Markers + reference

Memecylon

2 species · Melastomataceae · Myrtales

Back to catalogue

Species 2
Genome length 157–157 kb
Candidate markers 263
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF LSC 1345 0.0045 1.00 54.3 yes View details
atpF-atpH LSC 564 0.0160 1.00 65.5 yes View details
trnE-UUC-trnT-GGU LSC 911 0.0066 1.00 54.7 yes View details
trnT-UGU-trnL-UAA LSC 1044 0.0118 0.98 67.8 yes View details
rbcL-accD LSC 867 0.0096 0.96 59.4 yes View details
clpP LSC 2117 0.0043 1.00 60.0 yes View details
rpl14-rps3 LSC 1734 0.0058 1.00 61.6 yes View details
ycf1 IRb 1887 0.0032 1.00 49.0 no View details
ndhF-rpl32 SSC 841 0.0109 0.98 66.7 yes View details
ycf1 SSC 5595 0.0059 1.00 53.8 yes View details
rpl2-trnH-GUG IRa 138 0.0072 1.00 74.4 no View details
ndhK-ndhC LSC 68 0.0476 0.93 70.2 yes View details
atpH-atpI LSC 938 0.0044 0.97 64.5 yes View details
trnS-GCU-trnR-UCU LSC 1808 0.0057 0.98 63.5 yes View details
rps16-trnQ-UUG LSC 1059 0.0076 1.00 63.2 yes View details
trnC-GCA-ndhJ LSC 855 0.0059 1.00 62.5 yes View details
trnT-GGU-psbD LSC 1381 0.0044 0.99 61.8 yes View details
atpB-rbcL LSC 824 0.0049 1.00 61.5 yes View details
petA-psbJ LSC 950 0.0032 0.99 61.3 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTGCTACCACATCGTTT GAGGTTCGAATCCTTCCGTC 1120–1121 1.000 79.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTGCTACCACATCGTT GAGGTTCGAATCCTTCCGTC 1121–1122 1.000 79.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ACGATCATGTCCGTCAAGTC GAGGTTCGAATCCTTCCGTC 1146–1147 1.000 77.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCTTGCTACCACATCGTTTC GAGGTTCGAATCCTTCCGTC 1119–1120 1.000 75.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGCTTGCTACCACATCGTTT TTCGGAGGTTCGAATCCTTC 1124–1125 1.000 74.4
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAACTTGCGTCCAATAGGA 1882–1923 1.000 70.6
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAACTTGCGTCCAATAGGA 1881–1922 1.000 70.6
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AAGAACTTGCGTCCAATAGGA 1883–1924 1.000 68.5
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AAGAACTTGCGTCCAATAGGA 1882–1923 1.000 68.5
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU AGCAATCCGACGCTTTAGTC AGAACTTGCGTCCAATAGGA 1884–1925 1.000 67.7
atpF_p1 atpF CGTCGGCTTTAATGGTTACC AGTGAAACAAAGGAGATTGT 1439 1.000 40.3
atpF_p2 atpF CGTCGGCTTTAATGGTTACC AAGTGAAACAAAGGAGATTGT 1440 1.000 40.3
atpF_p3 atpF CGTCGGCTTTAATGGTTACC TCTGTAAAAGTGAAACAAAGGAGA 1447 1.000 40.3
atpF_p4 atpF CGTCGGCTTTAATGGTTACC AAAGTGAAACAAAGGAGATTGT 1441 1.000 40.3
atpF_p5 atpF TCGTCGGCTTTAATGGTTACC AGTGAAACAAAGGAGATTGT 1440 1.000 40.3
atpF-atpH_p1 atpF-atpH GGCCCAAGGAAAGGAAAGAA GTCTGGCTTTTATGGAGGCA 681–682 1.000 80.1
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG GTCTGGCTTTTATGGAGGCA 713–714 1.000 79.1
atpF-atpH_p3 atpF-atpH TTGGCCCAAGGAAAGGAAAG GTCTGGCTTTTATGGAGGCA 683–684 1.000 77.9
atpF-atpH_p4 atpF-atpH GGCCCAAGGAAAGGAAAGAA AGTCTGGCTTTTATGGAGGC 682–683 1.000 77.7
atpF-atpH_p5 atpF-atpH CATTGGCCCAAGGAAAGGAA GTCTGGCTTTTATGGAGGCA 685–686 1.000 77.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGCCGCCGCTTATATAGGA 983–1014 1.000 81.4
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCC 995–1026 1.000 81.3
atpH-atpI_p3 atpH-atpI GAAGCAAGTCCGACAGCTAA TAGCCGCCGCTTATATAGGA 1013–1044 1.000 81.0
atpH-atpI_p4 atpH-atpI GGCAGAAATCAGTGGGTTCA TAGCCGCCGCTTATATAGGA 972–1003 1.000 81.0
atpH-atpI_p5 atpH-atpI GAAGCAAGTCCGACAGCTAA TTTTTGCAACTTTAGCCGCC 1025–1056 1.000 80.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 1052 1.000 79.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 1031 1.000 78.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 1028 1.000 78.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 1014 1.000 78.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 993 1.000 78.2

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
Memecylon ligustrifolium MK994913.1 157154 View on NCBI ↗
Memecylon pauciflorum NC_043809.1 157101 View on NCBI ↗