Markers + reference

Gyrosphragma

2 species · Lythraceae · Myrtales

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Species 2
Genome length 158–159 kb
Candidate markers 266
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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 461 0.0338 0.84 66.8 yes View details
trnK-UUU-rps16 LSC 880 0.0189 0.96 61.1 yes View details
rps16-trnQ-UUG LSC 1425 0.0155 0.82 60.1 yes View details
psbK-psbI LSC 403 0.0150 0.99 64.0 yes View details
trnR-UCU-atpA LSC 340 0.0240 0.98 59.9 yes View details
atpF-atpH LSC 529 0.0286 0.40 53.7 yes View details
trnE-UUC-trnT-GGU LSC 955 0.0150 0.98 63.4 yes View details
trnT-UGU-trnL-UAA LSC 1146 0.0214 0.98 65.7 yes View details
rbcL-accD LSC 788 0.0166 0.99 59.8 yes View details
accD-psaI LSC 557 0.0259 0.97 75.6 yes View details
pafII-cemA LSC 462 0.0290 0.97 61.0 yes View details
ndhF-rpl32 SSC 1011 0.0168 1.00 54.3 yes View details
rpl32-trnL-UAG SSC 788 0.0245 0.98 71.9 yes View details
ndhD-psaC SSC 113 0.0654 0.95 86.2 yes View details
psbT-pbf1 LSC 60 0.0500 1.00 78.8 yes View details
rpl2-trnH-GUG IRa 68 0.0536 0.82 75.4 no View details
ndhJ-ndhK LSC 113 0.0354 1.00 72.9 yes View details
trnP-UGG-psaJ LSC 450 0.0244 1.00 69.7 yes View details
rps19-rpl2 IRb 77 0.0448 0.87 68.8 yes View details
rps11-rpl36 LSC 112 0.0268 1.00 67.9 yes View details
psbZ-trnG-GCC LSC 373 0.0168 0.96 67.5 yes View details
trnQ-UUG-psbK LSC 389 0.0258 0.99 67.0 yes View details
trnS-GCU-trnG-UCC LSC 734 0.0141 0.96 66.0 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 110 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 CCTCTAGACCTAGCTGCTGT 452–528 1.000 84.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 466–542 1.000 84.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 465–541 1.000 84.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 467–543 1.000 84.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 455–531 1.000 84.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ACAGAATTTCATTTTAATCAAACG 924–950 1.000 44.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ACAGAATTTCATTTTAATCAAACG 923–949 1.000 44.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CAGAATTTCATTTTAATCAAACGA 923–949 1.000 44.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CAGAATTTCATTTTAATCAAACGA 922–948 1.000 44.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA ACAGAATTTCATTTTAATCAAACG 933–959 1.000 44.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ACCACATCGTTTCAACCGAA GAGGTTCGAATCCTTCCGTC 1218–1479 1.000 84.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 1232–1493 1.000 82.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCTGTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1248–1509 1.000 82.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGTCGCACGTTGCTTTTTAC GAGGTTCGAATCCTTCCGTC 1236–1497 1.000 81.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAAGTCGCACGTTGCTTTTT GAGGTTCGAATCCTTCCGTC 1238–1499 1.000 80.8
trnQ-UUG-psbK_p1 trnQ-UUG-psbK ATAGGTATTCCCTGGGACGG TCGGGCAATTTGGCTAAGAA 549–550 1.000 79.9
trnQ-UUG-psbK_p2 trnQ-UUG-psbK ATAGGTATTCCCTGGGACGG CTCGGGCAATTTGGCTAAGA 550–551 1.000 79.5
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GAATACCGGGACCAAAACCC TCGGGCAATTTGGCTAAGAA 513–514 1.000 75.9
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GAATACCGGGACCAAAACCC CTCGGGCAATTTGGCTAAGA 514–515 1.000 75.6
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA TCGGGCAATTTGGCTAAGAA 504–505 1.000 74.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGCCCAGGATTAC 541–548 1.000 77.7
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTCTTCACGCCCAGGATTAC 538–545 1.000 75.7
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTCTTCACGCCCAGGATTAC 539–546 1.000 75.7
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTCTTCACGCCCAGGATTAC 540–547 1.000 75.7
psbK-psbI_p5 psbK-psbI TGTTTGGCAAGCTGCTGTAA TTCTTCACGCCCAGGATTAC 542–549 1.000 73.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAATTAAACCGAGGGACCCC 822–847 1.000 83.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGAATTAAACCGAGGGACCC 823–848 1.000 83.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAATTAAACCGAGGGACCCC 821–846 1.000 83.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGAATTAAACCGAGGGACCC 822–847 1.000 83.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTCGTACAACGGATTAGCA GAATTAAACCGAGGGACCCC 840–865 1.000 82.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Gyrosphragma latipetala NC_082006.1 158746 View on NCBI ↗
Gyrosphragma santos-limae NC_082005.1 158147 View on NCBI ↗