Markers + reference

Scabiosa

2 species · Caprifoliaceae · Dipsacales

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Species 2
Genome length 158–160 kb
Candidate markers 274
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD LSC 1842 0.2083 0.80 78.7 yes View details
ycf1 IRb 1050 0.4583 0.25 69.6 no View details
ycf1-ccsA SSC 1138 0.4538 0.57 74.0 yes View details
ccsA SSC 972 0.4785 0.84 80.5 yes View details
trnL-UAG-rpl32 SSC 804 0.4630 0.86 81.0 yes View details
ndhF SSC 2268 0.4726 0.88 80.1 yes View details
ycf1 SSC 5769 0.0866 0.83 71.1 yes View details
psbE-petL LSC 1309 0.1770 0.90 91.0 yes View details
trnN-GUU-ycf1 IRb 471 0.2041 0.72 86.9 yes View details
ndhC-trnV-UAC LSC 1005 0.0608 0.95 86.5 yes View details
rbcL-accD LSC 837 0.1332 0.87 81.4 yes View details
infA-rps8 LSC 115 0.0435 1.00 77.5 yes View details
ycf1-trnN-GUU IRa 471 0.4324 0.79 77.2 yes View details
rpl32-ndhF SSC 138 0.3488 0.93 76.9 yes View details
rpl32 SSC 171 0.4699 0.97 75.3 yes View details
atpA-atpF LSC 77 0.0390 1.00 74.9 yes View details
trnL-UAG SSC 80 0.5125 1.00 72.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpA-atpF_p1 atpA-atpF CCTACTTGAAGTACGGTGCC TTGGGAGCGATGAACGAAAT 214–219 1.000 80.2
atpA-atpF_p2 atpA-atpF CCTACTTGAAGTACGGTGCC GGCGCTCTAGGAACTTTGAA 289–294 1.000 80.0
atpA-atpF_p3 atpA-atpF CCTACTTGAAGTACGGTGCC AAGGCGCTCTAGGAACTTTG 291–296 1.000 80.0
atpA-atpF_p4 atpA-atpF CCTACTTGAAGTACGGTGCC CAAGGCGCTCTAGGAACTTT 292–297 1.000 80.0
atpA-atpF_p5 atpA-atpF GAAGTACGGTGCCGGTATTT GGCGCTCTAGGAACTTTGAA 282–287 1.000 80.0
ndhC-trnV-UAC_p1 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT AGAAGGTCTACGGTTCGAGT 1136–1204 1.000 84.8
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CCTTTGCTAATCGGGGCTAA AGAAGGTCTACGGTTCGAGT 1148–1216 1.000 83.1
ndhC-trnV-UAC_p3 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT GAAGGTCTACGGTTCGAGTC 1135–1203 1.000 82.0
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TAATCGGGGCTAAAACTCCG AGAAGGTCTACGGTTCGAGT 1141–1209 1.000 81.0
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAT GTTCGAGTCCGTATAGCCCT 1124–1192 1.000 80.9
rbcL-accD_p1 rbcL-accD AATGAGGGACGTGATCTTGC AACCCGTCCTCAGTAGTCAA 1469 0.500 59.7
rbcL-accD_p2 rbcL-accD AATGAGGGACGTGATCTTGC ACCCGTCCTCAGTAGTCAAA 1468 0.500 59.7
rbcL-accD_p3 rbcL-accD AATGAGGGACGTGATCTTGC CATCGAAGGCAGTGGAATCA 1069 0.500 59.5
rbcL-accD_p4 rbcL-accD AGGGCTGTCTTTGCTAGAGA AACCCGTCCTCAGTAGTCAA 2006 0.500 59.5
rbcL-accD_p5 rbcL-accD AGGGCTGTCTTTGCTAGAGA ACCCGTCCTCAGTAGTCAAA 2005 0.500 59.5
accD_p1 accD TTTCTACCCGCGCTTTCTAC TATACGTAAGGCGGGAGGAG 2656 0.500 59.2
accD_p2 accD TTTCTACCCGCGCTTTCTAC CGGGAGGAGGAAATTCGTTT 2645 0.500 59.1
accD_p3 accD TCTACCCGCGCTTTCTACTA TATACGTAAGGCGGGAGGAG 2654 0.500 58.9
accD_p4 accD TCTACCCGCGCTTTCTACTA CGGGAGGAGGAAATTCGTTT 2643 0.500 58.8
accD_p5 accD AGTTTCCCTGGATCGAGACA TATACGTAAGGCGGGAGGAG 2694 0.500 58.7
psbE-petL_p1 psbE-petL CAACCCGCAATGAATAGGGA GTCGTATCTTGCTCAGACCA 1453–1501 1.000 84.1
psbE-petL_p2 psbE-petL AGAACGTTCTCCTGTGCTTC GTCGTATCTTGCTCAGACCA 1376–1424 1.000 83.2
psbE-petL_p3 psbE-petL ACGAATAACCAACCCGCAAT GTCGTATCTTGCTCAGACCA 1462–1510 1.000 83.1
psbE-petL_p4 psbE-petL TGCTGACGAATAACCAACCC GTCGTATCTTGCTCAGACCA 1467–1515 1.000 83.0
psbE-petL_p5 psbE-petL CGAATAACCAACCCGCAATG GTCGTATCTTGCTCAGACCA 1461–1509 1.000 83.0
infA-rps8_p1 infA-rps8 ACTCGGAACATACCATTGGG CGGGAAGCTCGACTAGAAAG 237 1.000 74.4
infA-rps8_p2 infA-rps8 ACTCGGAACATACCATTGGG TCGGCGGAGAAATTTTGTGT 215 1.000 73.0
infA-rps8_p3 infA-rps8 ACTCGGAACATACCATTGGG CGGCGGAGAAATTTTGTGTT 214 1.000 72.9
infA-rps8_p4 infA-rps8 ACTCGGAACATACCATTGGG AGAATTTTAGGCGGGATGGG 297 1.000 72.7
infA-rps8_p5 infA-rps8 ACTCGGAACATACCATTGGG CGGGATGGGGATTGTCATTC 286 1.000 72.6

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
Scabiosa comosa NC_065840.1 159651 View on NCBI ↗
Scabiosa tschiliensis NC_045050.1 158252 View on NCBI ↗