Markers + reference

Zostera

5 species · Zosteraceae · Alismatales

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Species 5
Genome length 145–146 kb
Candidate markers 271
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 612 0.0418 0.99 72.5 yes View details
accD LSC 1422 0.0345 1.00 63.3 yes View details
psbE-petL LSC 1086 0.0266 1.00 66.8 yes View details
rpl16 LSC 1373 0.0262 1.00 57.2 yes View details
rpl22 LSC 165 0.0788 1.00 65.7 yes View details
rpl22-trnH-GUG IRb 582 0.0440 1.00 73.9 yes View details
ycf2 IRb 5445 0.0165 1.00 44.5 no View details
ycf1-trnL-UAG IRb 1329 0.0408 1.00 68.5 yes View details
ndhG-ndhI SSC 443 0.0454 1.00 70.0 yes View details
ycf2 IRa 5445 0.0165 1.00 44.5 yes View details
petG-trnW-CCA LSC 123 0.0591 1.00 74.7 yes View details
psbH-petB LSC 105 0.0495 1.00 70.9 yes View details
rpl16-rps3 LSC 159 0.0790 1.00 70.1 yes View details
trnS-UCC-rps4 LSC 265 0.0370 1.00 67.7 yes View details
atpE-trnM-CAU LSC 185 0.0422 1.00 67.6 yes View details
ccsA-ndhD SSC 191 0.0524 1.00 67.6 yes View details
rpl32-ndhF SSC 746 0.0335 1.00 67.5 yes View details
trnF-GAA-ndhJ LSC 611 0.0288 1.00 66.4 yes View details
trnS-GCU-trnG-UCC LSC 745 0.0298 1.00 65.8 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 CCTTTCAGGATCAGTCGTGG CTTGAGCCGTACGAGGAAAA 1021–1038 1.000 86.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TGAGCCGTACGAGGAAAAAG 1019–1036 1.000 86.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CTTGAGCCGTACGAGGAAAA 1017–1034 1.000 86.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT TGAGCCGTACGAGGAAAAAG 1015–1032 1.000 86.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT TGAGCCGTACGAGGAAAAAG 1016–1033 1.000 86.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 811–823 1.000 76.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 810–822 1.000 76.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 811–823 1.000 76.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 810–822 1.000 76.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACGAATCGCACTTTTACCAC 812–824 1.000 74.4
trnS-UCC-rps4_p1 trnS-UCC-rps4 AGGCTTTTGTTTACCGAGGG AGTCGTAGAATATTATTCCCGTCA 330–336 1.000 48.7
trnS-UCC-rps4_p2 trnS-UCC-rps4 AGGCTTTTGTTTACCGAGGG TCGTAGAATATTATTCCCGTCAGA 328–334 1.000 48.7
trnS-UCC-rps4_p3 trnS-UCC-rps4 AGGCTTTTGTTTACCGAGGG AGTCGTAGAATATTATTCCCGTCAG 330–336 1.000 48.6
trnS-UCC-rps4_p4 trnS-UCC-rps4 AGGCTTTTGTTTACCGAGGG GTCGTAGAATATTATTCCCGTCAGA 329–335 1.000 48.6
trnS-UCC-rps4_p5 trnS-UCC-rps4 AGGCTTTTGTTTACCGAGGG GTCGTAGAATATTATTCCCGTCAG 329–335 1.000 48.6
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GGCTGGCCTTTACGTAAAGA 700–708 1.000 85.3
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA AGGCTGGCCTTTACGTAAAG 701–709 1.000 85.3
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TGAAAGTTGGATAGGCTGGC 713–721 1.000 85.0
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CGTTGGGATAGCTCAGTTGG GGCTGGCCTTTACGTAAAGA 740–748 1.000 82.7
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CGTTGGGATAGCTCAGTTGG AGGCTGGCCTTTACGTAAAG 741–749 1.000 82.6
atpE-trnM-CAU_p1 atpE-trnM-CAU ACGCGAGTCGAATCTATCAA ACGGCAGAAGTCATTGGTTC 250–255 1.000 74.4
atpE-trnM-CAU_p2 atpE-trnM-CAU ACGCGAGTCGAATCTATCAA CGGCAGAAGTCATTGGTTCA 249–254 1.000 74.4
atpE-trnM-CAU_p3 atpE-trnM-CAU ACGCGAGTCGAATCTATCAA TGCTTTCATACGGCAGAAGT 259–264 1.000 74.2
atpE-trnM-CAU_p4 atpE-trnM-CAU ACGCGAGTCGAATCTATCAA TACGGCAGAAGTCATTGGTT 251–256 1.000 71.4
atpE-trnM-CAU_p5 atpE-trnM-CAU ACGCGAGTCGAATCTATCAAT TGCTTTCATACGGCAGAAGT 259–264 1.000 70.2
accD_p1 accD TCTTGAAATACCGGGGTCCT ATGTGACCCAAGAAAACCCC 1756 0.600 63.8
accD_p2 accD TCTTGAAATACCGGGGTCCT GTGACCCAAGAAAACCCCAT 1754 0.600 63.8
accD_p3 accD GGTTCGAATCCGTATAGCCC GTGACCCAAGAAAACCCCAT 2244–2247 0.600 63.7
accD_p4 accD AGCTAGGACCCCTCCTTTTT ATGTGACCCAAGAAAACCCC 1775 0.600 63.6
accD_p5 accD AGCTAGGACCCCTCCTTTTT GTGACCCAAGAAAACCCCAT 1773 0.600 63.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Zostera capricorni OR538605.1 145822 View on NCBI ↗
Zostera japonica NC_058623.1 146090 View on NCBI ↗
Zostera muelleri NC_068805.1 145820 View on NCBI ↗
Zostera nigricaulis NC_058621.1 145883 View on NCBI ↗
Zostera pacifica PQ286553.1 144675 View on NCBI ↗