Markers + reference

Amomum

4 species · Zingiberaceae · Zingiberales

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Species 4
Genome length 163–164 kb
Candidate markers 273
Primer pairs 90

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
trnS-GCU-trnG-GCC LSC 748 0.0590 0.99 92.4 yes View details
atpH-atpI LSC 1394 0.0360 0.81 73.6 yes View details
trnE-UUC-trnT-GGU LSC 895 0.0338 0.94 72.8 yes View details
psbE-petL LSC 1252 0.0216 1.00 73.5 yes View details
rps19 IRb 279 0.0018 1.00 25.3 no View details
ycf1 IRb 3893 0.0028 1.00 43.9 no View details
ndhF-rpl32 SSC 623 0.0322 0.98 72.1 yes View details
ccsA-ndhD SSC 300 0.0529 0.96 79.1 yes View details
psaC-ndhE SSC 715 0.0326 0.92 71.9 yes View details
ycf1 IRa 5457 0.0173 1.00 55.9 yes View details
rps19 IRa 279 0.0108 1.00 36.3 yes View details
rps19-psbA IRa 247 0.0816 0.94 75.9 no View details
rpl22-rps19 IRb 180 0.0773 0.93 74.7 yes View details
atpF-atpH LSC 524 0.0347 0.97 74.4 yes View details
ndhC-trnV-UAC LSC 1582 0.0139 1.00 74.0 yes View details
trnH-GUG-rpl2 IRb 43 0.0736 1.00 73.2 yes View details
rpl2-trnH-GUG IRa 43 0.1047 1.00 73.2 yes View details
ycf1-ndhF SSC 68 0.0613 0.85 72.1 yes View details
rps11-rpl36 LSC 122 0.0441 0.99 71.4 yes View details
trnL-UAG-ccsA SSC 108 0.0324 1.00 71.2 yes View details
trnT-UGU-trnL-UAA LSC 1069 0.0210 0.99 70.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 817–990 1.000 62.5
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 816–989 1.000 62.5
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 820–993 1.000 61.4
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 819–992 1.000 61.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 818–991 1.000 61.4
atpF-atpH_p1 atpF-atpH AGTGGCCCAAGTAAACGAAA TGGTTGTGGCATTAGCACTT 592–608 1.000 84.8
atpF-atpH_p2 atpF-atpH CAGTGGCCCAAGTAAACGAA TGGTTGTGGCATTAGCACTT 593–609 1.000 84.4
atpF-atpH_p3 atpF-atpH TGGCCCAAGTAAACGAAAGA TGGTTGTGGCATTAGCACTT 590–606 1.000 82.5
atpF-atpH_p4 atpF-atpH GTGGCCCAAGTAAACGAAAG TGGTTGTGGCATTAGCACTT 591–607 1.000 82.0
atpF-atpH_p5 atpF-atpH TTAAACCCGAAACTTCCGGC TGGTTGTGGCATTAGCACTT 620–636 1.000 81.1
atpH-atpI_p1 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACCTTAGCCGC 976–1566 1.000 87.0
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA ATTTTTGCAACCTTAGCCGC 891–1481 1.000 86.8
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATTTTTGCAACCTTAGCCGC 949–1539 1.000 86.5
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC ATTTTTGCAACCTTAGCCGC 953–1543 1.000 85.9
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC ATTTTTGCAACCTTAGCCGC 908–1498 1.000 85.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 657–998 1.000 85.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 636–977 1.000 85.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 636–977 1.000 85.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 615–956 1.000 85.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 633–974 1.000 85.3
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 954–1176 1.000 85.8
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GAGTCGAACCGATGACCATC ACCAATTTCGCCATATCCCC 985–1207 1.000 85.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 962–1184 1.000 85.3
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GAGTCGAACCGATGACCATC TAGCGTCTACCAATTTCGCC 993–1215 1.000 85.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 977–1199 1.000 84.0
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CCTAACCGGGGCTAAAACTC AGAAGGTCTACGGTTCGAGT 1705–1846 1.000 84.1
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CTAACCGGGGCTAAAACTCC AGAAGGTCTACGGTTCGAGT 1704–1845 1.000 84.1
ndhC-trnV-UAC_p3 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT AGAAGGTCTACGGTTCGAGT 1698–1839 1.000 83.3
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TTTCTCCGGTCCTTCCCTAA AGAAGGTCTACGGTTCGAGT 1720–1861 1.000 81.7
ndhC-trnV-UAC_p5 ndhC-trnV-UAC CTAACCGGGGCTAAAACTCC GAAGGTCTACGGTTCGAGTC 1703–1844 1.000 81.3

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
Amomum cinnamomeum PX987620.1 163763 View on NCBI ↗
Amomum krervanh NC_036935.1 162766 View on NCBI ↗
Amomum longipetiolatum PP542016.1 163269 View on NCBI ↗
Amomum velutinum PP542018.1 163311 View on NCBI ↗