Markers + reference

Microula

2 species · Boraginaceae · Boraginales

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Species 2
Genome length 149–150 kb
Candidate markers 268
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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 303 0.0825 1.00 85.4 yes View details
rps16 LSC 1121 0.0126 0.99 54.4 yes View details
rps16-trnQ-UUG LSC 882 0.0249 0.91 68.0 yes View details
trnS-GCU-trnG-UCC LSC 758 0.0332 0.95 69.3 yes View details
rps4-trnT-UGU LSC 383 0.0437 0.96 81.8 yes View details
trnT-UGU-trnL-UAA LSC 701 0.0133 0.96 62.2 yes View details
atpB-rbcL LSC 700 0.0344 1.00 72.0 yes View details
trnP-UGG-psaJ LSC 418 0.0315 0.99 67.3 yes View details
rps8 LSC 408 0.0196 1.00 55.5 yes View details
ycf1 IRb 1077 0.0096 0.97 52.5 no View details
ndhF-rpl32 SSC 631 0.0281 0.96 65.2 yes View details
ycf1 SSC 5337 0.0146 0.99 46.9 yes View details
rps8-rpl14 LSC 160 0.0566 0.99 82.6 yes View details
atpA-atpF LSC 59 0.1053 0.97 78.0 yes View details
psbJ-psbL LSC 138 0.0376 0.96 77.5 yes View details
trnG-UCC-trnR-UCU LSC 202 0.0432 0.80 70.7 yes View details
rpoC1-rpoB LSC 32 0.0312 1.00 70.5 yes View details
ycf3-trnS-GGA LSC 756 0.0194 0.96 70.2 yes View details
psbT-psbN LSC 69 0.0290 1.00 69.2 yes View details
ndhD-psaC SSC 117 0.0431 0.99 68.5 yes View details
ccsA-ndhD SSC 183 0.0533 0.82 67.5 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 424–428 1.000 82.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 426–430 1.000 82.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 438–442 1.000 82.1
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 437–441 1.000 82.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 439–443 1.000 82.1
rps16_p1 rps16 TCCTTAATCCTTAATTGAATTCCGT CAACTCCATGCCGCTTCTAA 1180 0.500 20.0
rps16_p2 rps16 TCCTTAATCCTTAATTGAATTCCGT AACTCCATGCCGCTTCTAAA 1179 0.500 20.0
rps16_p3 rps16 CCTTAATCCTTAATTGAATTCCGT CAACTCCATGCCGCTTCTAA 1179 0.500 20.0
rps16_p4 rps16 TTCCTTAATCCTTAATTGAATTCCGT CAACTCCATGCCGCTTCTAA 1181 0.500 20.0
rps16_p5 rps16 TCCTTAATCCTTAATTGAATTCCGT ACTCCATGCCGCTTCTAAAT 1178 0.500 20.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 935–962 1.000 85.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TTGACTAGAAATGGGGCGTG 994–1021 1.000 84.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 928–955 1.000 84.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTGACTAGAAATGGGGCGTG 987–1014 1.000 83.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGCGGATCTTGTCTTT GAGGTTCGAATCCTTCCGTC 949–976 1.000 83.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GGGGTAATAGAACGAATCACACT 829–839 1.000 58.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGGGTAATAGAACGAATCACACT 824–834 1.000 57.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GGGGTAATAGAACGAATCACAC 829–839 1.000 55.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TAGTCCACTCAGCCATCTCT GGGGTAATAGAACGAATCACACT 825–835 1.000 54.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGGGTAATAGAACGAATCACAC 824–834 1.000 54.5
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAACAAATTGCGTCCAA 292–329 1.000 75.5
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAACAAATTGCGTCCAA 295–332 1.000 75.3
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC TGGAAACAAATTGCGTCCAA 296–333 1.000 73.1
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT TGGAAACAAATTGCGTCCAA 281–318 1.000 72.4
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU TAACGATGCGGGTTCGATTC TGGAAACAAATTGCGTCCAA 280–317 1.000 72.3
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC TTGGGGGCGATGAAAGAAAT 200–202 1.000 80.6
atpA-atpF_p2 atpA-atpF ACTAATTTCGTCGGCTCGAA TTGGGGGCGATGAAAGAAAT 117–119 1.000 78.4
atpA-atpF_p3 atpA-atpF CGTCGCCTACTTGAAGTACA TTGGGGGCGATGAAAGAAAT 199–201 1.000 76.4
atpA-atpF_p4 atpA-atpF AATTTCGTCGGCTCGAATGG TTGGGGGCGATGAAAGAAAT 114–116 1.000 75.8
atpA-atpF_p5 atpA-atpF CCGTCGCCTACTTGAAGTAC TGGGGGCGATGAAAGAAATA 199–201 1.000 73.5

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
Microula sikkimensis NC_085483.1 149428 View on NCBI ↗
Microula tibetica PP234551.1 149968 View on NCBI ↗