Markers + reference

Taeniophyllum

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 142–143 kb
Candidate markers 251
Primer pairs 95

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 251 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 816 0.1525 0.96 87.8 yes View details
trnS-GCU-trnG-GCC LSC 639 0.1318 0.95 87.2 yes View details
trnE-UUC-trnT-GGU LSC 758 0.1446 0.88 88.8 yes View details
trnF-GAA-trnV-UAC LSC 639 0.1698 0.90 85.6 yes View details
rpl16 LSC 1725 0.1072 0.91 81.9 yes View details
trnN-GUU-rpl32 IRb 1410 0.1098 0.59 70.8 yes View details
ccsA-psaC SSC 1142 0.0628 0.18 58.3 yes View details
ycf1 SSC 5307 0.0860 0.99 71.9 yes View details
trnT-GGU-psbD LSC 1012 0.0982 0.95 88.1 yes View details
rpl32-trnL-UAG SSC 521 0.1335 0.85 85.5 yes View details
ycf3-trnS-GGA LSC 614 0.0626 0.94 84.8 yes View details
psbM-trnD-GUC LSC 1044 0.0968 0.94 83.7 yes View details
psbE-petL LSC 1158 0.0983 0.94 83.2 yes View details
trnP-UGG-psaJ LSC 423 0.0926 0.87 82.9 yes View details
petA-psbJ LSC 975 0.1057 0.96 82.8 yes View details
psbK-psbI LSC 447 0.1058 0.93 82.6 yes View details
matK-trnK-UUU LSC 918 0.1025 0.97 82.3 yes View details
psaJ-rpl33 LSC 468 0.1303 0.95 82.3 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-trnK-UUU_p1 matK-trnK-UUU AGGAACATCTTTGAGCCAGC AACGGTAGAGTACTCGGCTT 1491–1688 1.000 85.0
matK-trnK-UUU_p2 matK-trnK-UUU AGGAACATCTTTGAGCCAGC ACGGTAGAGTACTCGGCTTT 1490–1687 1.000 85.0
matK-trnK-UUU_p3 matK-trnK-UUU AGGAACATCTTTGAGCCAGC TAGATGTTCGATCCCGACGA 2136 0.500 58.3
matK-trnK-UUU_p4 matK-trnK-UUU TTCTTGTGCAGCGAAAATGC TAGATGTTCGATCCCGACGA 1871 0.500 57.8
matK-trnK-UUU_p5 matK-trnK-UUU TTTGAGCCAGCATTGAAGGA TAGATGTTCGATCCCGACGA 2127 0.500 57.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 912–972 1.000 89.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 889–949 1.000 88.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 910–970 1.000 88.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 916–976 1.000 88.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 900–960 1.000 88.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GCCCCGGATCGTTAGATAAG 565–615 1.000 86.6
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGCCCAGGATTAC 585–635 1.000 86.1
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT GCCCCGGATCGTTAGATAAG 562–612 1.000 84.6
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT GCCCCGGATCGTTAGATAAG 563–613 1.000 84.6
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT GCCCCGGATCGTTAGATAAG 564–614 1.000 84.6
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 708–1196 1.000 61.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 707–1195 1.000 61.1
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 711–1199 1.000 60.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 710–1198 1.000 60.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 709–1197 1.000 60.0
psbM-trnD-GUC_p1 psbM-trnD-GUC AAGAATTCGAGGAGTTGGGC CCATGCATATGGCTGGGATT 1700 0.500 58.5
psbM-trnD-GUC_p2 psbM-trnD-GUC GAATTCGAGGAGTTGGGCTT CCATGCATATGGCTGGGATT 1698 0.500 58.5
psbM-trnD-GUC_p3 psbM-trnD-GUC AAGAATTCGAGGAGTTGGGC GTATGATGGCAGTCTAGGCG 2167 0.500 58.5
psbM-trnD-GUC_p4 psbM-trnD-GUC GAATTCGAGGAGTTGGGCTT GTATGATGGCAGTCTAGGCG 2165 0.500 58.5
psbM-trnD-GUC_p5 psbM-trnD-GUC GAATTCGAGGAGTTGGGCTT GGAAAGACTCCCCGGATCTA 2239 0.500 58.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 862–874 1.000 90.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 841–853 1.000 90.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 838–850 1.000 90.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 840–852 1.000 89.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 859–871 1.000 89.4

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
Taeniophyllum glandulosum MZ681475.1 141769 View on NCBI ↗
Taeniophyllum pusillum NC_082915.1 143223 View on NCBI ↗