Markers + reference

Scleromitrion

2 species · Rubiaceae · Gentianales

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Species 2
Genome length 154–154 kb
Candidate markers 267
Primer pairs 100

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 746 0.0242 1.00 59.2 yes View details
rps16-trnQ-UUG LSC 1393 0.0153 0.99 62.2 yes View details
trnS-GCU-trnG-GCC LSC 707 0.0227 1.00 66.0 yes View details
atpH-atpI LSC 1121 0.0213 0.97 61.1 yes View details
rpoB-trnC-GCA LSC 1253 0.0149 0.96 56.3 yes View details
ycf4-cemA LSC 895 0.0205 0.98 69.2 yes View details
petA-psbJ LSC 1039 0.0221 1.00 71.5 yes View details
rpl16 LSC 1504 0.0168 0.99 55.6 yes View details
ycf1 IRb 1770 0.0006 0.99 49.4 no View details
ndhF-rpl32 SSC 832 0.0350 1.00 70.3 yes View details
rpl32-trnL-UAG SSC 704 0.0345 0.99 71.9 yes View details
ycf1 SSC 5478 0.0128 1.00 46.1 yes View details
trnD-GUC-trnY-GUA LSC 107 0.0374 1.00 74.0 yes View details
rps11-rpl36 LSC 132 0.0268 0.85 69.4 yes View details
petN-psbM LSC 688 0.0174 1.00 68.6 yes View details
ndhC-trnV-UAC LSC 514 0.0146 0.94 67.7 yes View details
rpl22-rps19 LSC 130 0.0396 0.78 66.7 yes View details
psbA-trnK-UUU LSC 197 0.0203 1.00 64.1 yes View details
trnS-UGA-psbZ LSC 320 0.0187 1.00 63.2 yes View details
trnR-ACG-trnN-GUU IRb 577 0.0104 1.00 62.7 yes View details
trnN-GUU-trnR-ACG IRa 577 0.0104 1.00 62.7 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
psbA-trnK-UUU_p1 psbA-trnK-UUU TTGCAGAAACGACCCCATAG GGAGGGGTGTTTCCTTGTTT 336–346 1.000 79.4
psbA-trnK-UUU_p2 psbA-trnK-UUU AAACGACCCCATAGGCTTTC GGAGGGGTGTTTCCTTGTTT 330–340 1.000 79.3
psbA-trnK-UUU_p3 psbA-trnK-UUU GAAACGACCCCATAGGCTTT GGAGGGGTGTTTCCTTGTTT 331–341 1.000 79.3
psbA-trnK-UUU_p4 psbA-trnK-UUU GTTGCAGAAACGACCCCATA GGAGGGGTGTTTCCTTGTTT 337–347 1.000 78.8
psbA-trnK-UUU_p5 psbA-trnK-UUU TTGCAGAAACGACCCCATAG CTAGTTCCGGGTTCGAATCC 284–294 1.000 78.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CTCTCCTTCAACCCGACATG TTTCCTTGAAAGGGGTGCTC 1008–1011 1.000 81.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGTGAATACACTCATGGGCA TTTCCTTGAAAGGGGTGCTC 1248–1251 1.000 81.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 CTCTCCTTCAACCCGACATG CTTGAAAGGGGTGCTCAACT 1004–1007 1.000 81.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGTGAATACACTCATGGGCA CTTGAAAGGGGTGCTCAACT 1244–1247 1.000 81.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CTCTCCTTCAACCCGACATG AGCTCTTCAAAACGTGGGTT 1080–1083 1.000 81.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1466–1469 1.000 80.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAAAATCGAAATGGGGCGTG 1525–1528 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1470–1473 1.000 75.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1496–1499 1.000 75.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1458–1461 1.000 75.1
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AAACCGAAAGCAAAGACCCT 820–858 1.000 81.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AACCGAAAGCAAAGACCCTT 819–857 1.000 81.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACCGAAAGCAAAGACCCTTT 818–856 1.000 81.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AACCGAAAGCAAAGACCCTT 818–856 1.000 81.0
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACCGAAAGCAAAGACCCTTT 817–855 1.000 81.0
atpH-atpI_p1 atpH-atpI CTCTACAGCTTGACCTGCAG ACGCAGGTCTTACCAAAAGG 1508–1528 1.000 82.5
atpH-atpI_p2 atpH-atpI CTCTACAGCTTGACCTGCAG TGCTTTGGCTTTACTCACGT 1563 0.500 59.6
atpH-atpI_p3 atpH-atpI CAAACCAGCAGCAATAACGG TGCTTTGGCTTTACTCACGT 1497 0.500 59.5
atpH-atpI_p4 atpH-atpI CCAAACCAGCAGCAATAACG TGCTTTGGCTTTACTCACGT 1498 0.500 59.5
atpH-atpI_p5 atpH-atpI AGTCGGGTCGGTATACCAAT TGCTTTGGCTTTACTCACGT 1863 0.500 59.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CCGGATTTGAACTGGGGAAA 1975–2019 1.000 82.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTCCCTCATTTCCATCCCCT AAGTCTCAACAGCCCGTTTT 1383 0.500 59.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG AAGTCTCAACAGCCCGTTTT 2062 0.500 59.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCCTCATTTCCATCCCCT CCGGATTTGAACTGGGGAAA 1340 0.500 59.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTCCCTCATTTCCATCCCCT GTTGAAGAGCATCCCGAAGT 1489 0.500 59.2

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
Scleromitrion brachypodum NC_057984.1 153617 View on NCBI ↗
Scleromitrion diffusum NC_057985.1 153653 View on NCBI ↗