Markers + reference

Scorzonera

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–153 kb
Candidate markers 272
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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 855 0.0243 0.96 63.3 yes View details
rps16-trnQ-UUG LSC 988 0.0173 0.99 65.8 yes View details
trnC-GCA-petN LSC 779 0.0104 0.99 57.2 yes View details
psbM-trnD-GUC LSC 664 0.0151 1.00 58.7 yes View details
trnY-GUA-trnE-UUC LSC 192 0.0312 1.00 63.6 yes View details
trnE-UUC-rpoB LSC 798 0.0177 0.99 60.9 yes View details
rpoC2 LSC 4146 0.0065 1.00 42.7 yes View details
trnT-trnL LSC 577 0.0210 0.99 67.9 yes View details
ndhK LSC 678 0.0103 1.00 50.7 yes View details
psaI-ycf4 LSC 402 0.0149 1.00 50.8 yes View details
ycf1 IRb 495 0.0021 0.98 55.1 no View details
ycf1 SSC 5031 0.0122 1.00 52.7 yes View details
trnW-trnP LSC 164 0.0488 1.00 75.9 yes View details
atpA-trnR-UCU LSC 141 0.0426 1.00 75.1 yes View details
rpl14-rpl16 LSC 127 0.0242 0.98 68.2 yes View details
ycf3-trnS LSC 941 0.0160 0.99 67.6 yes View details
ndhC-trnV-UAC LSC 1242 0.0068 0.94 67.2 yes View details
petD-rpoA LSC 212 0.0283 1.00 64.1 yes View details
rpl16-rps3 LSC 166 0.0316 0.95 63.7 yes View details
rps7-rps12 IRb 53 0.0189 1.00 63.3 yes View details
rps12-rps7 IRa 53 0.0189 1.00 63.3 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TGCCCTAATCAAACGAAATTCA 951–977 1.000 56.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGATGGTATGGACGAATCCC TGCCCTAATCAAACGAAATTCA 950–976 1.000 56.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCCCTAATCAAACGAAATTCA 890–916 1.000 56.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCCCTAATCAAACGAAATTCA 889–915 1.000 56.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC TGCCCTAATCAAACGAAATTCA 905–931 1.000 55.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1061–1067 1.000 80.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1076–1082 1.000 78.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1075–1081 1.000 78.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCAAGAGCACCTTCATTCCT GAGGTTCGAATCCTTCCGTC 1132–1138 1.000 77.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1065–1071 1.000 75.3
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 827–835 1.000 79.7
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 845–853 1.000 77.5
trnC-GCA-petN_p3 trnC-GCA-petN ATTATGTATCGTGGCGGCAT AGCCCAAGCGAGACTTACTA 881–889 1.000 76.5
trnC-GCA-petN_p4 trnC-GCA-petN TTATGTATCGTGGCGGCATG AGCCCAAGCGAGACTTACTA 880–888 1.000 76.3
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 826–834 1.000 73.7
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 779–781 1.000 51.7
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 773–775 1.000 51.3
psbM-trnD-GUC_p3 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 776–778 1.000 50.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCAG TTCAATAGGCAAGAGCACCG 780–782 1.000 49.7
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCA TTCAATAGGCAAGAGCACCG 780–782 1.000 48.8
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC AAAACGAGGGTTCAAGTCCC 265 1.000 78.8
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC ACGAATTTACAGTCCGTCCC AAAACGAGGGTTCAAGTCCC 266 1.000 78.6
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC CGGAGAAAACGAGGGTTCAA 270 1.000 78.0
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC CCCCTATGGTCCAGTGGTTA 306 1.000 77.9
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC TTTCACGGAGAAAACGAGGG 275 1.000 77.9
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCTGA 940–962 1.000 63.7
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 899–921 1.000 63.1
trnE-UUC-rpoB_p3 trnE-UUC-rpoB CCCTCGTTTTCTCCGTGAAA AGTTCTTCTGTCAAACCCTGA 930–952 1.000 62.9
trnE-UUC-rpoB_p4 trnE-UUC-rpoB TTGAACCCTCGTTTTCTCCG AGTTCTTCTGTCAAACCCTGA 935–957 1.000 62.9
trnE-UUC-rpoB_p5 trnE-UUC-rpoB GGGACTTGAACCCTCGTTTT TCAAACCCTGATCAATGAACCT 930–952 1.000 62.3

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
Scorzonera tragopogonoides PX924389.1 152061 View on NCBI ↗
Scorzonera turkestanica PX924391.1 152860 View on NCBI ↗