Markers + reference

Rochelia

6 species · Boraginaceae · Boraginales

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Species 6
Genome length 147–147 kb
Candidate markers 264
Primer pairs 105

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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF-atpH LSC 389 0.0043 1.00 30.0 yes View details
ycf3-trnS-GGA LSC 895 0.0044 1.00 40.7 yes View details
rbcL-psaI LSC 1393 0.0047 0.99 46.2 yes View details
cemA-petA LSC 212 0.0173 1.00 42.8 yes View details
petA-psbJ LSC 563 0.0089 1.00 39.2 yes View details
psbB-psbT LSC 172 0.0039 1.00 29.4 yes View details
ycf1 IRb 1098 0.0000 1.00 33.7 no View details
ndhF-rpl32 SSC 584 0.0055 1.00 43.2 yes View details
rpl32-trnL-UAG SSC 576 0.0075 1.00 39.1 yes View details
ndhD SSC 1551 0.0034 1.00 34.6 yes View details
psaC SSC 246 0.0035 1.00 29.3 yes View details
ycf1 SSC 3846 0.0037 1.00 43.2 yes View details
trnS-GCU-trnG-UCC LSC 655 0.0025 0.99 58.7 yes View details
trnT-GGU-psbD LSC 1162 0.0017 0.99 57.0 yes View details
trnL-UAA-trnF-GAA LSC 319 0.0050 1.00 55.9 yes View details
ndhA SSC 2091 0.0025 1.00 54.8 yes View details
clpP LSC 1929 0.0018 1.00 53.2 yes View details
trnC-GCA-petN LSC 783 0.0021 1.00 50.7 yes View details
atpH-atpI LSC 1094 0.0030 1.00 49.9 yes View details
trnE-UUC-trnT-GGU LSC 502 0.0007 1.00 49.3 yes View details
ycf4-cemA LSC 839 0.0032 1.00 49.1 yes View details
rps12-trnV-GAC IRb 1412 0.0000 1.00 49.0 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TGAATCAAACCGAAAGACCCT 732–782 1.000 72.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACCGAAAGACCCT 781–831 1.000 71.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACAACAACGGAAAGAGAGGG TGAATCAAACCGAAAGACCCT 787–837 1.000 70.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAAAGACCCT 718–768 1.000 69.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TGAATCAAACCGAAAGACCCT 713–763 1.000 68.4
atpF-atpH_p1 atpF-atpH GCCCAAAGAAACGAAAGAATC GGACTGGTTGTAGCATTAGCA 473–479 1.000 49.2
atpF-atpH_p2 atpF-atpH GCCCAAAGAAACGAAAGAATC TGGACTGGTTGTAGCATTAGC 474–480 1.000 49.2
atpF-atpH_p3 atpF-atpH GCCCAAAGAAACGAAAGAATC CTGAGGGAAAAATACGAGGCA 538–544 1.000 49.1
atpF-atpH_p4 atpF-atpH GCCCAAAGAAACGAAAGAATC TGAGGGAAAAATACGAGGCA 537–543 1.000 47.9
atpF-atpH_p5 atpF-atpH GCCCAAAGAAACGAAAGAATC AGCTGAGGGAAAAATACGAGG 540–546 1.000 47.0
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTGCAACTTTAGCTGCGG 1174–1185 1.000 79.5
atpH-atpI_p2 atpH-atpI AACAGAAGCGGCAGAAATCA TAGCTGCGGCGTATATAGGT 1163–1174 1.000 79.2
atpH-atpI_p3 atpH-atpI TACCCTCTACAGCTTGACCC TTTTGCAACTTTAGCTGCGG 1259–1270 1.000 79.1
atpH-atpI_p4 atpH-atpI GCGATACCCTCTACAGCTTG TTTTGCAACTTTAGCTGCGG 1263–1274 1.000 79.1
atpH-atpI_p5 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCTGCGG 1192–1203 1.000 79.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 846–873 1.000 81.4
trnC-GCA-petN_p2 trnC-GCA-petN GTATCATTTTGGCGGCATGG TTAAAGCAGCCCAAGCAAGA 898–925 1.000 81.0
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CGCTTCTTCCCCATACTACG 894–921 1.000 80.3
trnC-GCA-petN_p4 trnC-GCA-petN GTATCATTTTGGCGGCATGG CGCTTCTTCCCCATACTACG 946–973 1.000 79.8
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 864–891 1.000 79.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 588–615 1.000 81.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 586–613 1.000 81.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 642–669 1.000 81.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 567–594 1.000 81.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 565–592 1.000 81.1
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1293–1322 1.000 81.0
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1296–1325 1.000 80.8
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1283–1312 1.000 79.9
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1286–1315 1.000 79.7
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1270–1299 1.000 79.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Rochelia bungei PQ580731.1 146781 View on NCBI ↗
Rochelia campanulata PV548698.1 146654 View on NCBI ↗
Rochelia cardiosepala PQ585759.1 146674 View on NCBI ↗
Rochelia leiocarpa PQ580730.1 146814 View on NCBI ↗
Rochelia rectipes PV548696.1 147266 View on NCBI ↗
Rochelia sessiliflora PV548699.1 146993 View on NCBI ↗