Markers + reference

Chusquea

2 species · Poaceae · Poales

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Species 2
Genome length 138–138 kb
Candidate markers 268
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-psbD LSC 984 0.0092 1.00 57.2 yes View details
psaA-ycf3 LSC 617 0.0162 1.00 68.1 yes View details
trnT-UGU-trnL-UAA LSC 701 0.0118 0.97 63.2 yes View details
rbcL-psaI LSC 1298 0.0146 1.00 55.6 yes View details
rps15-ndhF IRb 457 0.0159 0.96 68.7 yes View details
rpl32-trnL-UAG SSC 739 0.0176 1.00 57.4 yes View details
ndhG SSC 531 0.0038 1.00 59.0 yes View details
rpl36-infA LSC 111 0.0183 0.98 64.8 yes View details
atpH-atpF LSC 454 0.0154 1.00 64.6 yes View details
rrn23-rrn4.5 IRb 95 0.0211 1.00 64.6 yes View details
rrn4.5-rrn23 IRa 95 0.0211 1.00 64.6 yes View details
ndhG-ndhI SSC 232 0.0388 1.00 63.6 yes View details
rps4 LSC 606 0.0083 1.00 63.5 yes View details
trnH-GUG-rpl2 IRb 55 0.0182 1.00 63.0 yes View details
rpl2-trnH-GUG IRa 55 0.0182 1.00 63.0 yes View details
psbM-petN LSC 733 0.0068 1.00 62.7 yes View details
ndhC-trnV-UAC LSC 647 0.0062 1.00 62.3 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1128–1129 1.000 79.0
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1115–1116 1.000 78.4
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1114–1115 1.000 76.1
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1107–1108 1.000 75.9
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1101–1102 1.000 75.5
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 895 1.000 68.0
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT GTAGTATGGGGGAGGAGTGG 839 1.000 67.0
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT TAGTATGGGGGAGGAGTGGA 838 1.000 66.2
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTC TAGTAAGTCTCGCTTGGGCT 895 1.000 63.8
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT AGTAGTATGGGGGAGGAGTG 840 1.000 63.0
atpH-atpF_p1 atpH-atpF AGTTGTGGCACTAGCACTTT GGATGGCCAGTGAGCTAAAA 545 1.000 77.2
atpH-atpF_p2 atpH-atpF AGTTGTGGCACTAGCACTTT ATTAAGCCCGAAACTCCCAG 566 1.000 74.8
atpH-atpF_p3 atpH-atpF CTAGTTGTGGCACTAGCACT GGATGGCCAGTGAGCTAAAA 547 1.000 74.0
atpH-atpF_p4 atpH-atpF CTAGTTGTGGCACTAGCACT ATTAAGCCCGAAACTCCCAG 568 1.000 71.6
atpH-atpF_p5 atpH-atpF CTAGTTGTGGCACTAGCACTT GGATGGCCAGTGAGCTAAAA 547 1.000 71.6
psaA-ycf3_p1 psaA-ycf3 TGTTCTTGAGAAATGGCCGG TATAGCGCTTACTCCGGGAA 798–800 1.000 77.2
psaA-ycf3_p2 psaA-ycf3 TTTTACTTCTGGTTCCGGCG TATAGCGCTTACTCCGGGAA 726–728 1.000 77.1
psaA-ycf3_p3 psaA-ycf3 TGTTCTTGAGAAATGGCCGG GCGCTTACTCCGGGAAATTA 794–796 1.000 76.8
psaA-ycf3_p4 psaA-ycf3 TTTTACTTCTGGTTCCGGCG GCGCTTACTCCGGGAAATTA 722–724 1.000 76.8
psaA-ycf3_p5 psaA-ycf3 GGTTTGGCCCATTCCTCAAA TATAGCGCTTACTCCGGGAA 779–781 1.000 75.7
rps4_p1 rps4 AGGTCGATTTAGTTCGGGGA TCAGTTTTAATTTCGATGTATTCTGT 759 1.000 40.5
rps4_p2 rps4 CGGGGAAAGGGGAAGAAAAT TCAGTTTTAATTTCGATGTATTCTGT 745 1.000 40.5
rps4_p3 rps4 TTAGTTCGGGGAAAGGGGAA TCAGTTTTAATTTCGATGTATTCTGT 751 1.000 40.5
rps4_p4 rps4 TTTAGTTCGGGGAAAGGGGA TCAGTTTTAATTTCGATGTATTCTGT 752 1.000 40.5
rps4_p5 rps4 AGGTCGATTTAGTTCGGGGA CAGTTTTAATTTCGATGTATTCTGT 758 1.000 40.5
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG CCGTAGCGTCTACCGATTTC 775–792 1.000 80.8
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA CGATGACCCTCGCATTACAA CCGTAGCGTCTACCGATTTC 767–784 1.000 80.5
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 745–762 1.000 80.0
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG CGTCTACCGATTTCGCCATA 769–786 1.000 79.5
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA CGATGACCCTCGCATTACAA CGTCTACCGATTTCGCCATA 761–778 1.000 79.2

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
Chusquea circinata NC_027490.1 137951 View on NCBI ↗
Chusquea culeou NC_042672.1 138137 View on NCBI ↗