Markers + reference

Iseilema

7 species · Poaceae · Poales

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Species 7
Genome length 140–140 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

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbZ-trnG-GCC LSC 289 0.0081 1.00 56.7 yes View details
trnG-UCC-trnM-CAU LSC 2003 0.0038 1.00 52.9 yes View details
trnT-GGU-trnE-UUC LSC 469 0.0041 1.00 43.1 yes View details
petA-psbJ LSC 905 0.0073 1.00 56.2 yes View details
psbE-petL LSC 1270 0.0040 1.00 62.5 yes View details
rps8 LSC 411 0.0049 1.00 32.8 yes View details
rpl32-trnL-UAG SSC 535 0.0091 1.00 57.1 yes View details
ccsA SSC 966 0.0033 1.00 36.8 yes View details
rps16-trnQ-UUG LSC 1075 0.0037 1.00 57.1 yes View details
psaA-ycf3 LSC 609 0.0026 0.99 56.8 yes View details
atpB-rbcL LSC 797 0.0020 1.00 55.8 yes View details
rps12-trnV-GAC IRb 1740 0.0012 1.00 55.2 yes View details
trnV-GAC-rps12 IRa 1740 0.0012 1.00 55.2 yes View details
trnD-GUC-psbM LSC 1055 0.0042 1.00 54.2 yes View details
ndhD SSC 1503 0.0021 1.00 53.5 yes View details
ndhF-rpl32 SSC 892 0.0012 1.00 52.8 yes View details
rps16 LSC 1096 0.0019 1.00 52.6 yes View details
ycf3-trnS-GGA LSC 608 0.0044 1.00 52.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GCAAAACTCAGATTGCTCTT GAGCGTCCGGTGTAATTTCA 2652–2656 1.000 50.3
trnK-UUU_p2 trnK-UUU GCAAAACTCAGATTGCTCTT AGCGTCCGGTGTAATTTCAT 2651–2655 1.000 49.4
trnK-UUU_p3 trnK-UUU GCAAAACTCAGATTGCTCTTT GAGCGTCCGGTGTAATTTCA 2652–2656 1.000 48.9
trnK-UUU_p4 trnK-UUU GCAAAACTCAGATTGCTCTT ATGTTTTGACAGGAGCGTCC 2664–2668 1.000 48.7
trnK-UUU_p5 trnK-UUU GCAAAACTCAGATTGCTCTTT AGCGTCCGGTGTAATTTCAT 2651–2655 1.000 48.0
rps16_p1 rps16 TGGCACGATATAAATGTAGCA TCTCGATACCTTTTTGCAATGA 1243–1252 1.000 40.8
rps16_p2 rps16 GGTACTAAGGACCCTCTCC TCTCGATACCTTTTTGCAATGA 1174–1183 1.000 40.8
rps16_p3 rps16 AGAAAGAGGCAAATTGTGTC TCTCGATACCTTTTTGCAATGA 1207–1216 1.000 40.8
rps16_p4 rps16 GGACTAAGAAAGAGGCAAATTGT TCTCGATACCTTTTTGCAATGA 1213–1222 1.000 40.8
rps16_p5 rps16 TGGCACGATATAAATGTAGCAA TCTCGATACCTTTTTGCAATGA 1243–1252 1.000 40.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1141–1152 1.000 79.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1152–1163 1.000 79.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1145–1156 1.000 78.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1156–1167 1.000 77.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1147–1158 1.000 76.7
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TCGAACCCGTATCTTCTCCT 452–457 1.000 76.8
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC TCGAACCCGTATCTTCTCCT 450–455 1.000 76.4
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TTACCACTGAACTACGCTCG 417–422 1.000 75.5
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC TTACCACTGAACTACGCTCG 415–420 1.000 75.1
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CCGTATCTTCTCCTTGGCAA 446–451 1.000 74.8
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TCGAACCGATGACTTCTGTC 1981–2222 1.000 51.3
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CGAACCGATGACTTCTGTCT 1980–2221 1.000 51.2
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU AGAACGAATCACACTTTTACCAC TCGAACCGATGACTTCTGTC 1984–2225 1.000 50.2
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT TCGAACCGATGACTTCTGTC 1983–2224 1.000 50.2
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT CGAACCGATGACTTCTGTCT 1982–2223 1.000 50.2
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GACAGAAGTCATCGGTTCGA GCTGCCTCCTTGAAAGAGAG 546–555 1.000 74.2
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GACAGAAGTCATCGGTTCGA TGTCCTGAACCACTAGACGA 525–534 1.000 74.1
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC GACAGAAGTCATCGGTTCGA CCTGAACCACTAGACGATGG 522–531 1.000 71.6
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GACAGAAGTCATCGGTTCGA CTGAACCACTAGACGATGGG 521–530 1.000 71.6
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC GACAGAAGTCATCGGTTCGAA GCTGCCTCCTTGAAAGAGAG 546–555 1.000 70.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Iseilema anthephoroides NC_059831.1 139777 View on NCBI ↗
Iseilema hubbardii NC_059832.1 139716 View on NCBI ↗
Iseilema laxum NC_059833.1 139580 View on NCBI ↗
Iseilema macratherum NC_030611.1 139643 View on NCBI ↗
Iseilema membranaceum NC_059834.1 139582 View on NCBI ↗
Iseilema prostratum NC_059835.1 139806 View on NCBI ↗
Iseilema vaginiflorum NC_059836.1 139635 View on NCBI ↗