Markers + reference

Sasaella

2 species · Poaceae · Poales

Back to catalogue

Species 2
Genome length 139–140 kb
Candidate markers 283
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 283 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 404 0.0050 1.00 45.0 yes View details
psbM-petN LSC 772 0.0053 0.98 60.6 yes View details
trnC-GCA-rpoB LSC 1160 0.0043 1.00 52.8 yes View details
rpoC2-rps2 LSC 302 0.0133 0.99 59.9 yes View details
ndhC-trnV-UAC LSC 744 0.0081 1.00 63.4 yes View details
atpB LSC 1497 0.0040 1.00 55.7 yes View details
rpl33-rps18 LSC 262 0.0154 0.99 61.5 yes View details
psbB LSC 1527 0.0020 1.00 50.4 yes View details
rpl16 LSC 1502 0.0040 1.00 48.8 yes View details
rpl32-trnL-UAG SSC 703 0.0085 1.00 63.8 yes View details
ndhG SSC 531 0.0038 1.00 54.5 yes View details
psbT-psbN LSC 48 0.1042 1.00 87.5 yes View details
rps14-psaB LSC 155 0.0195 0.99 64.3 yes View details
rps3 LSC 720 0.0083 1.00 63.5 yes View details
ndhG-ndhI SSC 246 0.0366 1.00 62.4 yes View details
accD-psaI LSC 668 0.0060 1.00 62.2 yes View details
psbE-petL LSC 1228 0.0049 1.00 61.6 yes View details
ndhF-rpl32 SSC 864 0.0046 1.00 61.5 yes View details
petA-psbJ LSC 995 0.0041 0.99 61.3 yes View details
trnD-GUC-psbM LSC 986 0.0041 1.00 61.2 yes View details
ndhH-rps15 IRa 137 0.0146 1.00 60.9 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
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTACTCCTCACGCCCAG 548 1.000 78.4
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTTACTCCTCACGCCCAG 545 1.000 76.4
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTTTTACTCCTCACGCCCAG 546 1.000 76.4
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTTTTACTCCTCACGCCCAG 547 1.000 76.4
psbK-psbI_p5 psbK-psbI TGTTTGGCAAGCTGCTGTAA TTTTTACTCCTCACGCCCAG 549 1.000 74.0
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 1071–1072 1.000 48.4
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TGCGAGAATATTGACTTCCA 1103–1104 1.000 47.0
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 1072–1073 1.000 45.3
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 1071–1072 1.000 45.3
trnD-GUC-psbM_p5 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 1072–1073 1.000 44.2
psbM-petN_p1 psbM-petN TGGAAGTCAATATTCTCGCA TAGTAAGTCTCGCTTGGGCT 947–959 1.000 52.0
psbM-petN_p2 psbM-petN TGGAAGTCAATATTCTCGCA GTAGTATGGGGGAGGAGTGG 891–903 1.000 51.0
psbM-petN_p3 psbM-petN TGGAAGTCAATATTCTCGCA TAGTATGGGGGAGGAGTGGA 890–902 1.000 50.3
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTTATTCT TAGTAAGTCTCGCTTGGGCT 922–934 1.000 50.1
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTTATTCT GTAGTATGGGGGAGGAGTGG 866–878 1.000 49.2
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1244–1262 1.000 77.2
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1243–1261 1.000 77.2
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AAGTTCTTCTGCCAAGCCTT 1308–1326 1.000 76.8
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AGTTCTTCTGCCAAGCCTTG 1307–1325 1.000 76.6
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CAAGTTCTTCTGCCAAGCCT 1309–1327 1.000 76.6
rpoC2-rps2_p1 rpoC2-rps2 ATGAGACATCAGAACCCCCA ACCAAAATGAACTCCCGCTT 408–409 1.000 80.9
rpoC2-rps2_p2 rpoC2-rps2 TGAGACATCAGAACCCCCAT ACCAAAATGAACTCCCGCTT 407–408 1.000 80.9
rpoC2-rps2_p3 rpoC2-rps2 ATGAGACATCAGAACCCCCA TTTACGCTTTGCCGAGATGT 465–466 1.000 79.2
rpoC2-rps2_p4 rpoC2-rps2 TGAGACATCAGAACCCCCAT TTTACGCTTTGCCGAGATGT 464–465 1.000 79.2
rpoC2-rps2_p5 rpoC2-rps2 TGAGACATCAGAACCCCCAT CTTTGCCGAGATGTAAGGGG 458–459 1.000 78.2
rps14-psaB_p1 rps14-psaB CTCAAGGGGGAAACTTTGCT TGGATTAGCCCACTTTTCCG 352–353 1.000 79.9
rps14-psaB_p2 rps14-psaB CTCAAGGGGGAAACTTTGCT GGATTAGCCCACTTTTCCGT 351–352 1.000 79.9
rps14-psaB_p3 rps14-psaB CTCAAGGGGGAAACTTTGCT GCAGCTTTCTTGATTGCCTC 312–313 1.000 78.8
rps14-psaB_p4 rps14-psaB CTCAAGGGGGAAACTTTGCT GCTCTTTCCATTGTGCAAGC 381–382 1.000 78.5
rps14-psaB_p5 rps14-psaB CTCAAGGGGGAAACTTTGCT TGGCTCTTTCCATTGTGCAA 383–384 1.000 78.4

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
Sasaella glabra NC_069218.1 139067 View on NCBI ↗
Sasaella kogasensis NC_069219.1 139759 View on NCBI ↗