Markers + reference

Sarcopyramis

2 species · Melastomataceae · Myrtales

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Species 2
Genome length 153–153 kb
Candidate markers 262
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 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1036 0.0145 1.00 57.4 yes View details
rps16-trnQ-UUG LSC 946 0.0163 0.97 57.9 yes View details
trnQ-UUG-psbK LSC 322 0.0190 0.98 52.5 yes View details
trnE-UUC-trnT-GGU LSC 913 0.0133 0.99 59.3 yes View details
rps4-trnT-UGU LSC 391 0.0256 1.00 65.2 yes View details
rpl33-rps18 LSC 215 0.0140 1.00 47.5 yes View details
psbB-psbT LSC 175 0.0000 1.00 29.5 yes View details
ycf1 IRb 1905 0.0010 1.00 50.4 no View details
ndhF-rpl32 SSC 329 0.0304 1.00 57.7 yes View details
ndhE-ndhG SSC 230 0.0448 0.97 66.4 yes View details
rps15 SSC 264 0.0189 1.00 48.8 yes View details
ycf1 SSC 5451 0.0092 1.00 45.2 yes View details
psbT-psbN LSC 72 0.1389 1.00 83.3 yes View details
trnM-CAU-atpE LSC 177 0.0282 1.00 68.7 yes View details
trnT-GGU-psbD LSC 1161 0.0130 0.99 66.8 yes View details
trnC-GCA-petN LSC 820 0.0134 1.00 66.5 yes View details
trnR-ACG-trnN-GUU IRb 595 0.0035 0.96 64.2 yes View details
trnN-GUU-trnR-ACG IRa 595 0.0035 0.96 64.2 yes View details
cemA-petA LSC 201 0.0199 1.00 63.9 yes View details
ndhD-psaC SSC 141 0.0429 0.99 63.7 yes View details
rpl2-trnH-GUG IRa 136 0.0000 1.00 63.5 no View details
matK-trnK-UUU LSC 775 0.0090 1.00 63.4 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
matK-trnK-UUU_p1 matK-trnK-UUU AGGAAGTTGTGTTGCCAAGA AACGGTAGAGTACTCGGCTT 855 1.000 75.8
matK-trnK-UUU_p2 matK-trnK-UUU AGGAAGTTGTGTTGCCAAGA ACGGTAGAGTACTCGGCTTT 854 1.000 75.8
matK-trnK-UUU_p3 matK-trnK-UUU AGGAAGTTGTGTTGCCAAGA GGGTTGCTAACTCAACGGTA 868 1.000 73.5
matK-trnK-UUU_p4 matK-trnK-UUU AGGAAGTTGTGTTGCCAAGA TTCGGGTTGCTAACTCAACG 871 1.000 73.2
matK-trnK-UUU_p5 matK-trnK-UUU AGGAAGTTGTGTTGCCAAGAT ACGGTAGAGTACTCGGCTTT 854 1.000 70.9
rps16_p1 rps16 AGGGAGAGGGGGATCTACTA ATACCAGTTAAAACCCGGGG 1131–1133 1.000 70.3
rps16_p2 rps16 AGGGAGAGGGGGATCTACTA ACATACCAGTTAAAACCCGGG 1133–1135 1.000 68.2
rps16_p3 rps16 GAGGGAGAGGGGGATCTACT ATACCAGTTAAAACCCGGGG 1132–1134 1.000 68.0
rps16_p4 rps16 GGGAGAGGGGGATCTACTAG ATACCAGTTAAAACCCGGGG 1130–1132 1.000 67.4
rps16_p5 rps16 AGGGAGAGGGGGATCTACTA TACCAGTTAAAACCCGGGGG 1130–1132 1.000 66.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1011–1013 1.000 76.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1014–1016 1.000 74.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TAAGAATCCACGGACGATCC GAGGTTCGAATCCTTCCGTC 1047–1049 1.000 73.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 1015–1017 1.000 71.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 1013–1015 1.000 70.9
trnQ-UUG-psbK_p1 trnQ-UUG-psbK CCTTACCACTTGGCCACG AGGGTGAAATGAAAACAGAAGT 392–394 1.000 42.4
trnQ-UUG-psbK_p2 trnQ-UUG-psbK CCTTACCACTTGGCCACG AAGGGTGAAATGAAAACAGAAGT 393–395 1.000 42.4
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GCCTTACCACTTGGCCAC AGGGTGAAATGAAAACAGAAGT 393–395 1.000 42.4
trnQ-UUG-psbK_p4 trnQ-UUG-psbK CCTTACCACTTGGCCACG GGGTGAAATGAAAACAGAAGT 391–393 1.000 42.4
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GCCTTACCACTTGGCCAC AAGGGTGAAATGAAAACAGAAGT 394–396 1.000 42.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 883–890 1.000 80.3
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACAACCATTAAAGCAGCCCA 890–897 1.000 80.3
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CCTTTAGAGTCCACTTCGCC 942–949 1.000 80.2
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CTTTAGAGTCCACTTCGCCC 941–948 1.000 80.2
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 877–884 1.000 78.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 1054–1067 1.000 80.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 1033–1046 1.000 80.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 1030–1043 1.000 79.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 995–1008 1.000 79.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 1051–1064 1.000 79.3

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
Sarcopyramis bodinieri MK994810.1 153312 View on NCBI ↗
Sarcopyramis napalensis MK994843.1 153291 View on NCBI ↗