Markers + reference

Taihangia

2 species · Rosaceae · Rosales

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Species 2
Genome length 155–155 kb
Candidate markers 271
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1108 0.0063 1.00 62.4 yes View details
rps16 LSC 1147 0.0026 1.00 58.3 yes View details
trnR-UCU-atpA LSC 692 0.0058 1.00 54.3 yes View details
trnT-UGU-trnL-UAA LSC 692 0.0072 1.00 62.9 yes View details
ndhC-trnV-UAC LSC 667 0.0060 1.00 52.9 yes View details
petA-psbJ LSC 1153 0.0139 1.00 66.9 yes View details
rpl22 LSC 429 0.0047 1.00 47.8 yes View details
ndhF SSC 2259 0.0018 1.00 43.5 yes View details
ndhF-rpl32 SSC 1076 0.0037 1.00 60.4 yes View details
ndhD SSC 1503 0.0033 1.00 46.5 yes View details
ycf1-ndhF SSC 47 0.0606 0.70 63.6 yes View details
trnG-GCC-trnfM-CAU LSC 177 0.0169 1.00 62.2 yes View details
trnT-GGU-psbD LSC 1260 0.0008 0.97 61.8 yes View details
rpl20-rps12 LSC 766 0.0039 1.00 61.0 yes View details
matK LSC 1512 0.0020 1.00 59.9 yes View details
trnA-UGC-rrn23 IRb 163 0.0123 1.00 59.6 yes View details
rrn23-trnA-UGC IRa 163 0.0123 1.00 59.6 yes View details
accD LSC 1542 0.0013 1.00 59.4 yes View details
psbD LSC 1062 0.0009 1.00 59.3 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU AACATCCGCCGATATCGATG TTTGATGGCGTTGTGCTAGT 2909 1.000 79.5
trnK-UUU_p2 trnK-UUU CATCCGCCGATATCGATGTT TTTGATGGCGTTGTGCTAGT 2907 1.000 79.5
trnK-UUU_p3 trnK-UUU CCGCCGATATCGATGTTCTT TTTGATGGCGTTGTGCTAGT 2904 1.000 79.0
trnK-UUU_p4 trnK-UUU AACATCCGCCGATATCGATG GTTTGATGGCGTTGTGCTAG 2910 1.000 78.3
trnK-UUU_p5 trnK-UUU CATCCGCCGATATCGATGTT GTTTGATGGCGTTGTGCTAG 2908 1.000 78.3
matK_p1 matK TTCCATATTCGCATAACCAA TGACCGAGGTATCCGTTTTT 1651 1.000 40.1
matK_p2 matK TTCCATATTCGCATAACCAA TTGACCGAGGTATCCGTTTT 1652 1.000 40.1
matK_p3 matK TTTCCATATTCGCATAACCA TGACCGAGGTATCCGTTTTT 1652 1.000 40.1
matK_p4 matK TTTCCATATTCGCATAACCA TTGACCGAGGTATCCGTTTT 1653 1.000 40.1
matK_p5 matK TTTCCATATTCGCATAACCAA TGACCGAGGTATCCGTTTTT 1652 1.000 40.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC GGGCAGGGGTTTTTAAGGAA 1263–1288 1.000 79.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT GGGCAGGGGTTTTTAAGGAA 1262–1287 1.000 79.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC AAGGGCAGGGGTTTTTAAGG 1265–1290 1.000 79.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT AAGGGCAGGGGTTTTTAAGG 1264–1289 1.000 79.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGGCAGGGGTTTTTAAGGAA 1179–1204 1.000 79.0
rps16_p1 rps16 AGGAACTGGCAAAGAAATGA TGTAACGACCGAACCAATGA 1328–1329 1.000 50.8
rps16_p2 rps16 ACTGGCAAAGAAATGAAAAGGT TGTAACGACCGAACCAATGA 1324–1325 1.000 49.5
rps16_p3 rps16 AAGGAACTGGCAAAGAAATGA TGTAACGACCGAACCAATGA 1329–1330 1.000 49.4
rps16_p4 rps16 AGGAACTGGCAAAGAAATGAA TGTAACGACCGAACCAATGA 1328–1329 1.000 49.4
rps16_p5 rps16 AGGAACTGGCAAAGAAATGAAA TGTAACGACCGAACCAATGA 1328–1329 1.000 47.4
trnR-UCU-atpA_p1 trnR-UCU-atpA AAAGGAGTGAAAAGCGTCCA AAGGAAGCGGAAACCCTTTT 852–858 1.000 77.0
trnR-UCU-atpA_p2 trnR-UCU-atpA AAAGGAGTGAAAAGCGTCCA TTACCAAGGAAGCGGAAACC 857–863 1.000 76.8
trnR-UCU-atpA_p3 trnR-UCU-atpA AAAGGAGTGAAAAGCGTCCA CAGGACCAGATGGAACGTTT 819–825 1.000 76.2
trnR-UCU-atpA_p4 trnR-UCU-atpA AAGGAGTGAAAAGCGTCCAT AAGGAAGCGGAAACCCTTTT 851–857 1.000 75.2
trnR-UCU-atpA_p5 trnR-UCU-atpA AGGAGTGAAAAGCGTCCATT AAGGAAGCGGAAACCCTTTT 850–856 1.000 75.2
trnT-GGU-psbD_p1 trnT-GGU-psbD ACTCATGGTGGCTACTGACT GGCCAGACCAACCTACAAAA 1450–1482 1.000 81.3
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGCCAGACCAACCTACAAAA 1392–1424 1.000 81.3
trnT-GGU-psbD_p3 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGCCAGACCAACCTACAAAA 1395–1427 1.000 81.2
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TAGGCCAGACCAACCTACAA 1394–1426 1.000 81.2
trnT-GGU-psbD_p5 trnT-GGU-psbD ACTCATGGTGGCTACTGACT TAGGCCAGACCAACCTACAA 1452–1484 1.000 81.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Taihangia rupestris var. ciliata PQ528002.1 155467 View on NCBI ↗
Taihangia rupestris var. rupestris ON873893.1 155496 View on NCBI ↗