Markers + reference

Kageneckia

3 species · Rosaceae · Rosales

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Species 3
Genome length 159–159 kb
Candidate markers 269
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 273 0.0113 0.97 56.0 yes View details
trnK-UUU-rps16 LSC 985 0.0140 0.99 56.6 yes View details
trnG-UCC-trnR-UCU LSC 202 0.0347 1.00 73.6 yes View details
trnR-UCU-atpA LSC 522 0.0226 0.88 63.5 yes View details
psbZ-trnG-GCC LSC 488 0.0148 0.92 61.1 yes View details
ndhC-trnV-UAC LSC 630 0.0313 0.96 75.5 yes View details
psaI-ycf4 LSC 411 0.0138 1.00 52.0 yes View details
petA-psbJ LSC 972 0.0100 1.00 66.2 yes View details
rpl16 LSC 1397 0.0067 1.00 50.9 yes View details
rpl32-trnL-UAG SSC 1538 0.0145 0.96 64.3 yes View details
ndhD SSC 1503 0.0071 1.00 51.0 yes View details
rpl2-trnH-GUG IRa 276 0.0785 1.00 82.9 no View details
psbF-psbE LSC 9 0.0741 1.00 75.0 yes View details
trnT-GGU-psbD LSC 1383 0.0091 0.98 68.8 yes View details
rpl14-rpl16 LSC 159 0.0126 1.00 66.1 yes View details
rps8-rpl14 LSC 179 0.0186 1.00 64.4 yes View details
trnT-UGU-trnL-UAA LSC 453 0.0089 1.00 63.3 yes View details
petL-petG LSC 157 0.0212 1.00 63.3 yes View details
rpl20-rps12 LSC 776 0.0043 1.00 62.6 yes View details
trnF-GAA-ndhJ LSC 543 0.0074 1.00 62.1 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
trnH-GUG-psbA_p1 trnH-GUG-psbA ATATTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 424–451 1.000 83.9
trnH-GUG-psbA_p2 trnH-GUG-psbA ATATTATGGGCGAACGACGG CCTCTAGACCTAGCTGCTGT 374–401 1.000 83.7
trnH-GUG-psbA_p3 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 377–404 1.000 83.6
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 363–390 1.000 83.6
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 377–404 1.000 83.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGGAACTTCGCCCTAATCAA 1147–1157 1.000 83.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CGGAACTTCGCCCTAATCAA 1143–1153 1.000 83.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT CGGAACTTCGCCCTAATCAA 1144–1154 1.000 83.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGACGAGAGGGAAGAGATCT 1301–1311 1.000 83.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1403–1414 1.000 82.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 259–282 1.000 70.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 262–285 1.000 70.0
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 265–288 1.000 69.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 268–291 1.000 69.3
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 263–286 1.000 67.8
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 517–733 1.000 69.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 516–732 1.000 69.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 456–672 1.000 69.1
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 491–707 1.000 66.1
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 517–733 1.000 65.9
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGCCAGACCAACCTACAAAA 1547–1611 1.000 83.3
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGCCAGACCAACCTACAAAA 1550–1614 1.000 83.1
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TAGGCCAGACCAACCTACAA 1549–1613 1.000 83.1
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACCTACAAAAACGAAGCGGT 1537–1601 1.000 83.0
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TAGGCCAGACCAACCTACAA 1552–1616 1.000 82.9
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTTGCTTCTCCTGAGGGTTG CGTCTTCTCCTTGGCAAAGA 600–646 1.000 81.6
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GGGTTGGTCGGGTAACAAAA CGTCTTCTCCTTGGCAAAGA 586–632 1.000 81.3
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTCCGGCACATCATTATGGA CGTCTTCTCCTTGGCAAAGA 556–602 1.000 75.7
psbZ-trnG-GCC_p4 psbZ-trnG-GCC AGGGTTGGTCGGGTAACAAA CGTCTTCTCCTTGGCAAAGA 587–633 1.000 74.6
psbZ-trnG-GCC_p5 psbZ-trnG-GCC ATTTGCTTCTCCTGAGGGTTG CGTCTTCTCCTTGGCAAAGA 601–647 1.000 74.2

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
Kageneckia angustifolia NC_045322.1 159097 View on NCBI ↗
Kageneckia lanceolata NC_045323.1 159027 View on NCBI ↗
Kageneckia oblonga NC_045324.1 159409 View on NCBI ↗