Markers + reference

Odontochilus

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 153–153 kb
Candidate markers 273
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 618 0.0130 1.00 54.5 yes View details
rpoC1 LSC 2808 0.0043 1.00 58.5 yes View details
trnT-GGU-psbD LSC 1008 0.0090 1.00 59.1 yes View details
trnT-UGU-trnL-UAA LSC 962 0.0084 0.99 64.8 yes View details
accD LSC 1455 0.0076 1.00 50.9 yes View details
petA-psbJ LSC 960 0.0115 1.00 65.4 yes View details
rpl33 LSC 201 0.0149 1.00 48.9 yes View details
ycf1 IRb 1068 0.0037 1.00 48.7 no View details
ndhA SSC 2253 0.0049 1.00 49.0 yes View details
ycf1 SSC 5445 0.0074 1.00 44.5 yes View details
psbT-psbN LSC 69 0.0290 1.00 69.2 yes View details
petN-psbM LSC 597 0.0102 0.98 66.3 yes View details
trnW-CCA-trnP-UGG LSC 160 0.0187 1.00 63.3 yes View details
ndhI-ndhA SSC 111 0.0180 1.00 62.9 yes View details
psaA-ycf3 LSC 720 0.0056 1.00 61.9 yes View details
atpF-atpH LSC 383 0.0131 1.00 61.7 yes View details
matK LSC 1560 0.0045 1.00 61.2 yes View details
rpl20-rps12 LSC 795 0.0038 1.00 60.9 yes View details
ndhC-trnV-UAC LSC 641 0.0031 1.00 60.7 yes View details
rpl14-rpl16 LSC 123 0.0084 0.97 60.4 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK TGAGCATTTCAGAATACAAATTCA GCCGTTCTGACCATATTGCA 1672–1673 1.000 40.3
matK_p2 matK TGAGCATTTCAGAATACAAATTCA TAAAATGTACACATGCGCCG 1688–1689 1.000 40.3
matK_p3 matK TGAGCATTTCAGAATACAAATTCATG GCCGTTCTGACCATATTGCA 1672–1673 1.000 40.3
matK_p4 matK TGAGCATTTCAGAATACAAATTCATG TAAAATGTACACATGCGCCG 1688–1689 1.000 40.3
matK_p5 matK TGAGCATTTCAGAATACAAATTCA CCGTTCTGACCATATTGCAC 1671–1672 1.000 40.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCTTGAGCCGTATGAGGAGA 991 1.000 76.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCTTGAGCCGTATGAGGAGA 990 1.000 76.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGACAACGAATTCCGGAACA 1297–1313 1.000 75.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGACAACGAATTCCGGAACA 1296–1312 1.000 75.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AACGAATTCCGGAACAAGGA 1292–1308 1.000 75.0
atpF-atpH_p1 atpF-atpH CCACGGAAACAAAAGAATCGG ATTTATGGACTGGTGGTGGC 471–521 1.000 71.1
atpF-atpH_p2 atpF-atpH CCCACGGAAACAAAAGAATCG ATTTATGGACTGGTGGTGGC 472–522 1.000 71.1
atpF-atpH_p3 atpF-atpH CCACGGAAACAAAAGAATCGG GGTGGTGGCATTAGCTCTTT 460–510 1.000 71.0
atpF-atpH_p4 atpF-atpH CCCACGGAAACAAAAGAATCG GGTGGTGGCATTAGCTCTTT 461–511 1.000 71.0
atpF-atpH_p5 atpF-atpH GCCCCACGGAAACAAAAGAA ATTTATGGACTGGTGGTGGC 474–524 1.000 69.6
rpoC1_p1 rpoC1 CCAGTGAAATTGGGGGAGAC TTGCTCGTTCGAGAACTACG 2995 1.000 78.7
rpoC1_p2 rpoC1 CCAGTGAAATTGGGGGAGAC CTTTGGCCCTGGAACTGAAT 2973 1.000 78.5
rpoC1_p3 rpoC1 CCAGTGAAATTGGGGGAGAC TTTGGCCCTGGAACTGAATC 2972 1.000 78.4
rpoC1_p4 rpoC1 GAGACCCAAATTCCCACGAG TTGCTCGTTCGAGAACTACG 2980 1.000 77.9
rpoC1_p5 rpoC1 CCAGTGAAATTGGGGGAGAC GGCCCTGGAACTGAATCATT 2969 1.000 77.8
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA CGTTTATTGCTACTGCGCTG 749–759 1.000 81.1
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA ACGTCAAAACAGTCAGCCAA 692–702 1.000 79.9
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA ATTGCTACTGCGCTGTTCAT 744–754 1.000 79.7
petN-psbM_p4 petN-psbM AGTAAGTCTTGCTTGGGCTG CGTTTATTGCTACTGCGCTG 755–765 1.000 79.6
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA TATTGCTACTGCGCTGTTCA 745–755 1.000 78.7
trnT-GGU-psbD_p1 trnT-GGU-psbD GTAACGTCATGGTAAGGCGT GAAACGGTCCCTACGTAACC 1140–1142 1.000 80.9
trnT-GGU-psbD_p2 trnT-GGU-psbD GTAACGTCATGGTAAGGCGT GGACCAGCCTACAAAAACGA 1158–1160 1.000 80.0
trnT-GGU-psbD_p3 trnT-GGU-psbD GTAACGTCATGGTAAGGCGT CGGTCCCTACGTAACCAATC 1136–1138 1.000 79.2
trnT-GGU-psbD_p4 trnT-GGU-psbD GTAACGTCATGGTAAGGCGT ACAAAAACGAAACGGTCCCT 1148–1150 1.000 78.9
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GAAACGGTCCCTACGTAACC 1125–1127 1.000 78.6

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
Odontochilus elwesii NC_061759.1 152568 View on NCBI ↗
Odontochilus tortus MW589530.1 153031 View on NCBI ↗