Markers + reference

Nekemias

4 species · Vitaceae · Vitales

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Species 4
Genome length 163–163 kb
Candidate markers 267
Primer pairs 95

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 2094 0.0039 1.00 54.2 yes View details
psbM-trnD-GUC LSC 1177 0.0050 1.00 62.2 yes View details
trnS-UGA-psbZ LSC 290 0.0000 1.00 21.8 yes View details
psbZ-trnG-GCC LSC 685 0.0071 1.00 50.3 yes View details
clpP LSC 2077 0.0027 1.00 59.8 yes View details
rpl22-rps19 IRb 332 0.0151 1.00 49.2 yes View details
rps19 IRb 279 0.0024 1.00 23.4 no View details
ycf1 SSC 5682 0.0027 1.00 54.4 yes View details
ndhD-ccsA SSC 269 0.0206 0.99 64.4 yes View details
ccsA SSC 969 0.0041 1.00 53.3 yes View details
rps19 IRa 279 0.0024 1.00 25.1 yes View details
psbT-psbN LSC 83 0.0382 1.00 70.7 yes View details
rps19-rpl2 IRb 253 0.0178 1.00 65.9 yes View details
rpl2-rps19 IRa 253 0.0152 1.00 64.2 yes View details
rpoB-trnC-GCA LSC 1208 0.0030 1.00 62.0 yes View details
ndhC-trnM-CAU LSC 1874 0.0037 1.00 61.5 yes View details
accD-psaI LSC 755 0.0033 1.00 61.3 yes View details
ndhI-ndhG SSC 371 0.0085 1.00 59.8 yes View details
psaB LSC 2205 0.0009 1.00 57.9 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 2164–2180 1.000 79.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 2175–2191 1.000 78.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 2168–2184 1.000 74.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 2194–2210 1.000 74.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 2176–2192 1.000 73.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CATTCCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 1295–1319 1.000 78.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CATTCCCTCATTTCCACCCC AAAAGGATTTGCAGTCCCCC 1277–1301 1.000 76.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ACATTCCCTCATTTCCACCC CCGGATTTGAACTGGGGAAA 1296–1320 1.000 76.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCTGTCAAGCCCTGA CCGGATTTGAACTGGGGAAA 1371–1395 1.000 76.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGTTCTTCTGTCAAGCCCTG CCGGATTTGAACTGGGGAAA 1372–1396 1.000 76.0
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TGGGCTATGGCTATACACCT 1326–1329 1.000 59.6
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTGGGCTATGGCTATACACC 1327–1330 1.000 59.1
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1287–1290 1.000 59.1
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TGGGCTATGGCTATACACCT 1333–1336 1.000 56.4
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA GTGGGCTATGGCTATACACC 1334–1337 1.000 55.9
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC TGCAAAAACAGCCAATTGGA 359 1.000 71.6
trnS-UGA-psbZ_p2 trnS-UGA-psbZ CTATCAACCACTCGGCCATC TGCAAAAACAGCCAATTGGA 348 1.000 71.0
trnS-UGA-psbZ_p3 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC TGCAAAAACAGCCAATTGGAA 359 1.000 69.4
trnS-UGA-psbZ_p4 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC AAACAGCCAATTGGAAAGCA 354 1.000 69.1
trnS-UGA-psbZ_p5 trnS-UGA-psbZ CAAGACCGGAGCTATCAACC AACAGCCAATTGGAAAGCAA 353 1.000 69.1
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG AATCGAACCCGCATCTTCTC 853–899 1.000 78.7
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG GAATCGAACCCGCATCTTCT 854–900 1.000 78.7
psbZ-trnG-GCC_p3 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC AATCGAACCCGCATCTTCTC 851–897 1.000 78.3
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC GAATCGAACCCGCATCTTCT 852–898 1.000 78.3
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG GCATTTCTTTACCTTGGGCG 882–928 1.000 76.9
psaB_p1 psaB GAACCCCTTCTCCATCGAAA ACAACATGGGCGTTCTTCTT 2348 1.000 73.7
psaB_p2 psaB AACCCCTTCTCCATCGAAAG ACAACATGGGCGTTCTTCTT 2347 1.000 73.7
psaB_p3 psaB ATCGCGGATACAGCACATTA ACAACATGGGCGTTCTTCTT 2317 1.000 73.5
psaB_p4 psaB TATCGCGGATACAGCACATT ACAACATGGGCGTTCTTCTT 2318 1.000 73.5
psaB_p5 psaB TCGCGGATACAGCACATTAT ACAACATGGGCGTTCTTCTT 2316 1.000 73.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Nekemias cantoniensis NC_061755.1 162655 View on NCBI ↗
Nekemias chaffanjonii NC_071890.1 163013 View on NCBI ↗
Nekemias grossedentata PV239776.1 162602 View on NCBI ↗
Nekemias rubifolia NC_071892.1 162813 View on NCBI ↗