Markers + reference

Azolla

5 species · Salviniaceae · Salviniales

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Species 5
Genome length 147–148 kb
Candidate markers 91
Primer pairs 75

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 91 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-Arg-tRNA-Asp LSC 17559 0.0152 1.00 54.9 yes View details
tRNA-Leu-tRNA-Phe LSC 367 0.0536 1.00 80.4 yes View details
tRNA-Pro-tRNA-Ile LSC 19653 0.0206 1.00 58.3 yes View details
tRNA-Asn-tRNA-Pro SSC 4474 0.0358 0.99 72.9 yes View details
tRNA-Leu-tRNA-Asn SSC 18057 0.0259 1.00 63.6 yes View details
tRNA-Arg-tRNA-Gln LSC 8758 0.0286 1.00 69.7 no View details
tRNA-Cys-tRNA-Gly LSC 289 0.0705 1.00 82.7 yes View details
tRNA-Trp-tRNA-Pro LSC 166 0.0719 1.00 82.3 yes View details
tRNA-Val-tRNA-Met LSC 210 0.0611 1.00 81.8 yes View details
tRNA-Pro-tRNA-Leu SSC 169 0.0556 1.00 80.4 yes View details
tRNA-Ser-tRNA-Leu LSC 1592 0.0319 1.00 74.6 yes View details
tRNA-Gln-tRNA-Ser LSC 1193 0.0317 1.00 72.6 yes View details
tRNA-Thr-tRNA-Met LSC 159 0.0704 1.00 71.2 yes View details
tRNA-Glu-tRNA-Cys LSC 1407 0.0303 0.99 71.0 yes View details
tRNA-Gly-tRNA-Gly LSC 855 0.0261 0.99 66.8 yes View details
tRNA-Tyr-tRNA-Glu LSC 179 0.0367 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
tRNA-Gln-tRNA-Ser_p1 tRNA-Gln-tRNA-Ser GATCAAAACCCGCTGCCTTA GGGTTCGAATCCCTCTCTCT 1251–1272 1.000 78.9
tRNA-Gln-tRNA-Ser_p2 tRNA-Gln-tRNA-Ser GATCAAAACCCGCTGCCTTA TAACGCGTCGGATTGCTAAT 1296–1317 1.000 78.8
tRNA-Gln-tRNA-Ser_p3 tRNA-Gln-tRNA-Ser GATCAAAACCCGCTGCCTTA CTAACGCGTCGGATTGCTAA 1297–1318 1.000 76.9
tRNA-Gln-tRNA-Ser_p4 tRNA-Gln-tRNA-Ser GATCAAAACCCGCTGCCTTA TTTTGCTTGGAGAGATGGCC 1324–1345 1.000 76.7
tRNA-Gln-tRNA-Ser_p5 tRNA-Gln-tRNA-Ser CGAATGACGGGATCAAAACC TAACGCGTCGGATTGCTAAT 1306–1327 1.000 76.4
tRNA-Gly-tRNA-Gly_p1 tRNA-Gly-tRNA-Gly TTGTGGCGGGTATGGTTTAG CCCGCATCATTAGCTTGGAA 910–932 1.000 81.0
tRNA-Gly-tRNA-Gly_p2 tRNA-Gly-tRNA-Gly TTAGACAGAGGACCCGTCTG CCCGCATCATTAGCTTGGAA 945–967 1.000 80.5
tRNA-Gly-tRNA-Gly_p3 tRNA-Gly-tRNA-Gly AGAGGACCCGTCTGTGTAAT CCCGCATCATTAGCTTGGAA 939–961 1.000 80.0
tRNA-Gly-tRNA-Gly_p4 tRNA-Gly-tRNA-Gly TTGTGGCGGGTATGGTTTAG ATCGAACCCGCATCATTAGC 916–938 1.000 79.7
tRNA-Gly-tRNA-Gly_p5 tRNA-Gly-tRNA-Gly TTAGACAGAGGACCCGTCTG ATCGAACCCGCATCATTAGC 951–973 1.000 79.1
