Markers + reference

Allomorphia

5 species · Melastomataceae · Myrtales

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Species 5
Genome length 156–156 kb
Candidate markers 265
Primer pairs 110

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 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0124 1.00 45.7 yes View details
trnQ-UUG-psbK LSC 331 0.0269 1.00 56.2 yes View details
trnS-GCU-trnR-UCU LSC 1788 0.0177 1.00 59.4 yes View details
trnE-UUC-trnT-GGU LSC 969 0.0197 1.00 66.2 yes View details
trnT-GGU-psbD LSC 1218 0.0125 1.00 55.0 yes View details
ndhC-trnV-UAC LSC 729 0.0173 1.00 63.5 yes View details
accD-psaI LSC 847 0.0177 0.99 60.9 yes View details
psbE-petL LSC 1145 0.0091 1.00 56.3 yes View details
ycf1 SSC 1926 0.0043 1.00 48.5 no View details
ndhF SSC 2238 0.0118 1.00 52.2 yes View details
ndhF-rpl32 SSC 908 0.0263 1.00 79.5 yes View details
ccsA-ndhD SSC 322 0.0360 1.00 66.0 yes View details
ycf1 SSC 5526 0.0098 1.00 46.1 yes View details
ndhD-psaC SSC 143 0.0396 1.00 73.1 yes View details
trnT-UGU-trnL-UAA LSC 838 0.0156 1.00 68.9 yes View details
atpH-atpI LSC 959 0.0105 0.98 66.9 yes View details
ndhK-ndhC LSC 60 0.0367 0.98 65.9 yes View details
rps8-rpl14 LSC 283 0.0223 1.00 65.5 yes View details
atpF-atpH LSC 513 0.0152 1.00 63.1 yes View details
petL-petG LSC 192 0.0391 1.00 63.0 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0407 1.00 62.5 yes View details
trnC-GCA-petN LSC 846 0.0087 1.00 62.1 yes View details
rpl20-rps12 LSC 836 0.0063 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA GATCCACTTGGCTACATCCG CTTAGAGCCCTGTCTACGGA 1737–1753 1.000 82.0
psbA_p2 psbA GATCCACTTGGCTACATCCG TAGAGCCCTGTCTACGGAAG 1735–1751 1.000 82.0
psbA_p3 psbA GATCCACTTGGCTACATCCG TCTTAGAGCCCTGTCTACGG 1738–1754 1.000 82.0
psbA_p4 psbA CAATCCACTGCCTTGATCCA CTTAGAGCCCTGTCTACGGA 1751–1767 1.000 82.0
psbA_p5 psbA CAATCCACTGCCTTGATCCA TAGAGCCCTGTCTACGGAAG 1749–1765 1.000 82.0
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GCTGACTGAGCGGGTTAAAT CTTACAGCAGCTTGCCAAAC 1173–1202 1.000 82.7
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GCTGACTGAGCGGGTTAAAT CCGGGATTACGTCTTGGATC 1657–1685 1.000 81.5
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GCTGACTGAGCGGGTTAAAT AAACTTACAGCAGCTTGCCA 1176–1205 1.000 80.7
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GCTGACTGAGCGGGTTAAAT AACTTACAGCAGCTTGCCAA 1175–1204 1.000 80.7
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GCTGACTGAGCGGGTTAAAT ACTTACAGCAGCTTGCCAAA 1174–1203 1.000 80.7
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU GCTTTAGTCCACTCAGCCAT AGAAGACCTATGTCCTATCCA 1850–1885 1.000 45.4
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AGTCCACTCAGCCATCTCTC AGAAGACCTATGTCCTATCCA 1845–1880 1.000 44.6
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU GCTTTAGTCCACTCAGCCAT AGAAGACCTATGTCCTATCCAT 1850–1885 1.000 43.9
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU TAGTCCACTCAGCCATCTCT AGAAGACCTATGTCCTATCCA 1846–1881 1.000 43.9
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AGTCCACTCAGCCATCTCTC AGAAGACCTATGTCCTATCCAT 1845–1880 1.000 43.9
atpF-atpH_p1 atpF-atpH GGCCCAAGGAAAGGAAAGAA GGATTGGTTGTCGCTTTAGC 591–598 1.000 79.1
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG GGATTGGTTGTCGCTTTAGC 623–630 1.000 78.0
atpF-atpH_p3 atpF-atpH TTGGCCCAAGGAAAGGAAAG GGATTGGTTGTCGCTTTAGC 593–600 1.000 76.8
atpF-atpH_p4 atpF-atpH CATTGGCCCAAGGAAAGGAA GGATTGGTTGTCGCTTTAGC 595–602 1.000 76.3
atpF-atpH_p5 atpF-atpH ATTGGCCCAAGGAAAGGAAA GGATTGGTTGTCGCTTTAGC 594–601 1.000 75.8
atpH-atpI_p1 atpH-atpI GAAGCAAGTCCGACAGCTAA TAGCCGCCGCTTATATAGGA 997–1065 1.000 84.0
atpH-atpI_p2 atpH-atpI GAAGCAAGTCCGACAGCTAA TTTTTGCAACTTTAGCCGCC 1009–1077 1.000 84.0
atpH-atpI_p3 atpH-atpI AACAGAAGCGGCAGAAATCA TAGCCGCCGCTTATATAGGA 965–1033 1.000 83.9
atpH-atpI_p4 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTTGCAACTTTAGCCGCC 977–1045 1.000 83.8
atpH-atpI_p5 atpH-atpI CAGCAGCAATAACAGAAGCG TAGCCGCCGCTTATATAGGA 975–1043 1.000 83.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 919 1.000 80.7
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CCTTTAGAGTCCACTTCGCC 978 1.000 80.6
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CTTTAGAGTCCACTTCGCCC 977 1.000 80.6
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 913 1.000 79.2
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGACGACCATTAAAGCAGCC 928 1.000 78.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Allomorphia arborescens NC_068155.1 156319 View on NCBI ↗
Allomorphia inaequata NC_068159.1 156415 View on NCBI ↗
Allomorphia malaccensis NC_068189.1 155845 View on NCBI ↗
Allomorphia setosa NC_068146.1 155933 View on NCBI ↗
Allomorphia sulcata NC_068167.1 156220 View on NCBI ↗