Markers + reference

Habenaria

7 species · Orchidaceae · Asparagales

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Species 7
Genome length 154–156 kb
Candidate markers 271
Primer pairs 85

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 8 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 638 0.0524 1.00 78.6 yes View details
rps16 LSC 1160 0.0335 1.00 59.9 yes View details
rps16-trnQ-UUG LSC 399 0.0555 0.99 81.7 yes View details
trnQ-UUG-psbK LSC 359 0.0412 1.00 66.5 yes View details
atpH-atpI LSC 736 0.0416 0.99 82.8 yes View details
clpP LSC 2254 0.0248 1.00 60.7 yes View details
ycf1 IRb 1032 0.0119 1.00 45.1 no View details
ndhF-rpl32 SSC 721 0.0492 0.99 79.4 yes View details
rpl32-trnL-UAG SSC 653 0.0549 0.97 78.3 yes View details
ycf1 SSC 5301 0.0360 1.00 64.3 yes View details
psaJ-rpl33 LSC 569 0.0404 0.97 78.7 yes View details
psbM-trnD-GUC LSC 945 0.0338 0.99 78.1 yes View details
trnS-GCU-trnG-GCC LSC 622 0.0488 0.99 77.7 yes View details
ndhC-trnV-UAC LSC 1139 0.0303 0.99 74.9 yes View details
rpl16-rps3 LSC 180 0.0617 1.00 74.7 yes View details
rps14-psaB LSC 132 0.0909 0.95 72.5 yes View details
rpl36-infA LSC 122 0.0845 0.98 72.3 yes View details
trnE-UUC-trnT-GGU LSC 867 0.0308 1.00 71.3 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGATCCCGAAGAGAAGGAA 851–893 0.571 66.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGATACCCCGGAGACAGAAG GCAAAGACAACGAATTCCGG 1953–1954 0.286 50.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCAAAGACAACGAATTCCGG 1264–1265 0.286 50.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCAAAGACAACGAATTCCGG 1263–1264 0.286 50.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGATACCCCGGAGACAGAAG TCGATCCCGAAGAGAAGGAA 1541–1542 0.286 50.0
rps16_p1 rps16 TATTTGTTCGAGACGCCGTT GAGGTTCGAATCCTTCCGTC 1890–1958 0.571 68.2
rps16_p2 rps16 AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 2255–2336 0.571 67.7
rps16_p3 rps16 AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 2254–2335 0.571 67.7
rps16_p4 rps16 TATTTGTTCGAGACGCCGTT AATCCTTCCGTCCCAGATCA 1882–1888 0.286 50.0
rps16_p5 rps16 AAGCCGAGTACTCTACCGTT AATCCTTCCGTCCCAGATCA 2246–2249 0.286 49.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCGGAATTCGTTGTCTTTGC GAGGTTCGAATCCTTCCGTC 1006–1060 1.000 88.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCGGAATTCGTTGTCTTTGC CTTACAGCAGCTTGCCAAAC 1593–1652 1.000 87.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCGTTGTCTTTGCTTTTCGC CTTACAGCAGCTTGCCAAAC 1586–1589 0.286 50.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGTCTTTGCTTTTCGCT CTTACAGCAGCTTGCCAAAC 1585–1588 0.286 50.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCGTTGTCTTTGCTTTTCGC GAGGTTCGAATCCTTCCGTC 1003–1007 0.286 50.2
trnQ-UUG-psbK_p1 trnQ-UUG-psbK TCATGTCCTTCAAGTCGCAC CTTACAGCAGCTTGCCAAAC 1059–1087 1.000 87.8
trnQ-UUG-psbK_p2 trnQ-UUG-psbK TGCTCGAGCTGCATCATATG CTTACAGCAGCTTGCCAAAC 1208–1236 1.000 87.2
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AAGTCGCACGTTGCTTTCTA CTTACAGCAGCTTGCCAAAC 1053–1076 0.857 80.7
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AAGTCGCACGTTGCTTTCTA ACGCCCCGGATCATTAGATA 1596–1636 0.429 60.6
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AAGTCGCACGTTGCTTTCTA TACGCCCCGGATCATTAGAT 1597–1637 0.429 60.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CATCGTTAGCTTGGAAGGCT 1376–1443 1.000 86.3
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CATCGTTAGCTTGGAAGGCT 1375–1442 1.000 86.3
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GATCAGGGGAATCGGAGAGA CATCGTTAGCTTGGAAGGCT 1445–1498 0.571 67.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATCAGGGGAATCGGAGAGAG CATCGTTAGCTTGGAAGGCT 1444–1497 0.571 67.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GATCAGGGGAATCGGAGAGA CGTTAGCTTGGAAGGCTAGG 1442–1495 0.571 67.3
atpH-atpI_p1 atpH-atpI AGCCAATCCAGCAGCAATAA GGCTGCGGCTTATATAGGTG 821–833 1.000 87.1
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC GGCTGCGGCTTATATAGGTG 820–832 1.000 86.6
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG GGCTGCGGCTTATATAGGTG 815–827 1.000 86.2
atpH-atpI_p4 atpH-atpI AATCCAGCAGCAATAACGGA GGCTGCGGCTTATATAGGTG 817–829 1.000 85.0
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAA GGCTGCGGCTTATATAGGTG 816–828 1.000 85.0

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
Habenaria aitchisonii NC_088438.1 155259 View on NCBI ↗
Habenaria chejuensis NC_046821.1 153896 View on NCBI ↗
Habenaria ciliolaris MN495954.1 154732 View on NCBI ↗
Habenaria cruciformis NC_059695.1 155708 View on NCBI ↗
Habenaria linearifolia NC_059696.1 155653 View on NCBI ↗
Habenaria radiata NC_035834.1 155353 View on NCBI ↗
Habenaria tibetica NC_088439.1 155269 View on NCBI ↗