Markers + reference

Neomicrocalamus

2 species · Poaceae · Poales

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Species 2
Genome length 139–139 kb
Candidate markers 263
Primer pairs 80

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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-UCC-trnT-GGU LSC 2013 0.0266 0.97 67.4 yes View details
trnC-GCA-rpoB LSC 1159 0.0138 1.00 64.2 yes View details
rbcL-psaI LSC 1248 0.0128 1.00 66.2 yes View details
trnP-UGG-psaJ LSC 388 0.0155 1.00 57.0 yes View details
petD LSC 1235 0.0024 1.00 47.5 yes View details
infA LSC 324 0.0062 1.00 44.8 yes View details
ndhG-ndhI SSC 238 0.0504 1.00 81.3 yes View details
psbT-psbN LSC 48 0.1042 1.00 87.5 yes View details
infA-rps8 LSC 112 0.0625 1.00 82.8 yes View details
rps3-rpl22 LSC 60 0.0339 0.98 73.5 yes View details
rps19-psbA LSC 118 0.0339 1.00 72.0 no View details
psbZ-trnfM-CAU LSC 800 0.0102 0.98 65.8 yes View details
psbM-petN LSC 736 0.0109 1.00 65.0 yes View details
psaA-ycf3 LSC 616 0.0081 1.00 63.6 yes View details
rpl32-trnL-UAG SSC 734 0.0082 1.00 63.5 yes View details
trnG-UCC LSC 48 0.0208 1.00 63.4 yes View details
atpI-atpH LSC 821 0.0061 1.00 62.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbZ-trnfM-CAU_p1 psbZ-trnfM-CAU TTGCTTCTCCTGATGGTTGG CGAGGCTCATAACCTTGAGG 948–957 1.000 78.4
psbZ-trnfM-CAU_p2 psbZ-trnfM-CAU GCTTCTCCTGATGGTTGGTC CGAGGCTCATAACCTTGAGG 946–955 1.000 78.0
psbZ-trnfM-CAU_p3 psbZ-trnfM-CAU TTGCTTCTCCTGATGGTTGG CAGTTTGGTAGCTCACGAGG 963–972 1.000 78.0
psbZ-trnfM-CAU_p4 psbZ-trnfM-CAU GCTTCTCCTGATGGTTGGTC CAGTTTGGTAGCTCACGAGG 961–970 1.000 77.6
psbZ-trnfM-CAU_p5 psbZ-trnfM-CAU TTGCTTCTCCTGATGGTTGG GAGCGGAGTAGAGCAGTTTG 976–985 1.000 77.3
trnG-UCC_p1 trnG-UCC CAAACTGCTCTACTCCGCTC AAGGAGCCGAATGAAATCCA 238 1.000 71.0
trnG-UCC_p2 trnG-UCC CAAACTGCTCTACTCCGCTC AGGAGCCGAATGAAATCCAA 237 1.000 71.0
trnG-UCC_p3 trnG-UCC TGGTGGACGAAAAAGGTTGA AAGGAGCCGAATGAAATCCA 203 1.000 70.6
trnG-UCC_p4 trnG-UCC TGGTGGACGAAAAAGGTTGA AGGAGCCGAATGAAATCCAA 202 1.000 70.6
trnG-UCC_p5 trnG-UCC ACTGGTGGACGAAAAAGGTT AGGAGCCGAATGAAATCCAA 204 1.000 70.5
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2149–2169 1.000 46.7
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTACGTCTTACCATGGCA 2162–2182 1.000 45.9
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTACCATGGC 2163–2183 1.000 45.9
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC CCATGGCATTACTCTACCACC 2152–2172 1.000 45.6
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT CCATGGCATTACTCTACCACC 2151–2171 1.000 45.6
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 898 1.000 68.2
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT GTAGTATGGGGGAGGAGTGG 842 1.000 67.2
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT TAGTATGGGGGAGGAGTGGA 841 1.000 66.5
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTC TAGTAAGTCTCGCTTGGGCT 898 1.000 64.1
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT AGTAGTATGGGGGAGGAGTG 843 1.000 63.3
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1243–1254 1.000 77.9
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1242–1253 1.000 77.9
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AAGTTCTTCTGCCAAGCCTT 1307–1318 1.000 77.4
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AGTTCTTCTGCCAAGCCTTG 1306–1317 1.000 77.3
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CAAGTTCTTCTGCCAAGCCT 1308–1319 1.000 77.3
atpI-atpH_p1 atpI-atpH TAGCCGCAGCCTATATAGGT GCAGTACCTTGACCAACTCC 955–957 1.000 74.8
atpI-atpH_p2 atpI-atpH TAGCCGCAGCCTATATAGGT AAGCAGCAGCAATTAGTGGA 888–890 1.000 74.8
atpI-atpH_p3 atpI-atpH TAGCCGCAGCCTATATAGGT GCCAATCCAGCAGCAATAAC 910–912 1.000 74.7
atpI-atpH_p4 atpI-atpH TAGCCGCAGCCTATATAGGT ATAACGGAAGCAGCAGCAAT 895–897 1.000 74.5
atpI-atpH_p5 atpI-atpH ATTTTTGCAACGTTAGCCGC GCAGTACCTTGACCAACTCC 968–970 1.000 74.4

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
Neomicrocalamus prainii NC_050769.1 139172 View on NCBI ↗
Neomicrocalamus yunnanensis NC_050767.1 139480 View on NCBI ↗