Markers + reference

Ampelocalamus

13 species · Poaceae · Poales

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Species 13
Genome length 139–140 kb
Candidate markers 264
Primer pairs 80

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 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnfM-CAU-trnT-GGU LSC 2778 0.0107 1.00 70.2 yes View details
rbcL-psaI LSC 1302 0.0088 0.99 55.5 yes View details
petA-psbJ LSC 984 0.0108 1.00 64.2 yes View details
rpl33-rps18 LSC 271 0.0310 0.96 64.0 yes View details
petD LSC 1232 0.0077 1.00 45.4 yes View details
rps15-ndhF IRb 445 0.0227 0.99 72.0 yes View details
ndhF SSC 2220 0.0041 1.00 43.7 yes View details
ndhF-rpl32 SSC 913 0.0136 0.97 75.0 yes View details
trnT-UGU-trnL-UAA LSC 816 0.0089 1.00 74.1 yes View details
trnD-GUC-psbM LSC 997 0.0077 0.99 68.8 yes View details
ycf4-cemA LSC 400 0.0108 1.00 66.3 yes View details
trnS-GCU-psbD LSC 981 0.0076 1.00 65.2 yes View details
rps14-psaB LSC 156 0.0178 0.99 65.1 yes View details
rps19-psbA LSC 127 0.0334 1.00 65.1 no View details
ndhC-trnV-UAC LSC 756 0.0102 1.00 65.0 yes View details
rpoC2-rps2 LSC 306 0.0129 0.94 63.0 yes View details
psbE-petL LSC 1227 0.0076 1.00 62.6 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 80 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 1105–1151 1.000 82.4
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1092–1138 1.000 81.8
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1091–1137 1.000 79.4
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1084–1130 1.000 79.3
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1078–1124 1.000 78.9
trnfM-CAU-trnT-GGU_p1 trnfM-CAU-trnT-GGU CCTCGTGAGCTACCAAACTG CCATGGCATTACTCTACCACC 2911–2987 1.000 74.2
trnfM-CAU-trnT-GGU_p2 trnfM-CAU-trnT-GGU CCTCGTGAGCTACCAAACTG GACTTACGTCTTACCATGGCA 2924–3000 1.000 73.5
trnfM-CAU-trnT-GGU_p3 trnfM-CAU-trnT-GGU CCTCAAGGTTATGAGCCTCG CCATGGCATTACTCTACCACC 2926–2972 0.923 71.5
trnfM-CAU-trnT-GGU_p4 trnfM-CAU-trnT-GGU CCTCAAGGTTATGAGCCTCG GACTTACGTCTTACCATGGCA 2939–2985 0.923 70.7
trnfM-CAU-trnT-GGU_p5 trnfM-CAU-trnT-GGU CCTCAAGGTTATGAGCCTCG TGACTTACGTCTTACCATGGC 2940–2986 0.923 70.7
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 1071–1142 1.000 53.8
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TGCGAGAATATTGACTTCCA 1103–1174 1.000 52.2
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 1072–1143 1.000 50.7
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 1071–1142 1.000 50.7
trnD-GUC-psbM_p5 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 1072–1143 1.000 49.6
rpoC2-rps2_p1 rpoC2-rps2 ATGAGACATCAGAACCCCCA ACTCCCGCCTCTATCATCTC 379–422 1.000 86.8
rpoC2-rps2_p2 rpoC2-rps2 TGAGACATCAGAACCCCCAT ACTCCCGCCTCTATCATCTC 378–421 1.000 86.8
rpoC2-rps2_p3 rpoC2-rps2 ATGAGACATCAGAACCCCCA TGAACTCCCGCCTCTATCAT 382–425 1.000 86.7
rpoC2-rps2_p4 rpoC2-rps2 TGAGACATCAGAACCCCCAT ATGAACTCCCGCCTCTATCA 382–425 1.000 86.7
rpoC2-rps2_p5 rpoC2-rps2 TGAGACATCAGAACCCCCAT TGAACTCCCGCCTCTATCAT 381–424 1.000 86.7
rps14-psaB_p1 rps14-psaB CTCAAGGGGGAAACTTTGCT TGGATTAGCCCACTTTTCCG 343–355 1.000 84.0
rps14-psaB_p2 rps14-psaB CTCAAGGGGGAAACTTTGCT GGATTAGCCCACTTTTCCGT 342–354 1.000 84.0
rps14-psaB_p3 rps14-psaB CTCAAGGGGGAAACTTTGCT GCAGCTTTCTTGATTGCCTC 303–315 1.000 83.4
rps14-psaB_p4 rps14-psaB CTCAAGGGGGAAACTTTGCT GCTCTTTCCATTGTGCAAGC 372–384 1.000 82.3
rps14-psaB_p5 rps14-psaB CTCAAGGGGGAAACTTTGCT TGGCTCTTTCCATTGTGCAA 374–386 1.000 82.2
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG ACAATCAAGTCCGTAGCGTC 908–922 1.000 86.4
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA CGATGACCCTCGCATTACAA ACAATCAAGTCCGTAGCGTC 900–914 1.000 86.1
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACAATCAAGTCCGTAGCGTC 878–892 1.000 85.7
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG CCGTAGCGTCTACCGATTTC 898–912 1.000 84.5
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA ATTTGAACCGATGACCCTCG CAATCAAGTCCGTAGCGTCT 907–921 1.000 84.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Ampelocalamus actinotrichus NC_036815.1 139774 View on NCBI ↗
Ampelocalamus breviligulatus MK393365.1 139311 View on NCBI ↗
Ampelocalamus hirsutissimus MK393366.1 139471 View on NCBI ↗
Ampelocalamus luodianensis PQ472910.1 139645 View on NCBI ↗
Ampelocalamus melicoideus NC_043932.1 139552 View on NCBI ↗
Ampelocalamus mianningensis MK393374.1 139600 View on NCBI ↗
Ampelocalamus microphyllus PQ472911.1 139617 View on NCBI ↗
Ampelocalamus naibunensis NC_030767.1 139860 View on NCBI ↗
Ampelocalamus patellaris MK393370.1 139588 View on NCBI ↗
Ampelocalamus saxatilis NC_043931.1 139618 View on NCBI ↗
Ampelocalamus scandens NC_059867.1 139448 View on NCBI ↗
Ampelocalamus sinovietnamensis NC_063907.1 139846 View on NCBI ↗
Ampelocalamus yongshanensis MK393373.1 139633 View on NCBI ↗