Markers + reference

Marathrum

2 species · Podostemaceae · Malpighiales

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Species 2
Genome length 132–132 kb
Candidate markers 260
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-atpB LSC 1005 0.0185 0.97 64.6 yes View details
ndhJ-trnF-GAA LSC 486 0.0289 1.00 62.0 yes View details
psbZ-trnS-UGA LSC 376 0.0187 1.00 57.3 yes View details
trnS-UGA-psbC LSC 283 0.0522 0.88 76.7 yes View details
trnT-GGU-trnE-UUC LSC 638 0.0215 0.95 61.9 yes View details
trnC-GCA-rpoB LSC 968 0.0213 0.97 61.6 yes View details
trnG-UCC-trnS-GCU LSC 651 0.0246 1.00 72.9 yes View details
psbI-psbK LSC 509 0.0246 0.96 70.0 yes View details
rpoA LSC 1017 0.0059 1.00 48.9 yes View details
petG-trnW-CCA LSC 121 0.0496 1.00 74.8 yes View details
trnQ-UUG-trnK-UUU LSC 644 0.0187 1.00 70.0 yes View details
trnV-UAC-ndhC LSC 218 0.0291 0.94 68.5 yes View details
petD-rpoA LSC 185 0.0541 1.00 67.2 yes View details
rpl32-trnL-UAG SSC 547 0.0203 0.99 66.1 yes View details
accD-psaI LSC 725 0.0138 1.00 65.5 yes View details
ycf3-psaA LSC 774 0.0116 1.00 65.4 yes View details
rps11-rpl36 LSC 172 0.0204 0.85 65.1 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
rbcL-atpB_p1 rbcL-atpB GCCTTGAATCCAACACTTGC TTCAAGCGCAGAAACTCCAA 1100–1118 1.000 80.4
rbcL-atpB_p2 rbcL-atpB GGTGACATAAGTCCCTCCCT TTCAAGCGCAGAAACTCCAA 1064–1082 1.000 80.2
rbcL-atpB_p3 rbcL-atpB GCCTTGAATCCAACACTTGC GCAGAAACTCCAAGACCTGA 1093–1111 1.000 78.7
rbcL-atpB_p4 rbcL-atpB GGTGACATAAGTCCCTCCCT GCAGAAACTCCAAGACCTGA 1057–1075 1.000 78.4
rbcL-atpB_p5 rbcL-atpB GCCTTGAATCCAACACTTGC CCAAGACCTGAAGTAGTCGG 1084–1102 1.000 77.8
trnV-UAC-ndhC_p1 trnV-UAC-ndhC GGTTCGAATCCGTATAGCCC TCGGCGATAAAATTCCAGAA 328–340 1.000 61.0
trnV-UAC-ndhC_p2 trnV-UAC-ndhC GGTTCGAATCCGTATAGCCC TCGGCGATAAAATTCCAGAAA 328–340 1.000 59.4
trnV-UAC-ndhC_p3 trnV-UAC-ndhC CGGTTCGAATCCGTATAGCC TCGGCGATAAAATTCCAGAA 329–341 1.000 59.1
trnV-UAC-ndhC_p4 trnV-UAC-ndhC GGTTCGAATCCGTATAGCCC ATCGGCGATAAAATTCCAGA 329–341 1.000 59.1
trnV-UAC-ndhC_p5 trnV-UAC-ndhC GGTTCGAATCCGTATAGCCC ATCGGCGATAAAATTCCAGAA 329–341 1.000 57.6
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA AGAAAGGATTATATTGCACCCA CGGTAGAGCAGAGGACTGAA 593–594 1.000 42.0
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA AGAAAGGATTATATTGCACCCAA CGGTAGAGCAGAGGACTGAA 593–594 1.000 42.0
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA AGAAAGGATTATATTGCACCCA CAAATGGTCGGGATAGCTCA 615–616 1.000 41.9
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA AGAAAGGATTATATTGCACCCA ACAAATGGTCGGGATAGCTC 616–617 1.000 41.9
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA AGAAAGGATTATATTGCACCCAA CAAATGGTCGGGATAGCTCA 615–616 1.000 41.9
trnL-UAA_p1 trnL-UAA GTAAGATGGGGTTTGTTAATTT GGGGATCTCAAATAGTTCGTGT 687–693 1.000 42.6
trnL-UAA_p2 trnL-UAA GTAAGATGGGGTTTGTTAATTTT GGGGATCTCAAATAGTTCGTGT 687–693 1.000 42.6
trnL-UAA_p3 trnL-UAA GTAAGATGGGGTTTGTTAATTT AGGGGATCTCAAATAGTTCGTG 688–694 1.000 42.5
trnL-UAA_p4 trnL-UAA GTAAGATGGGGTTTGTTAATTTT AGGGGATCTCAAATAGTTCGTG 688–694 1.000 42.5
trnL-UAA_p5 trnL-UAA GTAAGATGGGGTTTGTTAATTT AGGGGATCTCAAATAGTTCGT 688–694 1.000 42.5
ycf3-psaA_p1 ycf3-psaA CAGAAGCCTGGTTCGATCAA GCCCATTCCTCGAAAGAAGT 967–978 1.000 79.0
ycf3-psaA_p2 ycf3-psaA AGCGCTTACTCCGGAAAATT GCCCATTCCTCGAAAGAAGT 921–932 1.000 79.0
ycf3-psaA_p3 ycf3-psaA CAATAGCGCTTACTCCGGAA GCCCATTCCTCGAAAGAAGT 925–936 1.000 78.1
ycf3-psaA_p4 ycf3-psaA AGAAGCCTGGTTCGATCAAG GCCCATTCCTCGAAAGAAGT 966–977 1.000 76.7
ycf3-psaA_p5 ycf3-psaA TGGAAACAAGCAATAGCGCT GCCCATTCCTCGAAAGAAGT 935–946 1.000 76.1
psbZ-trnS-UGA_p1 psbZ-trnS-UGA AGCAATTAACGCAAAAACAGC CAAGACCGGAGCTATCAACC 454 1.000 63.9
psbZ-trnS-UGA_p2 psbZ-trnS-UGA GCAATTAACGCAAAAACAGCT CAAGACCGGAGCTATCAACC 453 1.000 63.9
psbZ-trnS-UGA_p3 psbZ-trnS-UGA AGCAATTAACGCAAAAACAGC CTATCAACCACTCGGCCATC 443 1.000 63.4
psbZ-trnS-UGA_p4 psbZ-trnS-UGA GCAATTAACGCAAAAACAGCT CTATCAACCACTCGGCCATC 442 1.000 63.4
psbZ-trnS-UGA_p5 psbZ-trnS-UGA TGTTACTTGACCATCCATCAGG CAAGACCGGAGCTATCAACC 521 1.000 63.0

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
Marathrum foeniculaceum NC_049108.1 131600 View on NCBI ↗
Marathrum utile NC_059857.1 131951 View on NCBI ↗