tRNA-Arg-tRNA-Asp_p1 tRNA-Arg-tRNA-Asp AAACAAAATCCACCGACGGA AATCCAGAAACTCGACGAGC 435–447 0.600 70.7
tRNA-Arg-tRNA-Asp_p2 tRNA-Arg-tRNA-Asp AAACAAAATCCACCGACGGA CAGAAACTCGACGAGCAGAA 431–443 0.600 70.3
tRNA-Arg-tRNA-Asp_p3 tRNA-Arg-tRNA-Asp AGTTCTGGTAGTACAGGCGT AATCCAGAAACTCGACGAGC 678–692 0.600 68.7
tRNA-Arg-tRNA-Asp_p4 tRNA-Arg-tRNA-Asp CCTTGTGAATCCATCCAGGG AATCCAGAAACTCGACGAGC 966–980 0.600 67.8
tRNA-Arg-tRNA-Asp_p5 tRNA-Arg-tRNA-Asp CTTGTGAATCCATCCAGGGG AATCCAGAAACTCGACGAGC 965–979 0.600 67.8
tRNA-Tyr-tRNA-Glu_p1 tRNA-Tyr-tRNA-Glu GTCCCCATTAACCACTCGAG CGTCTAGAGGCCTAGGACAA 269–273 1.000 84.5
tRNA-Tyr-tRNA-Glu_p2 tRNA-Tyr-tRNA-Glu CCCATTAACCACTCGAGCAT CGTCTAGAGGCCTAGGACAA 266–270 1.000 84.4
tRNA-Tyr-tRNA-Glu_p3 tRNA-Tyr-tRNA-Glu GTCCCCATTAACCACTCGAG GAGGCCTAGGACAACTCTCT 263–267 1.000 83.9
tRNA-Tyr-tRNA-Glu_p4 tRNA-Tyr-tRNA-Glu GTCCCCATTAACCACTCGAG AGAGGCCTAGGACAACTCTC 264–268 1.000 83.8
tRNA-Tyr-tRNA-Glu_p5 tRNA-Tyr-tRNA-Glu CCCATTAACCACTCGAGCAT GAGGCCTAGGACAACTCTCT 260–264 1.000 83.8
tRNA-Glu-tRNA-Cys_p1 tRNA-Glu-tRNA-Cys TTGTCCTAGGCCTCTAGACG CCTTGATTCCCCAGTTCGAG 1462–1474 1.000 84.5
tRNA-Glu-tRNA-Cys_p2 tRNA-Glu-tRNA-Cys TTGTCCTAGGCCTCTAGACG TGATTCCCCAGTTCGAGTCT 1459–1471 1.000 84.3
tRNA-Glu-tRNA-Cys_p3 tRNA-Glu-tRNA-Cys AGAGAGTTGTCCTAGGCCTC CCTTGATTCCCCAGTTCGAG 1468–1480 1.000 83.7
tRNA-Glu-tRNA-Cys_p4 tRNA-Glu-tRNA-Cys GAGAGTTGTCCTAGGCCTCT CCTTGATTCCCCAGTTCGAG 1467–1479 1.000 83.7
tRNA-Glu-tRNA-Cys_p5 tRNA-Glu-tRNA-Cys GAGAGTTGTCCTAGGCCTCT TGATTCCCCAGTTCGAGTCT 1464–1476 1.000 83.4
tRNA-Cys-tRNA-Gly_p1 tRNA-Cys-tRNA-Gly CTCGAACTGGGGAATCAAGG GTTCGATTCCCGCTATCCG 360–368 1.000 80.7
tRNA-Cys-tRNA-Gly_p2 tRNA-Cys-tRNA-Gly CTCGAACTGGGGAATCAAGG GGGTTCGATTCCCGCTATC 362–370 1.000 80.5
tRNA-Cys-tRNA-Gly_p3 tRNA-Cys-tRNA-Gly CTCGAACTGGGGAATCAAGG GGTTCGATTCCCGCTATCC 361–369 1.000 80.5
tRNA-Cys-tRNA-Gly_p4 tRNA-Cys-tRNA-Gly AGACTCGAACTGGGGAATCA GTTCGATTCCCGCTATCCG 363–371 1.000 80.4
tRNA-Cys-tRNA-Gly_p5 tRNA-Cys-tRNA-Gly TTTAGTAGGCGACACCCAGA GTTCGATTCCCGCTATCCG 380–388 1.000 79.9

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
Azolla caroliniana MF177092.1 147498 View on NCBI ↗
Azolla filiculoides MF177094.1 147665 View on NCBI ↗
Azolla mexicana MF177088.1 147232 View on NCBI ↗
Azolla microphylla MF177089.1 147136 View on NCBI ↗
Azolla rubra PQ616047.1 147792 View on NCBI ↗