Markers + reference

Sporoxeia

3 species · Melastomataceae · Myrtales

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Species 3
Genome length 156–157 kb
Candidate markers 263
Primer pairs 105

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 7 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 954 0.0115 1.00 52.7 yes View details
trnC-GCA-petN LSC 846 0.0095 1.00 52.1 yes View details
psbC-trnS-UGA LSC 278 0.0228 1.00 65.7 yes View details
trnS-UGA-psbZ LSC 377 0.0159 1.00 53.9 yes View details
accD-psaI LSC 864 0.0166 1.00 60.5 yes View details
petA-psbJ LSC 909 0.0114 1.00 62.4 yes View details
psbE-petL LSC 1132 0.0088 1.00 51.0 yes View details
petL-petG LSC 181 0.0516 1.00 70.2 yes View details
clpP LSC 2153 0.0085 1.00 48.9 yes View details
ndhF-rpl32 SSC 904 0.0186 0.99 61.5 yes View details
ndhE SSC 306 0.0044 1.00 42.3 yes View details
rps15 SSC 264 0.0076 1.00 43.2 yes View details
rps15-ycf1 SSC 377 0.0213 0.95 65.9 yes View details
rps8-rpl14 LSC 311 0.0266 0.97 74.5 yes View details
trnH-GUG-psbA LSC 231 0.0495 0.99 73.4 yes View details
rps4-trnT-UGU LSC 422 0.0166 1.00 68.5 yes View details
trnT-UGU-trnL-UAA LSC 839 0.0079 1.00 64.1 yes View details
psaC-ndhE SSC 240 0.0307 1.00 63.3 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0452 1.00 62.4 yes View details
rpl2-trnH-GUG IRa 136 0.0000 1.00 62.2 no 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 105 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 285–287 1.000 82.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCTGTTGAAGTTCCAT 299–301 1.000 82.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTGTTGAAGTTCCAT 298–300 1.000 82.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTGTTGAAGTTCCAT 300–302 1.000 82.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCTGCTGTTGAAGTTCCATC 284–286 1.000 79.9
psbA_p1 psbA TCAAAAACTCGTCTAAATTCAGACT CATTGGATGGTTTGGTGTTTTG 1013 1.000 41.3
psbA_p2 psbA TCAAAAACTCGTCTAAATTCAGACT TTGGATGGTTTGGTGTTTTG 1011 1.000 41.3
psbA_p3 psbA TCAAAAACTCGTCTAAATTCAGAC CATTGGATGGTTTGGTGTTTTG 1013 1.000 41.3
psbA_p4 psbA TCAAAAACTCGTCTAAATTCAGACT CATTGGATGGTTTGGTGTTT 1013 1.000 41.3
psbA_p5 psbA CAAAAACTCGTCTAAATTCAGACT CATTGGATGGTTTGGTGTTTTG 1012 1.000 41.3
trnK-UUU_p1 trnK-UUU CCCAAGCACACGAATTCTCT ATCCAACCAAACATTGCCAA 2867–2892 1.000 67.5
trnK-UUU_p2 trnK-UUU CCCAAGCACACGAATTCTCT TCCAACCAAACATTGCCAAT 2866–2891 1.000 67.5
trnK-UUU_p3 trnK-UUU CTCCCAAGCACACGAATTCT ATCCAACCAAACATTGCCAA 2869–2894 1.000 67.5
trnK-UUU_p4 trnK-UUU CTCCCAAGCACACGAATTCT TCCAACCAAACATTGCCAAT 2868–2893 1.000 67.5
trnK-UUU_p5 trnK-UUU TCCCAAGCACACGAATTCTC TCCAACCAAACATTGCCAAT 2867–2892 1.000 67.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 902–915 1.000 79.0
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCAAGACTTACT 920–933 1.000 76.8
trnC-GCA-petN_p3 trnC-GCA-petN ATTTTGGTTTGGCGACATGG CAGCCCAAGCAAGACTTACT 954–967 1.000 75.9
trnC-GCA-petN_p4 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC CAGCCCAAGCAAGACTTACT 897–910 1.000 72.9
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCAGCCCAAGCAAGACTTA 903–916 1.000 72.1
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CGGATCAGGGAATTCTTGGG AAGTATGCCCCCATCGTCTA 238–265 1.000 80.3
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC CGGATCAGGGAATTCTTGGG TAATATGATGGCGGTTGGGC 258–285 1.000 80.2
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC TCATTTCATGGCGGATCAGG TAATATGATGGCGGTTGGGC 269–296 1.000 80.2
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC TCATTTCATGGCGGATCAGG AAGTATGCCCCCATCGTCTA 249–276 1.000 80.2
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC CGGATCAGGGAATTCTTGGG TCGTCTAGTGGTTCAGGACA 225–252 1.000 78.9
psbC-trnS-UGA_p1 psbC-trnS-UGA AACCGGTTCTTTCCATGACC GGGTTCGAATCCCTCTCTCT 327–333 1.000 81.1
psbC-trnS-UGA_p2 psbC-trnS-UGA AACCGGTTCTTTCCATGACC GATGGCTCCGGTCTTGAAAA 377–383 1.000 81.0
psbC-trnS-UGA_p3 psbC-trnS-UGA AACCGGTTCTTTCCATGACC ATTCGATTGCGGAGAGATGG 407–413 1.000 80.9
psbC-trnS-UGA_p4 psbC-trnS-UGA GGTTCTTTCCATGACCCCTC GATGGCTCCGGTCTTGAAAA 373–379 1.000 80.7
psbC-trnS-UGA_p5 psbC-trnS-UGA GGTTCTTTCCATGACCCCTC ATTCGATTGCGGAGAGATGG 403–409 1.000 80.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Sporoxeia clavicalcarata NC_068151.1 156007 View on NCBI ↗
Sporoxeia latifolia MK994820.1 156188 View on NCBI ↗
Sporoxeia petelotii MK994904.1 156529 View on NCBI ↗