Markers + reference

Roscoea

9 species · Zingiberaceae · Zingiberales

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Species 9
Genome length 163–164 kb
Candidate markers 273
Primer pairs 100

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
rps16-trnQ-UUG LSC 1369 0.0086 0.99 59.8 yes View details
psbK-psbI LSC 534 0.0207 0.99 64.8 yes View details
trnS-GCU-trnG-UCC LSC 799 0.0147 0.95 63.6 yes View details
atpH-atpI LSC 1121 0.0321 0.98 73.7 yes View details
rpoB-trnC-GCA LSC 990 0.0096 1.00 53.9 yes View details
trnT-UGU-trnL-UAA LSC 1134 0.0167 0.97 63.9 yes View details
psbB LSC 1527 0.0021 1.00 37.6 yes View details
ycf1 IRb 3313 0.0014 1.00 47.8 no View details
ycf1-ndhF IRb 680 0.0215 0.96 59.7 yes View details
rps15-ycf1 SSC 457 0.0192 0.95 60.8 yes View details
ycf1 IRa 5451 0.0032 1.00 37.9 yes View details
trnH-GUG-rpl2 IRb 48 0.0336 1.00 71.7 yes View details
ndhG-ndhI SSC 469 0.0114 0.97 69.2 yes View details
ndhF-rpl32 SSC 688 0.0102 0.99 68.7 yes View details
atpB-rbcL LSC 809 0.0051 1.00 66.3 yes View details
petN-psbM LSC 1301 0.0068 1.00 65.9 yes View details
ndhC-trnV-UAC LSC 1590 0.0070 1.00 64.4 yes View details
psbM-trnD-GUC LSC 1126 0.0077 0.99 63.5 yes View details
trnT-GGU-psbD LSC 1286 0.0060 1.00 63.4 yes View details
ndhA SSC 2197 0.0043 0.99 62.9 yes View details
rpl2-trnH-GUG IRa 48 0.0247 1.00 62.1 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1456–1551 1.000 84.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1454–1549 1.000 84.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1462–1557 1.000 84.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1438–1533 1.000 83.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCGAGACAAGAGCATCCTCA GAGGTTCGAATCCTTCCGTC 1508–1603 1.000 82.9
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCCTCACGTCCAGGATTACG 650–722 1.000 79.4
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCCTCACGTCCAGGATTACG 647–719 1.000 77.4
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCCTCACGTCCAGGATTACG 648–720 1.000 77.4
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCCTCACGTCCAGGATTACG 649–721 1.000 77.4
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCCTCACGTCCAGGATTAC 651–723 1.000 75.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGAGATACCCCTTCCCTTAAC 847–936 1.000 69.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGAGATACCCCTTCCCTTAAC 846–935 1.000 69.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGAGATACCCCTTCCCTTAACT 847–936 1.000 68.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGAGATACCCCTTCCCTTAACT 846–935 1.000 68.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC GGAGATACCCCTTCCCTTAAC 849–938 1.000 66.9
atpH-atpI_p1 atpH-atpI GCGGCAGAAATCAGTGGATT ATTTTTGCAACCTTAGCCGC 1179–1267 1.000 81.3
atpH-atpI_p2 atpH-atpI CGGCAGAAATCAGTGGATTC ATTTTTGCAACCTTAGCCGC 1178–1266 1.000 79.5
atpH-atpI_p3 atpH-atpI GCGGCAGAAATCAGTGGAT ATTTTTGCAACCTTAGCCGC 1179–1267 1.000 78.8
atpH-atpI_p4 atpH-atpI AAGCGGCAGAAATCAGTGG ATTTTTGCAACCTTAGCCGC 1181–1269 1.000 77.0
atpH-atpI_p5 atpH-atpI GAAGCGGCAGAAATCAGTGG ATTTTTGCAACCTTAGCCGC 1182–1270 1.000 76.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCTCATTTCCATCATTCCAGA AAAGGATTTGCAGTCCCCTG 1050–1291 1.000 66.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATCATTCCAG AAAGGATTTGCAGTCCCCTG 1051–1292 1.000 66.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCATTTCCATCATTCCAGAGCA AAAGGATTTGCAGTCCCCTG 1047–1288 1.000 66.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCTCATTTCCATCATTCCA AAAGGATTTGCAGTCCCCTG 1051–1292 1.000 65.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCTCATTTCCATCATTCCAGA GCGACACCCAGATTTGAACT 1076–1317 1.000 63.2
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1397–1467 1.000 71.3
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1396–1466 1.000 71.3
petN-psbM_p3 petN-psbM ATGGGGAAGGAGTGGACTTT TGCTACTGCACTGTTCATTCT 1394–1464 1.000 70.4
petN-psbM_p4 petN-psbM ATTGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 1456–1526 1.000 70.1
petN-psbM_p5 petN-psbM TGGGGAAGGAGTGGACTTTA TGCTACTGCACTGTTCATTCT 1393–1463 1.000 68.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Roscoea alpina NC_050946.1 163395 View on NCBI ↗
Roscoea cautleyoides NC_070285.1 163089 View on NCBI ↗
Roscoea cautleyoides var. pubescens OP219812.1 163783 View on NCBI ↗
Roscoea debilis NC_070286.1 163565 View on NCBI ↗
Roscoea forrestii NC_070287.1 163616 View on NCBI ↗
Roscoea praecox NC_070283.1 163420 View on NCBI ↗
Roscoea schneideriana NC_070288.1 163389 View on NCBI ↗
Roscoea scillifolia NC_070284.1 163426 View on NCBI ↗
Roscoea tibetica NC_047420.1 163515 View on NCBI ↗