Markers + reference

Reevesia

9 species · Malvaceae · Malvales

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Species 9
Genome length 162–162 kb
Candidate markers 271
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1148 0.0051 1.00 46.3 yes View details
rps2 LSC 711 0.0015 1.00 28.3 yes View details
petN-psbM LSC 1157 0.0064 0.99 51.4 yes View details
rps4-trnT-UGU LSC 566 0.0100 0.97 61.4 yes View details
clpP LSC 2164 0.0043 1.00 57.0 yes View details
rps19 LSC 279 0.0018 1.00 23.2 yes View details
rpl2 IRb 1519 0.0004 1.00 27.2 no View details
ccsA-ndhD SSC 316 0.0200 1.00 47.9 yes View details
ycf1 SSC 5700 0.0017 1.00 34.8 yes View details
rpl2 IRa 1519 0.0004 1.00 27.2 yes View details
rpl33-rps18 LSC 410 0.0051 1.00 56.5 yes View details
ndhF-rpl32 SSC 1281 0.0039 0.99 56.3 yes View details
rpl2-trnH-GUG IRa 167 0.0216 0.91 55.0 no View details
psbE-petL LSC 906 0.0026 1.00 54.0 yes View details
atpF-atpH LSC 598 0.0043 1.00 53.6 yes View details
trnT-UGU-trnL-UAA LSC 1519 0.0028 1.00 52.2 yes View details
rps19-rpl2 IRb 159 0.0228 0.91 52.0 yes View details
trnE-UUC-trnT-GGU LSC 812 0.0018 1.00 50.2 yes View details
ndhA SSC 2199 0.0013 1.00 50.2 yes View details
rpoB-trnC-GCA LSC 1254 0.0024 0.99 49.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 TGAGTCATCCACACCCTCTT TGTATCGACTGAACCAATGACT 1241–1250 1.000 58.9
rps16_p2 rps16 ATGAGTCATCCACACCCTCT TGTATCGACTGAACCAATGACT 1242–1251 1.000 57.0
rps16_p3 rps16 TGAGTCATCCACACCCTCTT TGTATCGACTGAACCAATGAC 1241–1250 1.000 55.1
rps16_p4 rps16 TGAGTCATCCACACCCTCTT ATGTATCGACTGAACCAATGACT 1242–1251 1.000 54.5
rps16_p5 rps16 TGAGTCATCCACACCCTCTT TCGACTGAACCAATGACTATTCA 1237–1246 1.000 54.1
trnG-GCC_p1 trnG-GCC CTTGATTACGCGCAATTCCC TGCGTGGAATTGCGTATTTA 991–995 1.000 65.2
trnG-GCC_p2 trnG-GCC GCGGCAAGGCTATCATTTTC TGCGTGGAATTGCGTATTTA 1045–1049 1.000 65.0
trnG-GCC_p3 trnG-GCC TGCTCCTATCTTGTGCTCCT TGCGTGGAATTGCGTATTTA 1014–1018 1.000 65.0
trnG-GCC_p4 trnG-GCC ATTCCCCTGTTCGACAAAGG TGCGTGGAATTGCGTATTTA 977–981 1.000 64.5
trnG-GCC_p5 trnG-GCC CTTGATTACGCGCAATTCCC TGCGTGGAATTGCGTATTTAT 991–995 1.000 61.5
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA TGGTTGTAGCATTGGCACTT 682–685 1.000 80.8
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGTTGTAGCATTGGCACTT 710–713 1.000 80.1
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA CTGGTTGTAGCATTGGCACT 683–686 1.000 77.2
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA ATGGGCTGGTTGTAGCATTG 688–691 1.000 76.7
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CTGGTTGTAGCATTGGCACT 711–714 1.000 76.5
rps2_p1 rps2 TCTCTTTTGTGCGATTCAGGA AGAGAGAGGAAGTGTGAAGAGA 818 1.000 50.0
rps2_p2 rps2 TCTCTTTTGTGCGATTCAGGA GAGAGAGGAAGTGTGAAGAGA 817 1.000 46.1
rps2_p3 rps2 TCTCTTTTGTGCGATTCAGGA AGAGAGAGGAAGTGTGAAGAG 818 1.000 46.1
rps2_p4 rps2 CTCTTTTGTGCGATTCAGGA AGAGAGAGGAAGTGTGAAGAGA 817 1.000 45.8
rps2_p5 rps2 TCTCTTTTGTGCGATTCAGG AGAGAGAGGAAGTGTGAAGAGA 818 1.000 45.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTTCTGTTAAGCCCCGATCC CCGGATTTGAACTGGGGAAT 1399–1417 1.000 79.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTTCCCCATTTTCATCCCCG CCGGATTTGAACTGGGGAAT 1324–1342 1.000 79.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCGATCCATGAACCCACAAA CCGGATTTGAACTGGGGAAT 1386–1404 1.000 78.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCATTTTCATCCCCGAGCAT CCGGATTTGAACTGGGGAAT 1319–1337 1.000 77.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTAAGCCCCGATCCATGAAC CCGGATTTGAACTGGGGAAT 1393–1411 1.000 77.5
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA ATTGCTACAGCGCTGTTCAT 1301–1314 1.000 79.9
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA TATTGCTACAGCGCTGTTCA 1302–1315 1.000 78.9
petN-psbM_p3 petN-psbM AGTAAGTCTTGCTTGGGCTG ATTGCTACAGCGCTGTTCAT 1307–1320 1.000 78.4
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TTGCTACAGCGCTGTTCATT 1300–1313 1.000 78.1
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TATTGCTACAGCGCTGTTCA 1308–1321 1.000 77.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Reevesia glaucophylla NC_085247.1 161945 View on NCBI ↗
Reevesia lofouensis NC_063748.1 161894 View on NCBI ↗
Reevesia longipetiolata NC_085245.1 161826 View on NCBI ↗
Reevesia membranacea NC_085248.1 161852 View on NCBI ↗
Reevesia orbicularifolia NC_063747.1 161764 View on NCBI ↗
Reevesia pubescens NC_063749.1 161784 View on NCBI ↗
Reevesia thyrsoidea NC_041441.1 161786 View on NCBI ↗
Reevesia tomentosa NC_085246.1 161830 View on NCBI ↗
Reevesia xuefengensis NC_063750.1 161859 View on NCBI ↗