1.000 44.1
rpl33-psaJ_p4 rpl33-psaJ TATCTTTACCCTTGGCCAT GATGCATTGATATTCCCGTTTT 537–554 1.000 44.1
rpl33-psaJ_p5 rpl33-psaJ TATCTTTACCCTTGGCCAT TGCATTGATATTCCCGTTTTT 535–552 1.000 44.1

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
Cytisus austriacus PQ469243.1 153182 View on NCBI ↗
Cytisus nigricans PQ484033.1 151225 View on NCBI ↗
Cytisus scoparius PQ469245.1 153205 View on NCBI ↗