Markers + reference

Echinochloa

7 species · Poaceae · Poales

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Species 7
Genome length 140–140 kb
Candidate markers 340
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 340 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 554 0.0105 1.00 47.7 yes View details
trnD-GUC-psbM LSC 1072 0.0052 1.00 45.2 yes View details
psbM-petN LSC 818 0.0063 1.00 63.5 yes View details
trnT-UGU-trnL-UAA LSC 800 0.0049 1.00 45.3 yes View details
ndhC-trnV-UAC LSC 947 0.0103 1.00 61.4 yes View details
rpl23 LSC 282 0.0162 1.00 41.7 yes View details
petA-psbJ LSC 916 0.0048 1.00 41.1 yes View details
rpl23 IRb 282 0.0020 1.00 35.1 no View details
rpl32-trnL-UAG SSC 517 0.0111 1.00 42.8 yes View details
ccsA SSC 969 0.0022 1.00 36.3 yes View details
rpl23 IRa 282 0.0020 1.00 35.1 no View details
trnF-GAA-ndhJ LSC 588 0.0021 1.00 54.8 yes View details
ccsA-ndhD SSC 200 0.0186 1.00 53.3 yes View details
psbE-petL LSC 1283 0.0036 1.00 51.0 yes View details
trnS-GCU-psbD LSC 989 0.0030 1.00 50.4 yes View details
AU144_gp052 IRb 738 0.0014 1.00 49.2 yes View details
AU144_gp009 IRa 738 0.0014 1.00 49.2 yes View details
trnC-GCA-rpoB LSC 1145 0.0037 1.00 48.4 yes View details
atpH-atpF LSC 474 0.0034 1.00 48.1 yes View details
psaI-ycf4 LSC 357 0.0067 1.00 48.1 yes View details
ndhF-rpl32 SSC 791 0.0031 1.00 48.0 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 623–627 1.000 81.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 634–638 1.000 80.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 627–631 1.000 79.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTAAAACGAAATGGGGCGTG 682–686 1.000 79.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 638–642 1.000 79.3
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1121–1134 1.000 80.2
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1108–1121 1.000 79.7
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1107–1120 1.000 77.3
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1100–1113 1.000 77.1
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1094–1107 1.000 76.7
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TCATTTTGGCTGGCTGTTTT 1237–1265 1.000 67.1
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TCATTTTGGCTGGCTGTTTT 1269–1297 1.000 65.7
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAATGCGGTAGC 1183–1211 1.000 65.6
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AATCATTTTGGCTGGCTGTT 1239–1267 1.000 65.3
trnD-GUC-psbM_p5 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATCATTTTGGCTGGCTGTTT 1238–1266 1.000 65.3
psbM-petN_p1 psbM-petN TGCTACCGCATTGTTCATTC TAGTAAGTCTCGCTTGGGCT 958–980 1.000 73.3
psbM-petN_p2 psbM-petN AAAACAGCCAGCCAAAATGA TAGTAAGTCTCGCTTGGGCT 903–925 1.000 72.8
psbM-petN_p3 psbM-petN TGCTACCGCATTGTTCATTCT TAGTAAGTCTCGCTTGGGCT 958–980 1.000 72.6
psbM-petN_p4 psbM-petN TGCTACCGCATTGTTCATTC GTAGTATGGGGGAGGAGTGG 902–924 1.000 72.5
psbM-petN_p5 psbM-petN TGCTACCGCATTGTTCATTCT GTAGTATGGGGGAGGAGTGG 902–924 1.000 71.8
trnC-GCA-rpoB_p1 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1229–1235 1.000 77.6
trnC-GCA-rpoB_p2 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1228–1234 1.000 77.6
trnC-GCA-rpoB_p3 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AAGTTCTTCTGCCAAGCCTT 1293–1299 1.000 77.1
trnC-GCA-rpoB_p4 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG AGTTCTTCTGCCAAGCCTTG 1292–1298 1.000 77.0
trnC-GCA-rpoB_p5 trnC-GCA-rpoB AAAGGATTTGCAGTCCCCTG CAAGTTCTTCTGCCAAGCCT 1294–1300 1.000 77.0
atpH-atpF_p1 atpH-atpF TTATGGACTGGTTGTGGCAC CGAATGGCCAGTGAGCTAAA 575 1.000 77.8
atpH-atpF_p2 atpH-atpF TGTGGCACTAGCGCTTTTAT CGAATGGCCAGTGAGCTAAA 563 1.000 77.7
atpH-atpF_p3 atpH-atpF TTGTGGCACTAGCGCTTTTA CGAATGGCCAGTGAGCTAAA 564 1.000 77.7
atpH-atpF_p4 atpH-atpF TTATGGACTGGTTGTGGCAC GCCAGTGAGCTAAAAACACG 569 1.000 77.4
atpH-atpF_p5 atpH-atpF TGTGGCACTAGCGCTTTTAT GCCAGTGAGCTAAAAACACG 557 1.000 77.3

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
Echinochloa crus-galli NC_028719.1 139857 View on NCBI ↗
Echinochloa crus-galli var. crus-galli KR822685.1 139860 View on NCBI ↗
Echinochloa crus-galli var. praticola KR822686.1 139846 View on NCBI ↗
Echinochloa esculenta NC_032379.1 139851 View on NCBI ↗
Echinochloa haploclada MW672445.1 139844 View on NCBI ↗
Echinochloa stagnina NC_036128.1 139886 View on NCBI ↗
Echinochloa ugandensis NC_036127.1 139592 View on NCBI ↗