Markers + reference

Calypso

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 149–149 kb
Candidate markers 262
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 988 0.0253 1.00 73.3 yes View details
trnS-GCU-trnG-GCC LSC 1143 0.0174 0.95 60.2 yes View details
petN-psbM LSC 821 0.0341 0.93 82.3 yes View details
psbB-psbT LSC 417 0.0635 0.94 89.6 yes View details
rpl16 LSC 1588 0.0166 0.99 57.4 yes View details
trnN-GUU-rpl32 SSC 1383 0.0426 0.88 85.6 yes View details
ndhD-psaC SSC 376 0.0347 1.00 62.7 yes View details
ndhI-rps15 SSC 1875 0.0201 0.98 61.0 yes View details
psbL-psbF LSC 22 0.0455 1.00 74.1 yes View details
trnK-UUU-rps16 LSC 539 0.0261 1.00 72.4 yes View details
rpl36-infA LSC 92 0.0326 1.00 71.2 yes View details
rpl20-rps12 LSC 777 0.0096 0.93 68.6 yes View details
trnR-UCU-atpA LSC 181 0.0237 0.93 68.1 yes View details
rpl32-trnL-UAG SSC 657 0.0188 0.97 68.1 yes View details
atpH-atpI LSC 768 0.0130 1.00 66.4 yes View details
trnH-GUG-rpl2 IRb 43 0.0233 1.00 65.9 yes View details
rpl2-trnH-GUG IRa 43 0.0233 1.00 65.9 yes View details
accD-psaI LSC 745 0.0179 0.98 65.6 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GTGCTCAACCCACAGGAAC 632–644 1.000 67.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GTGCTCAACCCACAGGAAC 631–643 1.000 67.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACCCACAGGAACT 631–643 1.000 66.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACCCACAGGAACT 630–642 1.000 66.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGGATCAGTCGCGGTCTTAT GTGCTCAACCCACAGGAAC 717–729 1.000 66.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 1084–1127 1.000 80.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1061–1104 1.000 80.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC AGACCAAATCAAGATGGGGC 1146–1189 1.000 80.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1082–1125 1.000 80.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 1088–1131 1.000 79.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 1173–1198 1.000 52.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 1172–1197 1.000 52.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 1174–1199 1.000 51.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 1173–1198 1.000 51.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TAAAGTGATCAGGGGTCGGA TACCACTAAACTATACCCGC 1242–1267 1.000 50.6
trnR-UCU-atpA_p1 trnR-UCU-atpA AGGGCGTCCATTGTCTAATG CCGAAGAAGCTGAAACCCTT 322–333 1.000 80.4
trnR-UCU-atpA_p2 trnR-UCU-atpA AGGGCGTCCATTGTCTAATG TCACCGAAGAAGCTGAAACC 325–336 1.000 80.2
trnR-UCU-atpA_p3 trnR-UCU-atpA GAAGGGCGTCCATTGTCTAA CCGAAGAAGCTGAAACCCTT 324–335 1.000 79.9
trnR-UCU-atpA_p4 trnR-UCU-atpA GAAGGGCGTCCATTGTCTAA TCACCGAAGAAGCTGAAACC 327–338 1.000 79.7
trnR-UCU-atpA_p5 trnR-UCU-atpA TAGGAATGAAGGGCGTCCAT CCGAAGAAGCTGAAACCCTT 331–342 1.000 79.0
atpH-atpI_p1 atpH-atpI CGCAATACCTTCTACGGCTT AACTTTGGCTGCGGCTTATA 937–943 1.000 79.4
atpH-atpI_p2 atpH-atpI TCCGATAGAAGCAAGCCCTA AACTTTGGCTGCGGCTTATA 886–892 1.000 79.4
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 865–871 1.000 78.8
atpH-atpI_p4 atpH-atpI CCGATAGAAGCAAGCCCTAC AACTTTGGCTGCGGCTTATA 885–891 1.000 78.8
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC AACTTTGGCTGCGGCTTATA 864–870 1.000 78.3
petN-psbM_p1 petN-psbM AATAAGTCTCGCTTGGGCTG CTTGCGCTTATTGCTACTGC 985–993 1.000 85.1
petN-psbM_p2 petN-psbM GGGACATCATTCGCATGGAT CTTGCGCTTATTGCTACTGC 1007–1015 1.000 84.5
petN-psbM_p3 petN-psbM AATAAGTCTCGCTTGGGCTG ACGTCAAAACAGTCAGCCAA 924–932 1.000 84.0
petN-psbM_p4 petN-psbM AATAAGTCTCGCTTGGGCTG ATTGCTACTGCGCTGTTCAT 976–984 1.000 83.8
petN-psbM_p5 petN-psbM GGGACATCATTCGCATGGAT ACGTCAAAACAGTCAGCCAA 946–954 1.000 83.4

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
Calypso bulbosa MN990433.1 149451 View on NCBI ↗
Calypso bulbosa var. occidentalis NC_040980.1 149313 View on NCBI ↗