Markers + reference

Myrsine

4 species · Primulaceae · Ericales

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Species 4
Genome length 155–160 kb
Candidate markers 273
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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1755 0.0184 0.98 64.7 yes View details
trnS-GCU-trnS-CGA LSC 720 0.0199 0.95 65.7 yes View details
trnT-GGU-psbD LSC 1342 0.0129 0.99 63.0 yes View details
atpB-rbcL LSC 761 0.0484 1.00 77.8 yes View details
petA-psbJ LSC 651 0.0297 1.00 71.0 yes View details
psaJ-rpl33 LSC 519 0.0225 1.00 63.6 yes View details
rpl16 LSC 1429 0.0102 1.00 53.2 yes View details
ycf1 IRb 977 0.0015 1.00 45.4 no View details
ndhF-rpl32 SSC 836 0.0212 1.00 63.8 yes View details
ccsA-ndhD SSC 272 0.0482 0.94 74.2 yes View details
ycf1 SSC 5571 0.0121 1.00 46.9 yes View details
rpoC1-rpoB LSC 27 0.0370 1.00 82.8 yes View details
rpl16-rps3 LSC 165 0.0646 1.00 76.2 yes View details
trnM-CAU-atpE LSC 217 0.0330 1.00 71.2 yes View details
trnE-UUC-trnT-GGU LSC 871 0.0098 0.97 69.7 yes View details
atpH-atpI LSC 743 0.0100 0.99 66.7 yes View details
trnF-GAA-ndhJ LSC 717 0.0126 1.00 64.7 yes View details
atpF-atpH LSC 387 0.0103 0.99 63.4 yes View details
psaI-ycf4 LSC 423 0.0110 1.00 62.9 yes View details
petN-psbM LSC 981 0.0133 1.00 62.4 yes View details
trnT-UGU-trnL-UAA LSC 799 0.0090 1.00 61.4 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1779–1820 1.000 79.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1782–1823 1.000 77.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GGGTTTTGGTCCCGGTATTC 1800–1841 1.000 75.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 1783–1824 1.000 74.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TAAGGCAACGGGTTTTGGTC 1809–1850 1.000 74.3
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CTTTCGTCCACTCAGCCATC ACCACTAAACTATACCCGCT 744–781 1.000 62.7
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA TTTCGTCCACTCAGCCATCT ACCACTAAACTATACCCGCT 743–780 1.000 59.6
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA TCCACTCAGCCATCTCTCC ACCACTAAACTATACCCGCT 738–775 1.000 59.1
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTT ACCACTAAACTATACCCGCT 759–796 1.000 58.0
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA TTCGTCCACTCAGCCATCT ACCACTAAACTATACCCGCT 742–779 1.000 57.2
atpF-atpH_p1 atpF-atpH CCAGTAGCCGAAAGAAACGA CGGAGGGAAAAATACGAGGT 536–559 1.000 76.1
atpF-atpH_p2 atpF-atpH CCAGTAGCCGAAAGAAACGA CGAGGCGGAGGGAAAAATAC 541–564 1.000 76.0
atpF-atpH_p3 atpF-atpH CCAGTAGCCGAAAGAAACGA GAGGCGGAGGGAAAAATACG 540–563 1.000 76.0
atpF-atpH_p4 atpF-atpH CCAGTAGCCGAAAGAAACGA GCGGAGGGAAAAATACGAGG 537–560 1.000 76.0
atpF-atpH_p5 atpF-atpH CCAGTAGCCGAAAGAAACGA GGCGGAGGGAAAAATACGAG 538–561 1.000 76.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCCGCTG 823–834 1.000 80.9
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCCGCTG 815–826 1.000 80.7
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCCGCTG 879–890 1.000 80.1
atpH-atpI_p4 atpH-atpI AAGCGGCAGAAATCAATGGA TTTTGCAACTTTAGCCGCTG 816–827 1.000 79.9
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCCGCTG 824–835 1.000 79.7
rpoC1-rpoB_p1 rpoC1-rpoB TGGCCCAAGCACTTATTTGT CCTGAGGATGCTCCAGAATC 219–221 1.000 76.6
rpoC1-rpoB_p2 rpoC1-rpoB GATTTTCTTGGCCCAAGCAC CCTGAGGATGCTCCAGAATC 227–229 1.000 76.0
rpoC1-rpoB_p3 rpoC1-rpoB ATTTTCTTGGCCCAAGCACT CCTGAGGATGCTCCAGAATC 226–228 1.000 74.4
rpoC1-rpoB_p4 rpoC1-rpoB GGGTTTTGTCACCTCTCCAA CCTGAGGATGCTCCAGAATC 266–268 1.000 73.7
rpoC1-rpoB_p5 rpoC1-rpoB TTTCTTGGCCCAAGCACTTA CCTGAGGATGCTCCAGAATC 224–226 1.000 73.7
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TCTCGTGCCTACTGCTTTTC 1134–1166 1.000 80.2
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT CTCGTGCCTACTGCTTTTCT 1133–1165 1.000 80.1
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ACTGCATTGTTCGTTCTCGT 1148–1180 1.000 79.7
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT GTTCTCGTGCCTACTGCTTT 1136–1168 1.000 79.2
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT CTGCATTGTTCGTTCTCGTG 1147–1179 1.000 79.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Myrsine africana NC_045100.1 156433 View on NCBI ↗
Myrsine linearis NC_067768.1 159627 View on NCBI ↗
Myrsine semiserrata PZ095203.1 154796 View on NCBI ↗
Myrsine stolonifera NC_045112.1 156953 View on NCBI ↗