Markers + reference

Ruppia

3 species · Cymodoceaceae · Alismatales

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Species 3
Genome length 159–159 kb
Candidate markers 273
Primer pairs 85

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1353 0.0091 0.98 54.4 yes View details
rps16-trnQ-UUG LSC 1590 0.0160 1.00 64.1 yes View details
psbK-psbI LSC 477 0.0151 0.93 55.6 yes View details
petA-psbJ LSC 1010 0.0152 1.00 64.5 yes View details
ndhF-rpl32 SSC 1138 0.0217 0.99 62.5 yes View details
rpl32-trnL-UAG SSC 697 0.0234 0.92 63.0 yes View details
ccsA SSC 966 0.0048 1.00 46.8 yes View details
ycf1 SSC 5325 0.0122 1.00 58.3 yes View details
trnK-UUU-rps16 LSC 1002 0.0108 0.99 67.4 yes View details
trnH-GUG-psbA LSC 321 0.0230 0.99 66.8 yes View details
psaA-ycf3 LSC 698 0.0105 1.00 66.4 yes View details
trnQ-UUG-psbK LSC 690 0.0117 0.99 66.3 yes View details
petN-psbM LSC 1055 0.0114 1.00 65.9 yes View details
psbI-trnS-GCU LSC 137 0.0276 0.97 65.8 yes View details
trnT-UGU-trnL-UAA LSC 721 0.0160 0.98 65.1 yes View details
ccsA-ndhD SSC 233 0.0295 0.97 64.1 yes View details
petG-trnW-CCA LSC 107 0.0249 1.00 62.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 442–445 1.000 79.9
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 444–447 1.000 79.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 456–459 1.000 79.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 455–458 1.000 79.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 457–460 1.000 79.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CAACCCACAGAGACGGTTTA 1125–1134 1.000 73.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA CAACCCACAGAGACGGTTTA 1126–1135 1.000 72.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA CAACCCACAGAGACGGTTTA 1123–1132 1.000 72.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC CAACCCACAGAGACGGTTTA 1122–1131 1.000 71.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG ACCCACAGAGACGGTTTATG 1123–1132 1.000 71.7
rps16_p1 rps16 AGTTGTCCTAATCCACCTTT TGTACCGATCGAGCTAATGAC 1444–1473 1.000 42.7
rps16_p2 rps16 AGTTGTCCTAATCCACCTTTT TGTACCGATCGAGCTAATGAC 1444–1473 1.000 42.7
rps16_p3 rps16 AGTTGTCCTAATCCACCTTT GTACCGATCGAGCTAATGACT 1443–1472 1.000 42.7
rps16_p4 rps16 AGTTGTCCTAATCCACCTTTTT TGTACCGATCGAGCTAATGAC 1444–1473 1.000 42.7
rps16_p5 rps16 AGTTGTCCTAATCCACCTTTT GTACCGATCGAGCTAATGACT 1443–1472 1.000 42.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCCAAGAGCATTTTCGTTCC GAGGTTCGAATCCTTCCGTC 1729–1786 1.000 81.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1663–1720 1.000 80.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1674–1731 1.000 79.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCCAAGAGCATTTTCGTTCC TAAATCGAAATGGGGCGTGG 1787–1844 1.000 76.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCCAAGAGCATTTTCGTTCC TTCGGAGGTTCGAATCCTTC 1733–1790 1.000 76.6
trnQ-UUG-psbK_p1 trnQ-UUG-psbK TCAAAACCGGTTGCCTTACC GGGCAATTTGGCGAAGAAAA 797–809 1.000 78.1
trnQ-UUG-psbK_p2 trnQ-UUG-psbK AAAACCGGTTGCCTTACCAC GGGCAATTTGGCGAAGAAAA 795–807 1.000 75.9
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CGAACCTCCGAATAACAGGA GGGCAATTTGGCGAAGAAAA 817–829 1.000 75.8
trnQ-UUG-psbK_p4 trnQ-UUG-psbK TCGAACCTCCGAATAACAGG GGGCAATTTGGCGAAGAAAA 818–830 1.000 75.8
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CAAAACCGGTTGCCTTACCA GGGCAATTTGGCGAAGAAAA 796–808 1.000 75.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 790–828 1.000 85.1
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG GTGGACTAAAGCGTCGGATT 791–829 1.000 85.1
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG CCGGGGGAATCAAAAAGGAA 972–1016 1.000 84.5
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG ATTGGGAGAGATGGCTGAGT 809–847 1.000 84.2
psbK-psbI_p5 psbK-psbI TTTTCTTCGCCAAATTGCCC TGGACTAAAGCGTCGGATTG 885–923 1.000 84.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Ruppia brevipedunculata NC_051974.1 158943 View on NCBI ↗
Ruppia mongolica OP723916.1 158846 View on NCBI ↗
Ruppia sinensis NC_088726.1 158897 View on NCBI ↗