Markers + reference

Rhammatophyllum

3 species · Brassicaceae · Brassicales

Back to catalogue

Species 3
Genome length 154–154 kb
Candidate markers 266
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 312 0.0742 0.96 79.0 yes View details
trnK-AAA-rps16 LSC 691 0.0421 1.00 78.6 yes View details
trnS-AGC-trnG-GGA LSC 628 0.0321 0.96 74.3 yes View details
trnR-AGA-atpA LSC 308 0.0414 0.99 75.1 yes View details
rpoB-trnC-UGC LSC 970 0.0304 1.00 79.8 yes View details
trnE-GAA-trnT-ACC LSC 555 0.0309 0.99 72.2 yes View details
trnT-ACC-psbD LSC 1288 0.0248 0.99 72.4 yes View details
trnL-UUA-trnF-UUC LSC 666 0.0337 1.00 74.7 yes View details
ndhC-trnV-GUA LSC 881 0.0301 0.99 68.9 yes View details
petA-psbJ LSC 911 0.0242 1.00 69.8 yes View details
psbE-petL LSC 1274 0.0234 1.00 77.0 yes View details
ycf1 IRb 1035 0.0013 1.00 32.5 no View details
ycf1 SSC 5349 0.0165 1.00 54.7 yes View details
psaJ-rpl33 LSC 426 0.0377 1.00 81.4 yes View details
ndhK-ndhC LSC 64 0.0376 0.97 79.4 yes View details
ccsA-ndhD SSC 217 0.0586 1.00 78.5 yes View details
rps12-clpP LSC 182 0.0476 1.00 74.8 yes View details
trnS-UCC-rps4 LSC 307 0.0315 1.00 74.1 yes View details
ndhE-ndhG SSC 267 0.0433 0.98 72.6 yes View details
rpl32-trnL-CUA SSC 822 0.0240 0.96 71.3 yes View details
rpl16-rps3 LSC 175 0.0476 1.00 71.2 yes View details
psbM-trnD-GAC LSC 1027 0.0231 1.00 68.1 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TGAGGCTCCATCTACAAATGG 365–392 0.667 60.0
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC TGAGGCTCCATCTACAAATGG 366–393 0.667 59.8
trnH-CAC-psbA_p3 trnH-CAC-psbA AATCCACTTGGCTACATCCG TGAGGCTCCATCTACAAATGG 358–385 0.667 58.6
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTGAGGCTCCATCTACAAATGG 366–393 0.667 55.7
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC TTGAGGCTCCATCTACAAATGG 367–394 0.667 55.4
trnK-AAA-rps16_p1 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT AGGCAGGGATTTTTACAGAA 737–803 1.000 58.6
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT AAGGCAGGGATTTTTACAGA 739–805 1.000 58.5
trnK-AAA-rps16_p3 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT AGGCAGGGATTTTTACAGAA 738–804 1.000 58.5
trnK-AAA-rps16_p4 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT AAGGCAGGGATTTTTACAGA 738–804 1.000 58.5
trnK-AAA-rps16_p5 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT AAGGCAGGGATTTTTACAGAA 738–804 1.000 57.4
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 676–738 1.000 79.6
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 674–736 1.000 79.3
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 671–733 1.000 77.7
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA TCCAACGCTTTAGTCCACTC TGAATCAAACCGAGAGACCC 677–739 1.000 77.3
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GAATCAAACCGAGAGACCCT 675–737 1.000 77.2
trnR-AGA-atpA_p1 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC ACATTAACCGCTGAAGCAGA 452–471 1.000 75.3
trnR-AGA-atpA_p2 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC AGACATTAACCGCTGAAGCA 454–473 1.000 75.3
trnR-AGA-atpA_p3 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC GACATTAACCGCTGAAGCAG 453–472 1.000 72.6
trnR-AGA-atpA_p4 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC TAACCGCTGAAGCAGAAAGC 448–467 1.000 72.4
trnR-AGA-atpA_p5 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC ACCAAGACATTAACCGCTGA 458–477 1.000 72.3
rpoB-trnC-UGC_p1 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC CCGGATTTGAACTGGGGAAA 1058–1175 1.000 82.3
rpoB-trnC-UGC_p2 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC AAAAGGATTTGCAGTCCCCC 1040–1157 1.000 80.2
rpoB-trnC-UGC_p3 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC TCAAGTCTGTTGTTGAGGCG 1082–1199 1.000 79.6
rpoB-trnC-UGC_p4 rpoB-trnC-UGC TGTTCCCTCTTTTCCATCCC CCGGATTTGAACTGGGGAAA 1059–1176 1.000 76.3
rpoB-trnC-UGC_p5 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC AAGTCTGTTGTTGAGGCGG 1080–1197 1.000 74.9
psbM-trnD-GAC_p1 psbM-trnD-GAC TGAGAATGAAGAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1127–1150 1.000 63.2
psbM-trnD-GAC_p2 psbM-trnD-GAC GAGAATGAAGAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1126–1149 1.000 60.0
psbM-trnD-GAC_p3 psbM-trnD-GAC AGGAATGAGAATGAAGAGTGCA TTCAATTGGTCAGAGCACCG 1132–1155 1.000 59.9
psbM-trnD-GAC_p4 psbM-trnD-GAC TGAGAATGAAGAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1128–1151 1.000 59.1
psbM-trnD-GAC_p5 psbM-trnD-GAC AGAATGAAGAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1125–1148 1.000 57.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Rhammatophyllum erysimoides NC_050802.1 154246 View on NCBI ↗
Rhammatophyllum gaudanense NC_050803.1 154288 View on NCBI ↗
Rhammatophyllum pachyrhizum NC_050804.1 154116 View on NCBI ↗