Markers + reference

Bletilla

4 species · Orchidaceae · Asparagales

Back to catalogue

Species 4
Genome length 157–159 kb
Candidate markers 269
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 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
rps16-trnQ-UUG LSC 1019 0.0924 0.96 84.8 yes View details
trnC-GCA-petN LSC 841 0.0704 0.98 84.6 yes View details
petN-psbM LSC 734 0.2980 0.86 80.2 yes View details
trnE-UUC-trnT-GGU LSC 1084 0.0988 0.94 86.8 yes View details
ndhC-trnV-UAC LSC 1083 0.2071 0.60 77.1 yes View details
atpB-rbcL LSC 974 0.1057 0.98 84.2 yes View details
clpP-psbB LSC 818 0.1021 0.83 80.3 yes View details
ndhF SSC 2259 0.0729 1.00 82.8 yes View details
ndhF-rpl32 SSC 940 0.1152 0.59 76.3 yes View details
psaA-ycf3 LSC 585 0.0504 0.99 97.8 yes View details
ycf4-cemA LSC 747 0.0609 0.99 87.8 yes View details
rps11-rpl36 LSC 170 0.0559 1.00 86.8 yes View details
rpl32-trnL-UAG SSC 663 0.0837 0.98 85.7 yes View details
atpH-atpI LSC 728 0.0559 0.93 84.2 yes View details
psaJ-rpl33 LSC 582 0.0578 1.00 83.8 yes View details
psbK-psbI LSC 471 0.0725 1.00 83.2 yes View details
trnT-UGU-trnL-UAA LSC 558 0.0508 1.00 82.7 yes View details
rpoB-trnC-GCA LSC 1464 0.0518 0.94 81.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 906–1132 1.000 90.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 883–1109 1.000 90.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 904–1130 1.000 90.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 910–1136 1.000 89.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 894–1120 1.000 89.8
psbK-psbI_p1 psbK-psbI CGCCCCATTTTGATTTGGTC TGGACTAAAGCGTCGGATTG 1326–1379 1.000 90.4
psbK-psbI_p2 psbK-psbI CGCCCCATTTTGATTTGGTC GTGGACTAAAGCGTCGGATT 1327–1380 1.000 90.4
psbK-psbI_p3 psbK-psbI CTGATGCAAACGATCTGGGA TGGACTAAAGCGTCGGATTG 1405–1458 1.000 90.0
psbK-psbI_p4 psbK-psbI TCTGATGCAAACGATCTGGG TGGACTAAAGCGTCGGATTG 1406–1459 1.000 90.0
psbK-psbI_p5 psbK-psbI CTGATGCAAACGATCTGGGA GTGGACTAAAGCGTCGGATT 1406–1459 1.000 90.0
atpH-atpI_p1 atpH-atpI AGCCAATCCAGCAGCAATAA GGCTGCGGCTTATATAGGTG 711–819 1.000 87.8
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC GGCTGCGGCTTATATAGGTG 710–818 1.000 87.3
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG GGCTGCGGCTTATATAGGTG 705–813 1.000 87.0
atpH-atpI_p4 atpH-atpI AATCCAGCAGCAATAACGGA GGCTGCGGCTTATATAGGTG 707–815 1.000 85.7
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAA GGCTGCGGCTTATATAGGTG 706–814 1.000 85.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA AGTATCGACAGACCTAGCCC 1819–1900 1.000 89.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA GTATCGACAGACCTAGCCCT 1818–1899 1.000 89.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCAAATTAAGACCGCGGGTA GCCCTACGGGTTCTCAAAAT 1841–1922 1.000 88.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCCTACACAGGCAAATTGT AGTATCGACAGACCTAGCCC 2258–2339 1.000 88.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCCTACACAGGCAAATTGT GTATCGACAGACCTAGCCCT 2257–2338 1.000 88.3
trnC-GCA-petN_p1 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC GCTCTAAAGCCCACTCCTTC 950–967 0.500 65.3
trnC-GCA-petN_p2 trnC-GCA-petN TAAGCGACGCGTATTCTGAG GCTCTAAAGCCCACTCCTTC 1354 0.250 48.9
trnC-GCA-petN_p3 trnC-GCA-petN TAAGCGACGCGTATTCTGAG AGCCCAAGCGAGACTTACTA 1288 0.250 48.0
trnC-GCA-petN_p4 trnC-GCA-petN TAAGCGACGCGTATTCTGAG CCTTCCCCATACTACAAGCG 1339 0.250 47.3
trnC-GCA-petN_p5 trnC-GCA-petN GCGACGCGTATTCTGAGATA GCTCTAAAGCCCACTCCTTC 1351 0.250 47.3
petN-psbM_p1 petN-psbM TAGAGGCTCTTAGTGCTGCT AGCGGGAAAATGAAATGGGA 1540–1728 1.000 88.9
petN-psbM_p2 petN-psbM TAGAGGCTCTTAGTGCTGCT CGTTTATTGCTACTGCGCTG 1228–1259 0.500 67.4
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT CGTTTATTGCTACTGCGCTG 903–966 0.500 66.0
petN-psbM_p4 petN-psbM CGCTTGTAGTATGGGGAAGG CGTTTATTGCTACTGCGCTG 852–915 0.500 65.8
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT AGCGGGAAAATGAAATGGGA 1215–1264 0.500 64.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Bletilla formosana NC_045842.1 158968 View on NCBI ↗
Bletilla ochracea NC_029483.1 157431 View on NCBI ↗
Bletilla sinensis ON243844.1 156939 View on NCBI ↗
Bletilla striata NC_028422.1 157393 View on NCBI ↗