Markers + reference

Moerckia

2 species · Moerckiaceae · Pallaviciniales

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Species 2
Genome length 125–127 kb
Candidate markers 270
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf66 Genome 999 0.0251 1.00 59.7 yes View details
petN-trnC-GCA Genome 375 0.0749 0.93 77.6 yes View details
rpoC2-rps2 Genome 263 0.0539 0.78 67.6 yes View details
psaM-trnS-GCU Genome 387 0.0395 0.98 70.3 yes View details
ycf2 Genome 6378 0.0170 1.00 48.1 yes View details
ycf3-trnS-GGA Genome 249 0.0161 1.00 51.5 yes View details
rps12-trnV-GAC Genome 709 0.0527 0.99 80.3 yes View details
trnV-GAC-trnL-CAA Genome 397 0.0831 1.00 78.9 no View details
trnR-UCU-trnG-GCC Genome 84 0.0714 1.00 76.7 yes View details
trnE-UUC-CysA Genome 330 0.0484 0.94 76.6 yes View details
cemA-petA Genome 193 0.0582 0.98 75.7 yes View details
trnW-CCA-trnP-UGG Genome 51 0.0588 1.00 74.3 yes View details
trnD-GUC-trnY-GUA Genome 186 0.0383 0.98 73.7 yes View details
trnF-GAA-ndhJ Genome 129 0.1163 1.00 73.7 yes View details
rpl36-infA Genome 52 0.1346 1.00 72.9 yes View details
trnS-GGA-rps4 Genome 159 0.3019 1.00 72.6 yes View details
ycf66-petN Genome 90 0.0674 0.99 72.1 yes View details
psbM-ycf66 Genome 128 0.0547 1.00 71.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbM-ycf66_p1 psbM-ycf66 TCAATTCCAACCGCCTTTCT TACTGGGGCCCAATTCCATA 216 1.000 79.6
psbM-ycf66_p2 psbM-ycf66 TCTCAATTCCAACCGCCTTT TACTGGGGCCCAATTCCATA 218 1.000 79.6
psbM-ycf66_p3 psbM-ycf66 TCAATTCCAACCGCCTTTCT CCGCACCTATTACGGTACTG 231 1.000 79.1
psbM-ycf66_p4 psbM-ycf66 TCAATTCCAACCGCCTTTCT CGCACCTATTACGGTACTGG 230 1.000 79.1
psbM-ycf66_p5 psbM-ycf66 TCTCAATTCCAACCGCCTTT CGCACCTATTACGGTACTGG 232 1.000 79.1
ycf66_p1 ycf66 ATTCCATTGGCAGCACAGAA AAGTGGTAAGGCAGAGGACT 2007–2373 1.000 82.9
ycf66_p2 ycf66 ATTCCATTGGCAGCACAGAA CGCTTCGCCGACAAGATATA 1953–2319 1.000 82.9
ycf66_p3 ycf66 TGAAACGGTATACACGCGAG AAGTGGTAAGGCAGAGGACT 2126–2492 1.000 82.5
ycf66_p4 ycf66 GGACTACGACATAGGGGACA AAGTGGTAAGGCAGAGGACT 1677 0.500 59.2
ycf66_p5 ycf66 GGACTACGACATAGGGGACA CGCTTCGCCGACAAGATATA 1623 0.500 59.1
ycf66-petN_p1 ycf66-petN TGTTACGGAGAGAAAGAACGA TATGGGGAAGAAGCGGTTTG 143–151 1.000 64.7
ycf66-petN_p2 ycf66-petN TGTTACGGAGAGAAAGAACGA GTATGGGGAAGAAGCGGTTT 144–152 1.000 64.6
ycf66-petN_p3 ycf66-petN TTGTTACGGAGAGAAAGAACGA TATGGGGAAGAAGCGGTTTG 144–152 1.000 62.2
ycf66-petN_p4 ycf66-petN TTGTTACGGAGAGAAAGAACGA GTATGGGGAAGAAGCGGTTT 145–153 1.000 62.2
ycf66-petN_p5 ycf66-petN TGTTACGGAGAGAAAGAACGA GTTGTATGGGGAAGAAGCGG 147–155 1.000 60.6
petN-trnC-GCA_p1 petN-trnC-GCA TCGAAGCACCCCAAGCTATA AAGTGGTAAGGCAGAGGACT 466–815 1.000 82.4
petN-trnC-GCA_p2 petN-trnC-GCA CGAAGCACCCCAAGCTATAT AAGTGGTAAGGCAGAGGACT 465–814 1.000 82.1
petN-trnC-GCA_p3 petN-trnC-GCA TCGAAGCACCCCAAGCTATA CAAGTGGTAAGGCAGAGGAC 467–816 1.000 81.9
petN-trnC-GCA_p4 petN-trnC-GCA TCGAAGCACCCCAAGCTATA CAAATCCTTCATCCCCGGTT 445–794 1.000 81.8
petN-trnC-GCA_p5 petN-trnC-GCA CGAAGCACCCCAAGCTATAT CAAGTGGTAAGGCAGAGGAC 466–815 1.000 81.5
rpoC2-rps2_p1 rpoC2-rps2 TCCGAAATAGCAGAAATATCT ACCGAAATGAACACCTGCTT 301–358 1.000 46.7
rpoC2-rps2_p2 rpoC2-rps2 TCCGAAATAGCAGAAATATCTT ACCGAAATGAACACCTGCTT 301–358 1.000 46.7
rpoC2-rps2_p3 rpoC2-rps2 TCCGAAATAGCAGAAATATCT GGTGACCGAAATGAACACCT 305–362 1.000 46.6
rpoC2-rps2_p4 rpoC2-rps2 TCCGAAATAGCAGAAATATCT GCCATCTTGGGATTCCACTT 333–390 1.000 46.4
rpoC2-rps2_p5 rpoC2-rps2 TCCGAAATAGCAGAAATATCT ATAGGGTGCCATCTTGGGAT 340–397 1.000 46.4
trnR-UCU-trnG-GCC_p1 trnR-UCU-trnG-GCC AGGGTACAGCTACGTCCAAT ACCCTTAGCCTTCCAAGCTA 215–227 1.000 80.8
trnR-UCU-trnG-GCC_p2 trnR-UCU-trnG-GCC AGGGTACAGCTACGTCCAAT AACGAAAAGTACGATGCCGA 240–252 1.000 80.3
trnR-UCU-trnG-GCC_p3 trnR-UCU-trnG-GCC AGGGTACAGCTACGTCCAAT CAACGAAAAGTACGATGCCG 241–253 1.000 79.7
trnR-UCU-trnG-GCC_p4 trnR-UCU-trnG-GCC AGGGTACAGCTACGTCCAAT ACGAAAAGTACGATGCCGAT 239–251 1.000 78.5
trnR-UCU-trnG-GCC_p5 trnR-UCU-trnG-GCC AGGGTACAGCTACGTCCAAT TTTCCACGTTCGGTTCTGAA 272–284 1.000 78.1

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
Moerckia flotoviana NC_080366.1 124598 View on NCBI ↗
Moerckia hibernica PX421532.1 126538 View on NCBI ↗