Markers + reference

Globba

7 species · Zingiberaceae · Zingiberales

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Species 7
Genome length 162–163 kb
Candidate markers 273
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 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
trnK-UUU-rps16 LSC 808 0.0271 0.91 61.6 yes View details
trnS-GCU-trnG-GCC LSC 680 0.0279 1.00 68.1 yes View details
atpH-atpI LSC 1095 0.0181 0.98 65.1 yes View details
trnE-UUC-trnT-GGU LSC 846 0.0274 0.98 71.5 yes View details
ycf1 SSC 3918 0.0038 1.00 37.2 no View details
ndhF SSC 2220 0.0095 1.00 44.9 yes View details
rpl32-trnL-UAG SSC 877 0.0240 0.93 65.0 yes View details
ccsA-ndhD SSC 452 0.0405 0.69 52.3 yes View details
psaC-ndhE SSC 441 0.0485 0.99 81.7 yes View details
rps15-ycf1 SSC 468 0.0497 0.92 79.3 yes View details
ycf1 SSC 5394 0.0134 1.00 45.5 yes View details
accD-psaI LSC 425 0.0304 1.00 78.0 yes View details
trnT-UGU-trnL-UAA LSC 846 0.0189 1.00 67.7 yes View details
psbT-psbN LSC 59 0.0420 0.98 67.3 yes View details
psbC-trnS-UGA LSC 149 0.0410 1.00 65.3 yes View details
ndhF-rpl32 SSC 669 0.0202 1.00 63.3 yes View details
rpoB-trnC-GCA LSC 584 0.0252 1.00 62.6 yes View details
ndhG-ndhI SSC 312 0.0360 1.00 62.5 yes View details
rps16-trnQ-UUG LSC 1009 0.0239 1.00 62.4 yes View details
ycf1-ndhF SSC 42 0.2558 0.55 61.6 yes View details
psbE-petL LSC 1036 0.0141 0.99 61.1 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CCAATATCAACCGAACAGACG GGGGTCGTGCAGTCTAATTC 2866–2958 1.000 67.1
trnK-UUU_p2 trnK-UUU AAGGACTCCCAAGCATATGT GGGGTCGTGCAGTCTAATTC 2966 0.143 28.5
trnK-UUU_p3 trnK-UUU AAGGACTCCCAAGCATATGT GGGTCGTGCAGTCTAATTCA 2965 0.143 28.2
trnK-UUU_p4 trnK-UUU CCAATATCAACCGAACAGACG AGTTGGTCCGTCGGAATTTT 2993 0.143 28.2
trnK-UUU_p5 trnK-UUU CCAATATCAACCGAACAGACG GTTGGTCCGTCGGAATTTTG 2992 0.143 27.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT AGGATTCCCCTGGGACTATG 1245–1290 1.000 86.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AATCAATGGTCTCCGAACGG AGGATTCCCCTGGGACTATG 1654 0.143 44.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AATCAATGGTCTCCGAACGG GGATTCCCCTGGGACTATGT 1653 0.143 44.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 AATCAATGGTCTCCGAACGG CGTTTCTGGGGGAGATTGTT 1548 0.143 43.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AATCAATGGTCTCCGAACGG TGCTGCCCTTTTGAAAAGGA 1840 0.143 43.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACCGATCATGTCCTT CTTACAGCAGCTTGCCAAAC 1665–2071 1.000 85.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTTACAGCAGCTTGCCAAAC 1644–2050 1.000 85.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAACCGATCATGTCCTT CGGGCAATTTGGCAAAGAAA 1571–1977 1.000 85.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1103–1510 0.857 78.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1082–1489 0.857 77.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CCGAGATACCCCTTCCCTTA 779–850 1.000 85.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CCGAGATACCCCTTCCCTTA 778–849 1.000 85.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GAGCGGAGAAAGAGGGATTC CCGAGATACCCCTTCCCTTA 835–906 1.000 82.9
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGCAATCCGACGCTTTAGTC CCGAGATACCCCTTCCCTTA 781–852 1.000 82.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CGACGCTTTAGTCCACTCAG CCGAGATACCCCTTCCCTTA 774–845 1.000 82.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCGCGGCTTATATAGGTGAA 1168–1611 1.000 80.4
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCTTGGCCT CCGCGGCTTATATAGGTGAA 1251–1694 1.000 80.2
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT GGTGAATCCATGGAAGGTCA 1154–1597 1.000 79.8
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT CCGCGGCTTATATAGGTGAA 1224–1667 1.000 79.7
atpH-atpI_p5 atpH-atpI TACCTTCTACAGCTTGGCCT GGTGAATCCATGGAAGGTCA 1237–1680 1.000 79.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AACCCATAGCCGACGATAGA CGACCTCTGATTTTCGTCGT 1468–2106 1.000 82.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ACCCATAGCCGACGATAGAA CGACCTCTGATTTTCGTCGT 1467–2105 1.000 82.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AACCCATAGCCGACGATAGA TCAGAGACCCTCGTGAGTTT 1702–2329 0.571 63.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACCCATAGCCGACGATAGAA TCAGAGACCCTCGTGAGTTT 1701–2328 0.571 63.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG TCAGAGACCCTCGTGAGTTT 1847–2474 0.571 63.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Globba atrosanguinea PP542021.1 161896 View on NCBI ↗
Globba lancangensis MT473704.1 163306 View on NCBI ↗
Globba marantina MT473705.1 162774 View on NCBI ↗
Globba multiflora MT473706.1 163199 View on NCBI ↗
Globba racemosa PX430557.1 163321 View on NCBI ↗
Globba schomburgkii MK262735.1 163325 View on NCBI ↗
Globba schomburgkii var. angustata MT473707.1 163432 View on NCBI ↗