Markers + reference

Masdevallia

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 156–157 kb
Candidate markers 271
Primer pairs 100

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 934 0.0231 0.98 63.0 yes View details
rpoB-trnC-GCA LSC 1322 0.0228 1.00 70.5 yes View details
petN-psbM LSC 859 0.0247 0.94 70.2 yes View details
ndhC-trnV-UAC LSC 619 0.0230 0.98 61.7 yes View details
atpB-rbcL LSC 1093 0.0397 0.95 78.4 yes View details
rbcL-accD LSC 842 0.0297 1.00 63.6 yes View details
ycf4-cemA LSC 748 0.0269 0.99 67.7 yes View details
clpP-psbB LSC 845 0.0221 0.96 66.7 yes View details
ndhF-rpl32 SSC 843 0.0242 0.93 76.5 yes View details
rpl32-trnL-UAG SSC 811 0.0380 0.94 78.6 yes View details
ycf1 SSC 5472 0.0159 1.00 54.1 yes View details
trnG-UCC-trnR-UCU LSC 114 0.0495 0.89 76.2 yes View details
psaA-ycf3 LSC 639 0.0180 0.96 73.1 yes View details
trnE-UUC-trnT-GGU LSC 721 0.0148 0.94 71.6 yes View details
trnS-UGA-psbZ LSC 238 0.0270 0.93 69.9 yes View details
trnF-GAA-ndhJ LSC 171 0.0307 0.95 69.0 yes View details
psaJ-rpl33 LSC 589 0.0204 1.00 68.8 yes View details
trnT-UGU-trnL-UAA LSC 635 0.0163 0.96 66.6 yes View details
atpF LSC 1511 0.0094 0.98 65.7 yes View details
ndhE-ndhG SSC 152 0.0461 1.00 65.1 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGGAAAGACCCCTTAACTGT 1039–1062 1.000 67.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGGAAAGACCCCTTAACTGT 1038–1061 1.000 67.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGAAAGACCCCTTAACTGTTGA 1038–1061 1.000 66.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGAAAGACCCCTTAACTGTTGA 1037–1060 1.000 66.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGGAAAGACCCCTTAACTGTTG 1039–1062 1.000 65.9
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 194–211 1.000 69.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 197–214 1.000 69.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 200–217 1.000 68.6
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 203–220 1.000 68.3
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCAACGTCGACTATAACCCC AGAAGACCTCTGTCCTATCCA 215–232 1.000 67.7
atpF_p1 atpF TTCGGAAGGAAAGGGAAAAA AGCGGAGTGATACAAAAAGAAC 1630–1636 1.000 41.9
atpF_p2 atpF TTCGGAAGGAAAGGGAAAAA GCGGAGTGATACAAAAAGAACT 1629–1635 1.000 41.9
atpF_p3 atpF TTTCGGAAGGAAAGGGAAAA AGCGGAGTGATACAAAAAGAAC 1631–1637 1.000 41.9
atpF_p4 atpF TTTCGGAAGGAAAGGGAAAA GCGGAGTGATACAAAAAGAACT 1630–1636 1.000 41.9
atpF_p5 atpF TTTTCGGAAGGAAAGGGAAA GCGGAGTGATACAAAAAGAACT 1631–1637 1.000 41.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TAAAGGATTTGCAGTCCCCC 1470–1494 1.000 76.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG CGACACCCAGATTCGAACTG 1494–1518 1.000 75.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTTGTTGATCAGGCGACACC 1507–1531 1.000 74.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT TAAAGGATTTGCAGTCCCCC 1471–1495 1.000 72.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG ATAAAGGATTTGCAGTCCCCC 1471–1495 1.000 72.2
petN-psbM_p1 petN-psbM GGGACATCATTCGCATGGAT ACGTCAAAACAGTCAGCCAA 968–992 1.000 82.7
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTCAAAACAGTCAGCCAA 947–971 1.000 82.4
petN-psbM_p3 petN-psbM GGGACATCATTCGCATGGAT GCGCTTATTGCTACTACGCT 1026–1050 1.000 80.4
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT GCGCTTATTGCTACTACGCT 1005–1029 1.000 80.0
petN-psbM_p5 petN-psbM GGGACATCATTCGCATGGAT TACGTCAAAACAGTCAGCCA 969–993 1.000 79.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 791–825 1.000 83.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CACCGCTGAAAAACGAAGAC 851–885 1.000 83.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA ACCGCTGAAAAACGAAGACT 850–884 1.000 83.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TCACCGCTGAAAAACGAAGA 852–886 1.000 83.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 770–804 1.000 83.1

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
Masdevallia coccinea NC_026541.1 157423 View on NCBI ↗
Masdevallia picturata NC_026777.1 156045 View on NCBI ↗