Markers + reference

Tripsacum

2 species · Poaceae · Poales

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Species 2
Genome length 141–141 kb
Candidate markers 239
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 239 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ LSC 1514 0.0020 0.99 60.8 yes View details
trnS-psbD LSC 1005 0.0020 1.00 60.1 yes View details
trnG-trnT LSC 1951 0.0010 1.00 49.3 yes View details
trnT-trnE LSC 461 0.0000 1.00 45.7 yes View details
trnY-trnD LSC 337 0.0148 1.00 61.8 yes View details
rps2-atpI LSC 250 0.0080 1.00 57.1 yes View details
atpB-rbcL LSC 821 0.0024 1.00 60.4 yes View details
rpl33-rps18 LSC 305 0.0098 1.00 47.6 yes View details
infA LSC 324 0.0031 1.00 54.8 yes View details
ndhF-rpl32 SSC 852 0.0024 0.99 60.8 yes View details
trnT LSC 72 0.0139 1.00 60.5 yes View details
petA-psbJ LSC 915 0.0011 0.99 60.4 yes View details
rpl20-rps12 LSC 684 0.0015 0.99 60.3 yes View details
trnD-psbM LSC 1058 0.0010 0.99 60.2 yes View details
petD LSC 1226 0.0024 1.00 60.2 yes View details
atpI-atpH LSC 824 0.0024 1.00 60.1 yes View details
ndhC-trnV LSC 949 0.0021 1.00 60.0 yes View details
trnC-rpoB LSC 1241 0.0008 0.99 59.8 yes View details
ndhH SSC 1182 0.0017 1.00 59.7 yes View details
trnT LSC 73 0.0000 1.00 33.8 no View details
trnT LSC 72 0.0000 1.00 19.1 no 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
trnK_p1 trnK TGAAAAACTCAGATTGCTCT TGTCTTGCTAATTCAATGTGGTG 2656–2696 1.000 40.1
trnK_p2 trnK TGAAAAACTCAGATTGCTCT GTCTTGCTAATTCAATGTGGTGT 2655–2695 1.000 40.1
trnK_p3 trnK TGAAAAACTCAGATTGCTCTTTTCT TGTCTTGCTAATTCAATGTGGTG 2656–2696 1.000 40.1
trnK_p4 trnK TGAAAAACTCAGATTGCTCTTTTCT GTCTTGCTAATTCAATGTGGTGT 2655–2695 1.000 40.1
trnK_p5 trnK TGAAAAACTCAGATTGCTCTT TGTCTTGCTAATTCAATGTGGTG 2656–2696 1.000 40.1
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1572–1587 1.000 79.2
rps16-trnQ_p2 rps16-trnQ TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1583–1598 1.000 78.7
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1576–1591 1.000 78.1
rps16-trnQ_p4 rps16-trnQ TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1587–1602 1.000 77.6
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1578–1593 1.000 76.3
trnS-psbD_p1 trnS-psbD ATTAGCAATCCGCCGCTTTA ATAAGCCGGACCATCCTACA 1152–1154 1.000 79.2
trnS-psbD_p2 trnS-psbD ATTAGCAATCCGCCGCTTTA TAAGCCGGACCATCCTACAA 1151–1153 1.000 78.9
trnS-psbD_p3 trnS-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1148–1150 1.000 78.6
trnS-psbD_p4 trnS-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1135–1137 1.000 78.0
trnS-psbD_p5 trnS-psbD GCTTTAGTCCACTCAGCCAT ATAAGCCGGACCATCCTACA 1138–1140 1.000 76.2
trnG-trnT_p1 trnG-trnT ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 2041–2046 1.000 41.0
trnG-trnT_p2 trnG-trnT ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 2037–2042 1.000 40.3
trnG-trnT_p3 trnG-trnT ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 2038–2043 1.000 40.3
trnG-trnT_p4 trnG-trnT AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 2044–2049 1.000 40.3
trnG-trnT_p5 trnG-trnT GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 2043–2048 1.000 40.3
trnT_p1 trnT AGCCCTTTTAACTCAGTGGT CCAAAAATGTGGGCATCTCG 238–239 1.000 67.6
trnT_p2 trnT AGGCATAAGTCATCGGTTCA CCAAAAATGTGGGCATCTCG 201–202 1.000 67.6
trnT_p3 trnT AGCCCTTTTAACTCAGTGGT CAAAAATGTGGGCATCTCGC 237–238 1.000 66.9
trnT_p4 trnT AGGCATAAGTCATCGGTTCA CAAAAATGTGGGCATCTCGC 200–201 1.000 66.9
trnT_p5 trnT TGGTAAGGCATAAGTCATCGG CCAAAAATGTGGGCATCTCG 206–207 1.000 66.8
trnT-trnE_p1 trnT-trnE GACAGAAGTCATCGGTTCGA GCTGCCTCCTTGAAAGAGAG 543–544 1.000 73.0
trnT-trnE_p2 trnT-trnE GACAGAAGTCATCGGTTCGA TGTCCTGAACCACTAGACGA 522–523 1.000 72.8
trnT-trnE_p3 trnT-trnE GACAGAAGTCATCGGTTCGA CCTGAACCACTAGACGATGG 519–520 1.000 70.4
trnT-trnE_p4 trnT-trnE GACAGAAGTCATCGGTTCGA CTGAACCACTAGACGATGGG 518–519 1.000 70.4
trnT-trnE_p5 trnT-trnE GACAGAAGTCATCGGTTCGAA GCTGCCTCCTTGAAAGAGAG 543–544 1.000 69.6

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
Tripsacum dactyloides NC_037087.1 141050 View on NCBI ↗
Tripsacum laxum NC_057482.1 140556 View on NCBI ↗