Markers + reference

Bothriospermum

2 species · Boraginaceae · Boraginales

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Species 2
Genome length 152–153 kb
Candidate markers 261
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnN-GUU-rps15 SSC 6072 0.2986 0.80 73.0 yes View details
ndhH SSC 1182 0.4608 0.87 81.5 yes View details
ndhA SSC 2166 0.4761 0.78 77.6 yes View details
ndhI SSC 501 0.5204 0.88 79.7 yes View details
ndhG SSC 531 0.4580 0.85 79.4 yes View details
ndhE SSC 306 0.4963 0.88 75.4 yes View details
ndhD SSC 1551 0.4741 0.83 80.2 yes View details
ccsA SSC 891 0.5020 0.86 81.5 yes View details
rpl32-ndhF SSC 671 0.4537 0.79 79.0 yes View details
trnL-UAG-rpl32 SSC 610 0.4111 0.89 81.8 yes View details
ndhF SSC 2211 0.4502 0.90 80.8 yes View details
rpl32 SSC 162 0.4444 0.94 77.2 yes View details
rps15-ndhH SSC 100 0.4255 0.94 77.1 yes View details
rps15 SSC 264 0.4453 0.94 76.9 yes View details
ccsA-trnL-UAG SSC 102 0.4000 0.93 76.8 yes View details
psaC SSC 246 0.4753 0.91 76.3 yes View details
ndhD-ccsA SSC 170 0.4605 0.89 75.8 yes View details
ndhG-ndhE SSC 230 0.5179 0.97 75.1 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
trnN-GUU-rps15_p1 trnN-GUU-rps15 AAAAGCTAAGCGTGTGGTCA AAATGAGGGGCGCTTTCTAG 805 0.500 59.3
trnN-GUU-rps15_p2 trnN-GUU-rps15 AAAAGCTAAGCGTGTGGTCA ACCAAGCCGGAGATTGAATC 1085 0.500 59.3
trnN-GUU-rps15_p3 trnN-GUU-rps15 AAAAGCTAAGCGTGTGGTCA GACCAAGCCGGAGATTGAAT 1086 0.500 59.3
trnN-GUU-rps15_p4 trnN-GUU-rps15 TTCTTGAACGGGCCATATCG AAATGAGGGGCGCTTTCTAG 1116 0.500 59.2
trnN-GUU-rps15_p5 trnN-GUU-rps15 TTCTTGAACGGGCCATATCG ACCAAGCCGGAGATTGAATC 1396 0.500 59.2
rps15_p1 rps15 ATGGTAAGGGTGCGGATAGA GGTCTGTGCCCCAATATCTG 1298 0.500 59.0
rps15_p2 rps15 ATGGTAAGGGTGCGGATAGA CACCAATAATGCCTACGCCT 1542 0.500 59.0
rps15_p3 rps15 ATGGTAAGGGTGCGGATAGA TCCACCAATAATGCCTACGC 1544 0.500 58.9
rps15_p4 rps15 ATGGTAAGGGTGCGGATAGA TCCTAACTGTTCGGGTCCAT 1181 0.500 58.8
rps15_p5 rps15 ATGGTAAGGGTGCGGATAGA AACACCATGCATTGATGGGT 986 0.500 58.8
rps15-ndhH_p1 rps15-ndhH TTGGGAAAACGTCAACGACT GGTCTGTGCCCCAATATCTG 592 0.500 59.6
rps15-ndhH_p2 rps15-ndhH TTGGGAAAACGTCAACGACT CACCAATAATGCCTACGCCT 836 0.500 59.5
rps15-ndhH_p3 rps15-ndhH TTGGGAAAACGTCAACGACT TCCACCAATAATGCCTACGC 838 0.500 59.5
rps15-ndhH_p4 rps15-ndhH TTGGGAAAACGTCAACGACT TCCTAACTGTTCGGGTCCAT 475 0.500 59.4
rps15-ndhH_p5 rps15-ndhH TTGGGAAAACGTCAACGACT AACACCATGCATTGATGGGT 280 0.500 59.3
ndhH_p1 ndhH TTGGGAAAACGTCAACGACT TAGGGCTTGAAGGATTCCCA 1616 0.500 59.6
ndhH_p2 ndhH TTGGGAAAACGTCAACGACT GCTAGGGCTTGAAGGATTCC 1618 0.500 59.6
ndhH_p3 ndhH TTGGGAAAACGTCAACGACT AGTCCAAGGGGAGCAATACT 1822 0.500 59.6
ndhH_p4 ndhH TTGGGAAAACGTCAACGACT CATCTGCTAGGGCTTGAAGG 1623 0.500 59.5
ndhH_p5 ndhH TTGGGAAAACGTCAACGACT CCATCTGCTAGGGCTTGAAG 1624 0.500 59.5
ndhA_p1 ndhA GAAACCCGGCGTTTTGTTAG GGTAACCGACCTAACGCAAT 2988 0.500 59.6
ndhA_p2 ndhA AGCCCCAAAAGGAGAATTGG GGTAACCGACCTAACGCAAT 2866 0.500 59.4
ndhA_p3 ndhA GCGTAGGCATTATTGGTGGA GCGTGGGACAAGGTAATCAT 2906 0.500 59.4
ndhA_p4 ndhA GAAACCCGGCGTTTTGTTAG GCGTGGGACAAGGTAATCAT 2649 0.500 59.4
ndhA_p5 ndhA AGCCCCAAAAGGAGAATTGG GCGTGGGACAAGGTAATCAT 2527 0.500 59.2
ndhI_p1 ndhI GCGATGGAGCAGTGATGTTA CCCACGGTCCAAAGATGAAA 1770 0.500 58.8
ndhI_p2 ndhI GCGATGGAGCAGTGATGTTA GCGGCAGCTACAAAATAGGA 1665 0.500 56.8
ndhI_p3 ndhI GCGATGGAGCAGTGATGTTA CGTAAATAAGGAGTTGCGCG 1682 0.500 56.7
ndhI_p4 ndhI GCGATGGAGCAGTGATGTTA TCCCGTACCATGACGTATCT 1850 0.500 56.7
ndhI_p5 ndhI GCGATGGAGCAGTGATGTTA CCCGATCCCAGAGAGACTAA 1536 0.500 56.6

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
Bothriospermum chinense PZ289360.1 152939 View on NCBI ↗
Bothriospermum zeylanicum NC_065834.1 152117 View on NCBI ↗