Markers + reference

Najas

2 species · Hydrocharitaceae · Alismatales

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Species 2
Genome length 156–158 kb
Candidate markers 252
Primer pairs 80

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 252 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1677 0.1237 0.95 83.5 yes View details
rps16-tRNA-Gln(UUG) LSC 1621 0.1211 0.87 85.5 yes View details
tRNA-Thr(UGU)-tRNA-Leu (AAA) LSC 832 0.1438 0.95 84.5 yes View details
psbE-petL LSC 1087 0.1131 0.97 82.7 yes View details
rpl22-rps19 LSC 924 0.1669 0.70 76.8 yes View details
ccsA SSC 927 0.4553 0.95 83.3 yes View details
psbZ-tRNA-Gly(GCC) LSC 634 0.1121 0.93 90.5 yes View details
petN-psbM LSC 698 0.0639 0.92 87.2 yes View details
psbM-tRNA-Tyr(GUA) LSC 1693 0.0795 0.93 87.0 yes View details
petA-psbJ LSC 857 0.1107 0.96 86.7 yes View details
tRNA-Ser(GCU)-tRNA-Gly(UCC) LSC 1118 0.0833 0.94 86.3 yes View details
rps18-rpl20 LSC 581 0.0954 0.94 84.2 yes View details
tRNA-Glu(UUC)-tRNA-Thr(GGU) LSC 665 0.1047 0.92 83.4 yes View details
tRNA-Lys(UUU)-rps16 LSC 751 0.1198 0.90 82.3 yes View details
tRNA-Gln(UUG)-psbK LSC 817 0.0833 0.91 81.9 yes View details
tRNA-Phe(GAA)-tRNA-Val(UAC) LSC 1627 0.1039 0.89 81.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
tRNA-Lys(UUU)-rps16_p1 tRNA-Lys(UUU)-rps16 TCCCTGGAATTGGAGCCTAA TCTTGAAAAGGGGGCTCAAC 1087–1124 1.000 90.8
tRNA-Lys(UUU)-rps16_p2 tRNA-Lys(UUU)-rps16 TTCCCTGGAATTGGAGCCTA TCTTGAAAAGGGGGCTCAAC 1088–1125 1.000 90.8
tRNA-Lys(UUU)-rps16_p3 tRNA-Lys(UUU)-rps16 TGAAGAACACAAGCCCCTTC TCTTGAAAAGGGGGCTCAAC 1116–1153 1.000 90.7
tRNA-Lys(UUU)-rps16_p4 tRNA-Lys(UUU)-rps16 TGTTTCCCTGGAATTGGAGC TCTTGAAAAGGGGGCTCAAC 1091–1128 1.000 90.3
tRNA-Lys(UUU)-rps16_p5 tRNA-Lys(UUU)-rps16 CCCCAAGAATCAAAGCGAGA TCTTGAAAAGGGGGCTCAAC 1052 0.500 59.1
rps16_p1 rps16 GGTTTAGGGTTGGATTGGCA GTAATAAATGCGATGCGGCC 2576 0.500 59.2
rps16_p2 rps16 GGTTTAGGGTTGGATTGGCA ACACAATCGCGACATACACA 2368 0.500 58.9
rps16_p3 rps16 CCAACCGGACAGAAATGGAT GTAATAAATGCGATGCGGCC 2703 0.500 58.7
rps16_p4 rps16 AGTCAAAAACCAACCGGACA GTAATAAATGCGATGCGGCC 2712 0.500 58.7
rps16_p5 rps16 CCAACCGGACAGAAATGGAT ACACAATCGCGACATACACA 2495 0.500 58.4
rps16-tRNA-Gln(UUG)_p1 rps16-tRNA-Gln(UUG) GTGTCCTTCAAGTCACACGT AAGGTTCGAATCCTTCCGTC 1592–1703 1.000 88.4
rps16-tRNA-Gln(UUG)_p2 rps16-tRNA-Gln(UUG) GTGTCCTTCAAGTCACACGT TAAATGGAAATGGGGCGTGG 1650–1761 1.000 87.3
rps16-tRNA-Gln(UUG)_p3 rps16-tRNA-Gln(UUG) ACACGTTGCTTTCTACCACA AAGGTTCGAATCCTTCCGTC 1578–1689 1.000 86.4
rps16-tRNA-Gln(UUG)_p4 rps16-tRNA-Gln(UUG) GTGTCCTTCAAGTCACACGT TAAGGCAACGGGTTTTGGTC 1622–1733 1.000 86.1
rps16-tRNA-Gln(UUG)_p5 rps16-tRNA-Gln(UUG) ACACGTTGCTTTCTACCACA TAAATGGAAATGGGGCGTGG 1636–1747 1.000 85.3
tRNA-Gln(UUG)-psbK_p1 tRNA-Gln(UUG)-psbK GACCAAAACCCGTTGCCTTA ACAGATACAGATGAAACTAAAGA 851–888 1.000 49.7
tRNA-Gln(UUG)-psbK_p2 tRNA-Gln(UUG)-psbK TAACAGGACCAAAACCCGTT ACAGATACAGATGAAACTAAAGA 857–894 1.000 49.7
tRNA-Gln(UUG)-psbK_p3 tRNA-Gln(UUG)-psbK AACAGGACCAAAACCCGTTG ACAGATACAGATGAAACTAAAGA 856–893 1.000 49.7
tRNA-Gln(UUG)-psbK_p4 tRNA-Gln(UUG)-psbK ATAACAGGACCAAAACCCGT ACAGATACAGATGAAACTAAAGA 858–895 1.000 49.7
tRNA-Gln(UUG)-psbK_p5 tRNA-Gln(UUG)-psbK AAAACCCGTTGCCTTACCAC ACAGATACAGATGAAACTAAAGA 847–884 1.000 49.7
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p1 tRNA-Ser(GCU)-tRNA-Gly(UCC) CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1187–1192 1.000 61.6
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p2 tRNA-Ser(GCU)-tRNA-Gly(UCC) AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1186–1191 1.000 61.6
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p3 tRNA-Ser(GCU)-tRNA-Gly(UCC) CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 1190–1195 1.000 60.5
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p4 tRNA-Ser(GCU)-tRNA-Gly(UCC) CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 1189–1194 1.000 60.5
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p5 tRNA-Ser(GCU)-tRNA-Gly(UCC) AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 1188–1193 1.000 60.5
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC AGTTCCGACTGCCTTTTTACT 747–781 1.000 75.4
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT AGTTCCGACTGCCTTTTTACT 746–780 1.000 75.4
petN-psbM_p3 petN-psbM TATGGGGAAGGAGTGGACTG AGTTCCGACTGCCTTTTTACT 745–779 1.000 75.4
petN-psbM_p4 petN-psbM GTATGGGGAAGGAGTGGACT TCTAGTTCCGACTGCCTTTT 749–783 1.000 75.2
petN-psbM_p5 petN-psbM GTATGGGGAAGGAGTGGACT TTCTAGTTCCGACTGCCTTT 750–784 1.000 75.2

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
Najas flexilis NC_021936.1 156366 View on NCBI ↗
Najas marina PZ087074.1 158013 View on NCBI ↗