Markers + reference

Hedychium

20 species · Zingiberaceae · Zingiberales

Back to catalogue

Species 20
Genome length 163–164 kb
Candidate markers 271
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0008 1.00 35.9 yes View details
trnS-GCU-trnG-GCC LSC 746 0.0079 0.95 57.3 yes View details
trnT-GGU-psbD LSC 1280 0.0091 1.00 60.4 yes View details
rps4-trnL-UAA LSC 1067 0.0051 1.00 48.6 yes View details
ndhC-trnV-UAC LSC 1710 0.0064 0.95 55.2 yes View details
trnI-CAU-ycf2 SSC 426 0.0648 0.30 59.7 yes View details
ycf1 SSC 3996 0.0039 0.96 49.6 yes View details
ndhF-rpl32 SSC 778 0.0049 0.84 47.0 yes View details
ccsA-ndhD SSC 272 0.0123 1.00 54.4 yes View details
ndhD SSC 1506 0.0011 1.00 34.5 yes View details
psaC-ndhE SSC 522 0.0065 1.00 60.4 yes View details
ycf1 SSC 5448 0.0008 1.00 43.1 no View details
rps19-psbA LSC 364 0.0643 0.70 75.7 no View details
psbC-trnS-UGA LSC 142 0.0183 1.00 60.7 yes View details
psbT-psbN LSC 64 0.0296 1.00 58.5 yes View details
accD-psaI LSC 521 0.0044 1.00 58.0 yes View details
rpl2-trnH-GUG IRa 47 0.0183 1.00 57.8 yes View details
atpH-atpI LSC 1104 0.0026 1.00 57.2 yes View details
rps16-trnQ-UUG LSC 1365 0.0020 0.99 55.9 yes View details
rps18-rpl20 LSC 203 0.0054 1.00 55.3 yes View details
petN-psbM LSC 1371 0.0028 1.00 55.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA ACCCCATATCTCGCTTAAGC ACATATGCTTGGGAGTCCTT 1203–1204 1.000 59.1
psbA_p2 psbA GCTTAAGCGAGATATGGGGT ACATATGCTTGGGAGTCCTT 1191–1192 1.000 59.1
psbA_p3 psbA ACCCCATATCTCGCTTAAGC TACATATGCTTGGGAGTCCT 1204–1205 1.000 51.9
psbA_p4 psbA GCTTAAGCGAGATATGGGGT TACATATGCTTGGGAGTCCT 1192–1193 1.000 51.9
psbA_p5 psbA GCTTAAGCGAGATATGGGGT ACATATGCTTGGGAGTCCTTA 1191–1192 1.000 50.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1447–1471 1.000 82.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1445–1469 1.000 82.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1453–1477 1.000 82.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1429–1453 1.000 81.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA CTCGGAGGTTCGAATCCTTC 1451–1475 1.000 81.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGGAGATACCCCTTCCCTTA 823–950 1.000 83.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGGAGATACCCCTTCCCTTA 822–949 1.000 83.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC AGTATCAAGCGGGTCGAGTA CGGAGATACCCCTTCCCTTA 907–1034 1.000 82.8
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC GAGCGGAGAAAGAGGGATTC CGGAGATACCCCTTCCCTTA 879–1006 1.000 81.3
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GTCGAGTAATCAGAGCGAGC CGGAGATACCCCTTCCCTTA 895–1022 1.000 81.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACCTTAGCCGC 1157–1678 1.000 84.2
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACCTTAGCCGC 1240–1761 1.000 84.2
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACCTTAGCCGC 1213–1734 1.000 83.7
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATTTTTGCAACCTTAGCCGC 1158–1679 1.000 83.1
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATTTTTGCAACCTTAGCCGC 1217–1738 1.000 83.0
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1379–1487 1.000 72.7
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1378–1486 1.000 72.7
petN-psbM_p3 petN-psbM ATGGGGAAGGAGTGGACTTT TGCTACTGCACTGTTCATTCT 1376–1484 1.000 71.8
petN-psbM_p4 petN-psbM ATTGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 1438–1546 1.000 71.5
petN-psbM_p5 petN-psbM TGGGGAAGGAGTGGACTTTA TGCTACTGCACTGTTCATTCT 1375–1483 1.000 70.3
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCCACAAAAACGAAACGGTC 1426–1483 1.000 83.2
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CCCACAAAAACGAAACGGTC 1429–1486 1.000 83.0
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG AACCCACAAAAACGAAACGG 1428–1485 1.000 82.3
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA AACCCACAAAAACGAAACGG 1431–1488 1.000 82.1
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGTCTCTGCGTAACCAATCA 1410–1467 1.000 81.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (20)

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

Species Accession Length (bp) Link
Hedychium aureum PP542023.1 163395 View on NCBI ↗
Hedychium bijiangense NC_085806.1 163883 View on NCBI ↗
Hedychium brevicaule NC_085801.1 163438 View on NCBI ↗
Hedychium chrysoleucum NC_085798.1 163977 View on NCBI ↗
Hedychium coccineum OP805574.1 163850 View on NCBI ↗
Hedychium coronarium NC_045863.1 163949 View on NCBI ↗
Hedychium flavescens NC_085797.1 163951 View on NCBI ↗
Hedychium flavum NC_085805.1 163850 View on NCBI ↗
Hedychium kwangsiense NC_085803.1 163423 View on NCBI ↗
Hedychium menghaiense NC_085804.1 163979 View on NCBI ↗
Hedychium neocarneum MT473709.1 163903 View on NCBI ↗
Hedychium philippinense NC_084246.1 163878 View on NCBI ↗
Hedychium puerense NC_085799.1 163941 View on NCBI ↗
Hedychium spicatum NC_047248.1 163531 View on NCBI ↗
Hedychium tienlinense NC_085807.1 163868 View on NCBI ↗
Hedychium villosum NC_060763.1 163540 View on NCBI ↗
Hedychium villosum f. albifihamentum OP805580.1 163442 View on NCBI ↗
Hedychium villosum var. tenuiflorum OP805576.1 163359 View on NCBI ↗
Hedychium viridibracteatum NC_085800.1 163338 View on NCBI ↗
Hedychium yunnanense NC_085802.1 163420 View on NCBI ↗