Markers + reference

Blastus

8 species · Melastomataceae · Myrtales

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Species 8
Genome length 155–156 kb
Candidate markers 255
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 9 remaining regions by MarkerSeek score (out of 255 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 997 0.0107 0.99 62.1 yes View details
trnS-GCU-trnG-UCC LSC 774 0.0158 1.00 58.9 yes View details
atpH-atpI LSC 940 0.0105 0.99 72.3 yes View details
psbZ-trnG-UCC LSC 312 0.0377 0.96 69.6 yes View details
trnL-UAA-trnF-GAA LSC 301 0.0227 0.99 64.1 yes View details
rps18-rpl20 LSC 340 0.0162 0.98 55.7 yes View details
rpl22 LSC 504 0.0068 1.00 50.3 yes View details
ndhF-rpl32 SSC 398 0.0416 0.97 80.3 yes View details
ccsA-ndhD SSC 318 0.0267 1.00 61.9 yes View details
psaC SSC 246 0.0010 1.00 22.2 yes View details
rps15-trnN-GUU SSC 6144 0.0072 0.99 47.5 yes View details
trnH-GUG-psbA LSC 199 0.0336 0.98 73.4 yes View details
ndhD-psaC SSC 143 0.0360 1.00 68.4 yes View details
rpl2-trnH-GUG IRa 136 0.0018 1.00 65.6 no View details
psbT-psbN LSC 72 0.0794 1.00 65.5 yes View details
ndhA-ndhH SSC 1 0.2500 1.00 63.7 yes View details
psbM-trnD-GUC LSC 718 0.0075 1.00 63.2 yes View details
trnR-UCU-atpA LSC 309 0.0142 1.00 63.1 yes View details
atpF LSC 1432 0.0059 0.95 62.7 yes View details
trnS-UGA-psbZ LSC 377 0.0113 1.00 61.0 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGCTGCTGTTGAAGTTCCAT 253–303 1.000 86.0
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTGTTGAAGTTCCAT 266–316 1.000 85.6
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCTGTTGAAGTTCCAT 267–317 1.000 85.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTGTTGAAGTTCCAT 268–318 1.000 85.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GACCTAGCTGCTGTTGAAGT 258–308 1.000 84.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 938–1085 1.000 79.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 941–1088 1.000 77.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 942–1089 1.000 75.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TAAGGCAACGGGTTTTGGTC 968–1115 1.000 74.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 940–1087 1.000 74.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 771–840 1.000 54.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 770–839 1.000 54.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 772–841 1.000 53.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 771–840 1.000 53.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTTACCACTAAACTATACCCGC 773–842 1.000 52.1
trnR-UCU-atpA_p1 trnR-UCU-atpA AACACCAAACCAGAAGCCAA CATTCACCGAGGAAGCAGAA 495–550 1.000 80.4
trnR-UCU-atpA_p2 trnR-UCU-atpA ACACCAAACCAGAAGCCAAA CATTCACCGAGGAAGCAGAA 494–549 1.000 80.4
trnR-UCU-atpA_p3 trnR-UCU-atpA AACACCAAACCAGAAGCCAA AAGACATTCACCGAGGAAGC 499–554 1.000 80.4
trnR-UCU-atpA_p4 trnR-UCU-atpA ACACCAAACCAGAAGCCAAA AAGACATTCACCGAGGAAGC 498–553 1.000 80.4
trnR-UCU-atpA_p5 trnR-UCU-atpA AGAACACCAAACCAGAAGCC CATTCACCGAGGAAGCAGAA 497–552 1.000 79.1
atpF_p1 atpF CGTCGGCTTTAATGGTTACC TCTGTAAAAGAAAGGGGATTGT 1462–1528 1.000 44.9
atpF_p2 atpF TCGTCGGCTTTAATGGTTACC TCTGTAAAAGAAAGGGGATTGT 1463–1529 1.000 44.9
atpF_p3 atpF CGTCGGCTTTAATGGTTACC ATCTGTAAAAGAAAGGGGATTGT 1463–1529 1.000 44.9
atpF_p4 atpF CGTCGGCTTTAATGGTTACCA TCTGTAAAAGAAAGGGGATTGT 1462–1528 1.000 44.9
atpF_p5 atpF CGTCGGCTTTAATGGTTACC CTGTAAAAGAAAGGGGATTGT 1461–1527 1.000 44.9
atpH-atpI_p1 atpH-atpI GAAGCAAGTCCGACAGCTAA TAGCCGCCGCTTATATAGGA 956–1066 1.000 84.3
atpH-atpI_p2 atpH-atpI GAAGCAAGTCCGACAGCTAA TTTTTGCAACTTTAGCCGCC 968–1078 1.000 84.2
atpH-atpI_p3 atpH-atpI AACAGAAGCGGCAGAAATCA TAGCCGCCGCTTATATAGGA 924–1034 1.000 84.2
atpH-atpI_p4 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTTGCAACTTTAGCCGCC 936–1046 1.000 84.1
atpH-atpI_p5 atpH-atpI CAGCAGCAATAACAGAAGCG TAGCCGCCGCTTATATAGGA 934–1044 1.000 83.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Blastus auriculatus MK335944.1 155981 View on NCBI ↗
Blastus borneensis NC_068158.1 155818 View on NCBI ↗
Blastus cavaleriei MK994908.1 155999 View on NCBI ↗
Blastus dunnianus MK994804.1 156004 View on NCBI ↗
Blastus eglandulosus NC_068154.1 155928 View on NCBI ↗
Blastus ernae MK994800.1 155994 View on NCBI ↗
Blastus mollissimus MK994863.1 155410 View on NCBI ↗
Blastus pauciflorus NC_046463.1 155983 View on NCBI ↗