Markers + reference

Cleisostoma

11 species · Orchidaceae · Asparagales

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Species 11
Genome length 147–149 kb
Candidate markers 267
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 474 0.0276 0.98 71.6 yes View details
trnS-GCU-trnG-GCC LSC 1219 0.0393 0.94 82.1 yes View details
rpoB-trnC-GCA LSC 1634 0.0321 0.97 80.0 yes View details
trnE-UUC-trnT-GGU LSC 820 0.0524 0.92 84.6 yes View details
trnT-UGU-trnL-UAA LSC 618 0.0443 0.95 85.3 yes View details
ndhC-trnV-UAC LSC 735 0.0380 0.93 77.0 yes View details
rpl16 LSC 1648 0.0260 0.99 71.9 yes View details
ycf1-rpl32 SSC 410 0.1449 0.86 73.0 yes View details
psaC-ndhE SSC 572 0.0344 0.98 75.5 yes View details
clpP-psbB LSC 619 0.0334 0.99 87.7 yes View details
psbB-psbT LSC 376 0.0502 0.93 84.3 yes View details
rpl32-trnL-UAG SSC 511 0.0463 1.00 83.8 yes View details
matK-trnK-UUU LSC 1133 0.0368 0.98 82.0 yes View details
rps16-trnQ-UUG LSC 840 0.0328 1.00 80.3 yes View details
trnL-UAG-ccsA SSC 141 0.0485 1.00 80.3 yes View details
trnT-GGU-psbD LSC 1014 0.0193 0.98 78.4 yes View details
rps15-ycf1 SSC 441 0.0435 0.96 78.4 yes View details
trnC-GCA-petN LSC 824 0.0219 0.99 77.9 yes View details
psbA-trnK-UUU LSC 248 0.0392 1.00 77.5 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
psbA-trnK-UUU_p1 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ACTCCATCCGACTAGTTCCG 315–347 1.000 87.0
psbA-trnK-UUU_p2 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ACTAGTTCCGGGTTCGAGTC 305–337 1.000 85.3
psbA-trnK-UUU_p3 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC GACTAGTTCCGGGTTCGAGT 306–338 1.000 85.3
psbA-trnK-UUU_p4 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ATCCGACTAGTTCCGGGTTC 310–342 1.000 84.8
psbA-trnK-UUU_p5 psbA-trnK-UUU AACACCAAACCATCCGATGT ACTCCATCCGACTAGTTCCG 381–413 1.000 84.0
matK-trnK-UUU_p1 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA GATCCGGGTTGCTAACTCAA 1042–1380 1.000 80.5
matK-trnK-UUU_p2 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TTGATCCGGGTTGCTAACTC 1044–1382 1.000 80.5
matK-trnK-UUU_p3 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TCCGGGTTGCTAACTCAATG 1040–1368 0.909 79.1
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA CGGGTTGCTAACTCAATGGT 1038–1366 0.909 78.6
matK-trnK-UUU_p5 matK-trnK-UUU TCCTGAAGGAGTAGCGGATAT TCCGGGTTGCTAACTCAATG 1040–1368 0.909 75.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 TAAGAAGGGAAGCTCGTTGC TCGATCCCGAAGAGAAGGAA 1028–1124 1.000 90.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCGCAACCCAATCACTCTTT TCGATCCCGAAGAGAAGGAA 1238–1335 0.818 80.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TTCGCAACCCAATCACTCTT TCGATCCCGAAGAGAAGGAA 1239–1336 0.818 80.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTTCGCAACCCAATCACTCT TCGATCCCGAAGAGAAGGAA 1240–1337 0.818 80.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 ATACCCCGGAGACAAAGAGT TCGATCCCGAAGAGAAGGAA 1430 0.091 40.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 904–1030 1.000 90.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 915–1041 1.000 89.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 908–1034 1.000 89.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 919–1045 1.000 88.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 910–1036 1.000 87.4
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1175–1288 1.000 63.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1174–1287 1.000 63.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 1178–1291 1.000 62.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 1177–1290 1.000 62.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 1176–1289 1.000 62.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT CCGGGGATAAAGGATTTGCA 1570–1812 1.000 86.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT ACCGGGGATAAAGGATTTGC 1571–1813 1.000 86.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTT CCGGGGATAAAGGATTTGCA 1789 0.091 38.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTT ACCGGGGATAAAGGATTTGC 1790 0.091 38.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTT TCGAACCGGGGATAAAGGAT 1794 0.091 37.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Cleisostoma arietinum MN124420.1 147021 View on NCBI ↗
Cleisostoma birmanicum MN124421.1 147943 View on NCBI ↗
Cleisostoma crochetii MN124440.1 147966 View on NCBI ↗
Cleisostoma fuerstenbergianum MN124417.1 146625 View on NCBI ↗
Cleisostoma linearilobatum MN124422.1 148494 View on NCBI ↗
Cleisostoma longioperculatum MN124423.1 149066 View on NCBI ↗
Cleisostoma paniculatum MN124416.1 149257 View on NCBI ↗
Cleisostoma rostratum MN124415.1 148747 View on NCBI ↗
Cleisostoma simondii var. guangdongense MN124424.1 148862 View on NCBI ↗
Cleisostoma striatum MN124425.1 149061 View on NCBI ↗
Cleisostoma williamsonii MN124426.1 146836 View on NCBI ↗