Markers + reference

Stachyphrynium

2 species · Marantaceae · Zingiberales

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Species 2
Genome length 162–168 kb
Candidate markers 273
Primer pairs 95

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1140 0.0347 0.99 70.4 yes View details
trnS-GCU-trnG-UCC LSC 1423 0.0929 0.95 83.8 yes View details
atpH-atpI LSC 883 0.0585 0.97 79.3 yes View details
trnE-UUC-trnT-GGU LSC 956 0.0570 0.94 83.7 yes View details
trnT-UGU-trnL-UAA LSC 1301 0.0588 0.88 78.5 yes View details
ndhF-rpl32 SSC 987 0.0584 0.94 79.6 yes View details
psaC-ndhE SSC 898 0.0777 0.87 78.3 yes View details
ndhG-ndhI SSC 501 0.1004 0.95 81.4 yes View details
rps15-ycf1 SSC 549 0.0857 0.91 79.0 yes View details
trnQ-UUG-psbK LSC 432 0.0576 0.97 78.5 yes View details
matK-trnK-UUU LSC 945 0.0489 0.97 77.9 yes View details
petN-psbM LSC 1153 0.0351 0.96 74.5 yes View details
trnD-GUC-trnY-GUA LSC 408 0.0444 0.94 73.1 yes View details
rps19-psbA LSC 198 0.0473 0.85 72.5 no View details
psbT-psbN LSC 65 0.0615 1.00 72.2 yes View details
rbcL-accD LSC 765 0.0419 1.00 72.0 yes View details
rpl16-rps3 LSC 152 0.0486 0.95 72.0 yes View details
psbB-psbT LSC 192 0.0729 1.00 71.7 yes View details
psaJ-rpl33 LSC 388 0.0398 0.97 71.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU AGATTTCTTTTCTATTTTCCGCA GGGGTGTGCAGTGTAATTCA 2954 0.500 20.0
trnK-UUU_p2 trnK-UUU AGATTTCTTTTCTATTTTCCGCA TGGGGTGTGCAGTGTAATTC 2955 0.500 20.0
trnK-UUU_p3 trnK-UUU AAGATTTCTTTTCTATTTTCCGCA GGGGTGTGCAGTGTAATTCA 2955 0.500 20.0
trnK-UUU_p4 trnK-UUU AAGATTTCTTTTCTATTTTCCGCA TGGGGTGTGCAGTGTAATTC 2956 0.500 20.0
trnK-UUU_p5 trnK-UUU AGATTTCTTTTCTATTTTCCGCA TTTAATGGGGTGTGCAGTGT 2960 0.500 20.0
matK-trnK-UUU_p1 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA TCGGGTTGCTAACTCAATGG 1040–1094 1.000 81.7
matK-trnK-UUU_p2 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA CGGGTTGCTAACTCAATGGT 1039–1093 1.000 81.1
matK-trnK-UUU_p3 matK-trnK-UUU AAGTGTTGTTGCCGAGATCT TCGGGTTGCTAACTCAATGG 1037–1091 1.000 79.9
matK-trnK-UUU_p4 matK-trnK-UUU AAGTGTTGTTGCCGAGATCT CGGGTTGCTAACTCAATGGT 1036–1090 1.000 79.4
matK-trnK-UUU_p5 matK-trnK-UUU AAAGTGTTGTTGCCGAGATCT TCGGGTTGCTAACTCAATGG 1038–1092 1.000 75.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1215–1231 1.000 82.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1213–1229 1.000 82.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1221–1237 1.000 82.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1197–1213 1.000 81.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA CTCGGAGGTTCGAATCCTTC 1219–1235 1.000 81.7
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GAAGGATTCGAACCTCCGAG GCTTCAGGCAATTTGGCAAA 582–596 1.000 82.7
trnQ-UUG-psbK_p2 trnQ-UUG-psbK AGGATTCGAACCTCCGAGTA GCTTCAGGCAATTTGGCAAA 580–594 1.000 80.9
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AAGGATTCGAACCTCCGAGT GCTTCAGGCAATTTGGCAAA 581–595 1.000 80.8
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GAGTAACGGGACCAAAACCC GCTTCAGGCAATTTGGCAAA 565–579 1.000 80.7
trnQ-UUG-psbK_p5 trnQ-UUG-psbK ATTCGAACCTCCGAGTAACG GCTTCAGGCAATTTGGCAAA 577–591 1.000 79.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AAAACGGAGAGACCCCCTAA 1523–1724 1.000 86.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AAAAACGGAGAGACCCCCTA 1524–1725 1.000 85.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC AAAAACGGAGAGACCCCCTA 1519–1720 1.000 85.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC AAAACGGAGAGACCCCCTAA 1518–1719 1.000 85.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TAGTCCACTCAGCCATCTCT AAAACGGAGAGACCCCCTAA 1519–1720 1.000 82.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GGTGAATCCATGGAAGGTCA 942–989 1.000 79.7
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCTTGGCCT GGTGAATCCATGGAAGGTCA 1025–1072 1.000 79.1
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT GGTGAATCCATGGAAGGTCA 998–1045 1.000 78.8
atpH-atpI_p4 atpH-atpI AATAGAAGCAAGCCCCACAG GGTGAATCCATGGAAGGTCA 976–1023 1.000 78.7
atpH-atpI_p5 atpH-atpI AGCCAATCCAGCAGCAATAA GGTGAATCCATGGAAGGTCA 958–1005 1.000 78.7

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
Stachyphrynium placentarium PQ835443.1 162492 View on NCBI ↗
Stachyphrynium spicatum PQ835452.1 167870 View on NCBI ↗