Markers + reference

Homolepis

2 species · Poaceae · Poales

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Species 2
Genome length 139–139 kb
Candidate markers 267
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 11 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-psbD LSC 956 0.0032 0.99 61.3 yes View details
trnY-GUA-trnD-GUC LSC 351 0.0142 1.00 58.1 yes View details
trnD-GUC-psbM LSC 1058 0.0028 1.00 60.7 yes View details
atpI-atpH LSC 494 0.0041 1.00 56.0 yes View details
psaA LSC 2253 0.0009 1.00 56.2 yes View details
trnT-UGU-trnL-UAA LSC 700 0.0029 1.00 60.4 yes View details
rbcL-psaI LSC 730 0.0041 1.00 61.1 yes View details
psbE-petL LSC 1272 0.0008 1.00 48.7 yes View details
rps11 LSC 432 0.0023 1.00 46.2 yes View details
trnfM-CAU LSC 54 0.0185 1.00 63.1 yes View details
rps3-rpl22 LSC 60 0.0167 1.00 62.1 yes View details
ndhC-trnV-UAC LSC 871 0.0012 0.99 60.1 yes View details
trnL-UAG-ccsA SSC 77 0.0130 1.00 60.0 yes View details
psaA-ycf3 LSC 637 0.0016 1.00 59.7 yes View details
atpB-rbcL LSC 809 0.0000 0.99 59.7 yes View details
ndhF-rpl32 SSC 699 0.0000 0.99 59.7 yes View details
psbM-petN LSC 782 0.0013 1.00 59.5 yes View details
matK LSC 1542 0.0013 1.00 59.4 yes View details
rps16-trnQ-UUG LSC 1181 0.0008 1.00 59.4 yes View details
trnfM-CAU LSC 74 0.0000 1.00 19.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK TCAGAATGGAAAATGTGCAAGT GCAACACCTTGTTCTGACCA 1717 1.000 49.5
matK_p2 matK TCAGAATGGAAAATGTGCAAGT TGCAACACCTTGTTCTGACC 1718 1.000 49.5
matK_p3 matK TCAGAATGGAAAATGTGCAAGTT GCAACACCTTGTTCTGACCA 1717 1.000 46.9
matK_p4 matK TCAGAATGGAAAATGTGCAAGTT TGCAACACCTTGTTCTGACC 1718 1.000 46.9
matK_p5 matK TTCAGAATGGAAAATGTGCAAGT GCAACACCTTGTTCTGACCA 1718 1.000 46.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1253–1255 1.000 78.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1264–1266 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1257–1259 1.000 77.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1268–1270 1.000 76.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAACGAAATGAAATGGGGCG 1314–1316 1.000 76.2
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1094–1101 1.000 79.1
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1081–1088 1.000 78.5
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1080–1087 1.000 76.1
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1073–1080 1.000 75.9
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1067–1074 1.000 75.5
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 475–476 1.000 76.7
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 442–443 1.000 74.3
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 441–442 1.000 74.1
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 474–475 1.000 72.5
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 443–444 1.000 70.9
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTT 1221–1223 1.000 66.2
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AATCATTTTGGCTGGCTGTT 1223–1225 1.000 64.3
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATCATTTTGGCTGGCTGTTT 1222–1224 1.000 64.3
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTTT 1221–1223 1.000 64.1
trnD-GUC-psbM_p5 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TTTGGCTGGCTGTTTTTACA 1217–1219 1.000 63.4
psbM-petN_p1 psbM-petN AAAACAGCCAGCCAAAATGA TAGTAAGTCTCGCTTGGGCT 889 1.000 68.5
psbM-petN_p2 psbM-petN AAAACAGCCAGCCAAAATGA GGCTGCTTTAATGGTGGTCT 873 1.000 68.4
psbM-petN_p3 psbM-petN AAAACAGCCAGCCAAAATGA GTAGTATGGGGGAGGAGTGG 833 1.000 67.5
psbM-petN_p4 psbM-petN AAAACAGCCAGCCAAAATGA TAGTATGGGGGAGGAGTGGA 832 1.000 66.7
psbM-petN_p5 psbM-petN AACAGCCAGCCAAAATGATT TAGTAAGTCTCGCTTGGGCT 887 1.000 66.6

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
Homolepis aturensis NC_036125.1 138757 View on NCBI ↗
Homolepis isocalycia NC_036690.1 138875 View on NCBI ↗