Markers + reference

Subularia

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 152–153 kb
Candidate markers 261
Primer pairs 95

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
rps16 LSC 1121 0.0212 0.97 62.7 yes View details
trnS-trnG LSC 622 0.0322 1.00 75.1 yes View details
atpF-atpH LSC 442 0.0253 0.98 71.5 yes View details
ycf9-trnG LSC 413 0.0266 1.00 61.2 yes View details
trnT-trnL LSC 820 0.0134 1.00 60.6 yes View details
petA-psbJ LSC 867 0.0185 1.00 60.8 yes View details
petD LSC 1212 0.0066 0.99 50.7 yes View details
ndhF-rpl32 SSC 917 0.0179 0.97 57.7 yes View details
rpl32-trnL SSC 631 0.0211 0.98 72.5 yes View details
trnG-trnR LSC 153 0.0280 0.93 67.2 yes View details
psaJ-rpl33 LSC 457 0.0114 0.96 66.3 yes View details
rps15-ycf1 SSC 354 0.0210 0.94 65.9 yes View details
trnH-psbA LSC 289 0.0144 0.96 64.8 yes View details
petB-petD LSC 197 0.0326 0.93 63.8 yes View details
ndhG SSC 531 0.0113 1.00 63.8 yes View details
trnP-psaJ LSC 348 0.0203 0.99 63.4 yes View details
atpH-atpI LSC 500 0.0101 0.99 63.2 yes View details
trnL-ndhB IRb 609 0.0000 0.94 63.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 335–347 1.000 82.2
trnH-psbA_p2 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 350–362 1.000 82.0
trnH-psbA_p3 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 336–348 1.000 82.0
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 353–365 1.000 81.9
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 351–363 1.000 81.8
trnK_p1 trnK GACTCCCAAGCACACACATT CCCTGATACACACATGACTGG 2973–2992 1.000 69.6
trnK_p2 trnK ACTCCCAAGCACACACATTA CCCTGATACACACATGACTGG 2972–2991 1.000 65.1
trnK_p3 trnK GACTCCCAAGCACACACATT CCTGATACACACATGACTGGA 2972–2991 1.000 63.1
trnK_p4 trnK GACTCCCAAGCACACACATT TCCCTGATACACACATGACTG 2974–2993 1.000 63.1
trnK_p5 trnK GACTCCCAAGCACACACATTA CCCTGATACACACATGACTGG 2973–2992 1.000 62.9
rps16_p1 rps16 AAAGCCGAGTACTCTACCGT TCAATTACACAAACTAGAGGAATGT 1207–1233 1.000 44.1
rps16_p2 rps16 AAGCCGAGTACTCTACCGTT TCAATTACACAAACTAGAGGAATGT 1206–1232 1.000 44.1
rps16_p3 rps16 AAGCCGAGTACTCTACCGTT TGAATCAATTACACAAACTAGAGGA 1210–1236 1.000 44.1
rps16_p4 rps16 AAAGCCGAGTACTCTACCGT TCCATCATTGAATCAATTACACA 1219–1245 1.000 44.0
rps16_p5 rps16 AAGCCGAGTACTCTACCGTT TCCATCATTGAATCAATTACACA 1218–1244 1.000 44.0
trnS-trnG_p1 trnS-trnG CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTT 730–804 1.000 68.5
trnS-trnG_p2 trnS-trnG CCAACGCTTTAGTCCACTCA ATCAAACCGAGAGACCCTTT 729–803 1.000 68.5
trnS-trnG_p3 trnS-trnG AACGCTTTAGTCCACTCAGC AATCAAACCGAGAGACCCTT 728–802 1.000 68.2
trnS-trnG_p4 trnS-trnG AACGCTTTAGTCCACTCAGC ATCAAACCGAGAGACCCTTT 727–801 1.000 68.2
trnS-trnG_p5 trnS-trnG CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTTT 730–804 1.000 66.6
trnG-trnR_p1 trnG-trnR AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 265–275 1.000 51.3
trnG-trnR_p2 trnG-trnR ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 271–281 1.000 51.2
trnG-trnR_p3 trnG-trnR CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 285–295 1.000 50.8
trnG-trnR_p4 trnG-trnR AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 273–283 1.000 50.8
trnG-trnR_p5 trnG-trnR AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 266–276 1.000 50.3
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG CCCGAGGCAGAAGGAAAAAT 624–631 1.000 80.1
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 553–560 1.000 78.3
atpF-atpH_p3 atpF-atpH CCAGTGACCCAAGTAAACGA CCCGAGGCAGAAGGAAAAAT 597–604 1.000 76.8
atpF-atpH_p4 atpF-atpH GGCCAGTGACCCAAGTAAAC CCCGAGGCAGAAGGAAAAAT 599–606 1.000 75.1
atpF-atpH_p5 atpF-atpH CCAGTGACCCAAGTAAACGA TGGCCTGGTTGTAGCATTAG 526–533 1.000 75.1

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
Subularia aquatica MW018466.1 152501 View on NCBI ↗
Subularia monticola NC_065151.1 152135 View on NCBI ↗