Markers + reference

Ensete

4 species · Musaceae · Zingiberales

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Species 4
Genome length 168–168 kb
Candidate markers 277
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0074 1.00 49.6 yes View details
tRNA-Lys-rps16 LSC 741 0.0265 0.99 65.7 yes View details
rps16-trnQ-UUG LSC 1643 0.0193 0.98 67.3 yes View details
ndhC-trnV-UAC LSC 1009 0.0209 0.98 67.9 yes View details
ycf4-cemA LSC 670 0.0382 0.98 75.2 yes View details
rps19 LSC 279 0.0090 1.00 44.5 yes View details
ndhA IRb 567 0.0000 1.00 24.8 no View details
ndhA-ndhF IRb 515 0.0252 0.98 63.6 yes View details
ndhF SSC 2214 0.0195 1.00 56.3 yes View details
rpl32-trnL-UAG SSC 808 0.0421 0.97 77.7 yes View details
ndhD SSC 1506 0.0134 1.00 53.2 yes View details
psaC-ndhE SSC 714 0.0461 0.97 79.1 yes View details
ndhA SSC 2191 0.0161 1.00 56.4 yes View details
rpl22-rps19 LSC 215 0.0775 0.99 80.0 yes View details
ccsA-ndhD SSC 233 0.0568 1.00 78.3 yes View details
trnH-GUG-psbA LSC 361 0.0632 0.86 73.5 no View details
rps8-rpl14 LSC 229 0.0443 0.96 73.1 yes View details
trnE-UUC-trnT-GGU LSC 782 0.0213 0.99 69.1 yes View details
matK-tRNA-Lys LSC 856 0.0261 0.97 68.2 yes View details
ndhG-ndhI SSC 380 0.0352 0.98 65.5 yes View details
accD-psaI LSC 293 0.0347 1.00 63.8 yes View details
atpB-rbcL LSC 857 0.0113 1.00 63.5 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA AGCAATACCCCGTATCTTGC CATAGGGAAAGTCGTGTGCA 1541 0.500 57.9
psbA_p2 psbA GCAATACCCCGTATCTTGCT CATAGGGAAAGTCGTGTGCA 1540 0.500 57.9
psbA_p3 psbA GCAATACCCCGTATCTTGCT ACATAGGGAAAGTCGTGTGC 1541 0.500 57.9
psbA_p4 psbA AGCAATACCCCGTATCTTGC AATACGTGTGCTTGGGAGTC 1195 0.500 57.8
psbA_p5 psbA GCAATACCCCGTATCTTGCT AATACGTGTGCTTGGGAGTC 1194 0.500 57.8
matK-tRNA-Lys_p1 matK-tRNA-Lys TCTAAATATCCTTGTAATTCTTCCA AACGGTAGAGTACTCGGCTT 877–906 1.000 47.2
matK-tRNA-Lys_p2 matK-tRNA-Lys TCTAAATATCCTTGTAATTCTTCCA ACGGTAGAGTACTCGGCTTT 876–905 1.000 47.2
matK-tRNA-Lys_p3 matK-tRNA-Lys TTCTAAATATCCTTGTAATTCTTCCA AACGGTAGAGTACTCGGCTT 878–907 1.000 47.2
matK-tRNA-Lys_p4 matK-tRNA-Lys TTCTAAATATCCTTGTAATTCTTCCA ACGGTAGAGTACTCGGCTTT 877–906 1.000 47.2
matK-tRNA-Lys_p5 matK-tRNA-Lys TCTAAATATCCTTGTAATTCTTCCA GGGTTGCTAACTCAACGGTA 890–919 1.000 47.1
tRNA-Lys-rps16_p1 tRNA-Lys-rps16 AGAACTCACCCTTTCCCGTA TCGATCCCGAAGAGAAGGAA 1364–1382 1.000 84.0
tRNA-Lys-rps16_p2 tRNA-Lys-rps16 ACTCACCCTTTCCCGTATCA TCGATCCCGAAGAGAAGGAA 1361–1379 1.000 83.8
tRNA-Lys-rps16_p3 tRNA-Lys-rps16 AGAACTCACCCTTTCCCGTA AAGAGGTTAGAGACGGCTCA 1682–1710 1.000 82.7
tRNA-Lys-rps16_p4 tRNA-Lys-rps16 AGAACTCACCCTTTCCCGTA AGAGGTTAGAGACGGCTCAA 1681–1709 1.000 82.7
tRNA-Lys-rps16_p5 tRNA-Lys-rps16 TGAGGATCAGTCGTGGTCTT TCGATCCCGAAGAGAAGGAA 1040–1049 1.000 82.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1716–1773 1.000 83.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1714–1771 1.000 83.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA CCAAACAGGAAAAATGGGGC 1778–1835 1.000 82.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GCCAAACAGGAAAAATGGGG 1779–1836 1.000 82.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT CCAAACAGGAAAAATGGGGC 1776–1833 1.000 82.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG GAACCGATGACTTACGCCTT 732–925 1.000 85.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG CCATGGCGTTACTCTACCAC 711–904 1.000 85.0
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG TGGCGTTACTCTACCACTGA 708–901 1.000 84.8
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 696–889 1.000 84.5
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG TGGAAAAAGCCCCTTATCGG 756–949 1.000 84.2
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GCCAAGATAGGAATAACGCTTG AGAAGGTCTACGGTTCGAGT 1113–1548 1.000 64.8
ndhC-trnV-UAC_p2 ndhC-trnV-UAC GCCAAGATAGGAATAACGCT AGAAGGTCTACGGTTCGAGT 1113–1548 1.000 63.1
ndhC-trnV-UAC_p3 ndhC-trnV-UAC GCCAAGATAGGAATAACGCTTG AGCCCAATGCAACAAAATGC 1195–1630 1.000 62.4
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GCCAAGATAGGAATAACGCTTG GAAGGTCTACGGTTCGAGTC 1112–1547 1.000 62.0
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GCCAAGATAGGAATAACGCTT AGAAGGTCTACGGTTCGAGT 1113–1548 1.000 61.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Ensete glaucum NC_058947.1 168248 View on NCBI ↗
Ensete livingstonianum NC_058943.1 168258 View on NCBI ↗
Ensete superbum NC_058930.1 168332 View on NCBI ↗
Ensete ventricosum NC_058926.1 168411 View on NCBI ↗