Markers + reference

Isachne

2 species · Poaceae · Poales

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Species 2
Genome length 136–136 kb
Candidate markers 265
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-psbD LSC 991 0.0152 1.00 57.2 yes View details
trnG-UCC-trnT-GGU LSC 1713 0.0158 1.00 59.4 yes View details
trnD-GUC-psbM LSC 968 0.0166 1.00 62.1 yes View details
psbM-petN LSC 773 0.0230 0.95 69.7 yes View details
trnC-GCA-rpoB LSC 1157 0.0164 1.00 61.2 yes View details
atpI-atpH LSC 829 0.0134 0.99 67.2 yes View details
trnT-UGU-trnL-UAA LSC 778 0.0169 0.99 69.7 yes View details
rbcL-psaI LSC 920 0.0164 1.00 55.8 yes View details
psbE-petL LSC 1278 0.0157 1.00 62.5 yes View details
petD LSC 1220 0.0115 1.00 50.5 yes View details
ndhF-rpl32 SSC 864 0.0204 0.97 65.3 yes View details
psaC-ndhE SSC 483 0.0232 0.98 65.6 yes View details
rpl14-rpl16 LSC 88 0.0460 0.99 72.6 yes View details
atpF-atpA LSC 93 0.0323 1.00 71.0 yes View details
petG-trnW-CCA LSC 126 0.0246 0.97 69.6 yes View details
rps19-psbA LSC 117 0.0187 0.91 66.9 no View details
psaA-ycf3 LSC 635 0.0127 1.00 66.5 yes View details
ndhC-trnV-UAC LSC 870 0.0116 0.99 66.4 yes View details
trnT-GGU-trnE-UUC LSC 461 0.0174 1.00 66.1 yes View details
atpH-atpF LSC 465 0.0091 0.94 65.4 yes View details
trnF-GAA-ndhJ LSC 571 0.0158 1.00 65.0 yes View details
clpP-psbB LSC 505 0.0119 1.00 63.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TAGGCTTGTACTTTCGCGTC GGCGTACGGTGTAATTCCAT 2899–2912 1.000 80.2
trnK-UUU_p2 trnK-UUU GACTCCCAAGCACACGTATT GGCGTACGGTGTAATTCCAT 2830–2843 1.000 79.5
trnK-UUU_p3 trnK-UUU AAAACACCGAACCATCCGAT GGCGTACGGTGTAATTCCAT 2967–2980 1.000 78.7
trnK-UUU_p4 trnK-UUU TGCGGTCAATAAGGTAGGGA GGCGTACGGTGTAATTCCAT 2992 0.500 58.5
trnK-UUU_p5 trnK-UUU TAGGCTTGTACTTTCGCGTC CCGGATCTGCTCATTTTGGT 2988 0.500 57.9
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACTCTACCAAGGGCTATAGTCA 1052–1054 1.000 60.8
trnS-GCU-psbD_p2 trnS-GCU-psbD GTCCCAAATGATCCAAGGGG ACTCTACCAAGGGCTATAGTCA 1121–1123 1.000 59.2
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACTCTACCAAGGGCTATAGTCA 1038–1040 1.000 57.8
trnS-GCU-psbD_p4 trnS-GCU-psbD AGTCCACTCAGCCATCTCTC ACTCTACCAAGGGCTATAGTCA 1033–1035 1.000 57.0
trnS-GCU-psbD_p5 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACTCTACCAAGGGCTATAGTCAT 1052–1054 1.000 56.4
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT AGCACTAAACGAAAAGCCCT 1833–1844 1.000 50.8
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACTTCCCTCTTACCATGGCA 1860–1871 1.000 50.3
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC AGCACTAAACGAAAAGCCCT 1836–1847 1.000 49.7
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT AGCACTAAACGAAAAGCCCT 1835–1846 1.000 49.7
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACTTCCCTCTTACCATGGCA 1862–1873 1.000 49.2
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 581–582 1.000 68.3
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 560–561 1.000 68.2
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 544–545 1.000 68.2
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 523–524 1.000 68.1
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG GCTGCCTCCTTGAAAGAGAG 549–550 1.000 67.5
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TAATCATTTTGGCTGGCCGT 1133–1136 1.000 76.3
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGGCTGGCCGTTTTTACATA 1124–1127 1.000 75.9
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TTTTGGCTGGCCGTTTTTAC 1127–1130 1.000 75.7
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG CATTTTGGCTGGCCGTTTTT 1129–1132 1.000 74.3
trnD-GUC-psbM_p5 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TTGGCTGGCCGTTTTTACAT 1125–1128 1.000 72.2
psbM-petN_p1 psbM-petN ACGGCCAGCCAAAATGATTA AGTATGGGGGAGAAGTGGAC 785–819 1.000 83.0
psbM-petN_p2 psbM-petN ACGGCCAGCCAAAATGATTA GTATGGGGGAGAAGTGGACT 784–818 1.000 83.0
psbM-petN_p3 psbM-petN TATGTAAAAACGGCCAGCCA AGTATGGGGGAGAAGTGGAC 794–828 1.000 82.6
psbM-petN_p4 psbM-petN TATGTAAAAACGGCCAGCCA GTATGGGGGAGAAGTGGACT 793–827 1.000 82.6
psbM-petN_p5 psbM-petN ACGGCCAGCCAAAATGATTA TATGGGGGAGAAGTGGACTC 783–817 1.000 82.6

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
Isachne albens NC_035530.1 135867 View on NCBI ↗
Isachne distichophylla NC_025236.1 135782 View on NCBI ↗