Markers + reference

Echinacanthus

3 species · Acanthaceae · Lamiales

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Species 3
Genome length 152–153 kb
Candidate markers 265
Primer pairs 85

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ(UUG) LSC 1096 0.0612 0.94 84.2 yes View details
trnC(GCA)-petN LSC 889 0.0575 0.95 81.8 yes View details
rrn16 IRb 1491 0.1011 1.00 86.9 yes View details
ndhF SSC 2229 0.0476 1.00 73.3 yes View details
rpl32-trnL-UAG SSC 493 0.0914 0.95 81.8 yes View details
ndhA SSC 2145 0.0360 1.00 70.4 yes View details
ycf1 SSC 5478 0.0560 0.99 72.6 yes View details
rrn16 IRa 1491 0.1024 1.00 86.6 yes View details
ndhC-trnV(UAC) LSC 1050 0.0512 0.97 83.6 yes View details
petN-psbM LSC 996 0.0469 0.97 82.8 yes View details
petA-psbJ LSC 1013 0.0380 0.97 82.7 yes View details
trnE(UUC)-trnT(GGU) LSC 615 0.0509 0.98 82.4 yes View details
trnG(GCC)-trnfM(CAU) LSC 168 0.0646 0.95 82.0 yes View details
trnD(GUC)-trnY(GUA) LSC 80 0.0684 0.97 81.7 yes View details
ycf3-trnS(GGA) LSC 599 0.0544 0.98 81.0 yes View details
rpoB-trnC(GCA) LSC 1203 0.0503 0.95 80.6 yes View details
rps4-trnL(UUA) LSC 1054 0.0411 0.89 80.0 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ(UUG)_p1 rps16-trnQ(UUG) TGCTTTCTACCACATCGTTTCA GAGGTTCGAATCCTTCCGTC 1129–1172 1.000 71.8
rps16-trnQ(UUG)_p2 rps16-trnQ(UUG) GCTTTCTACCACATCGTTTCA GAGGTTCGAATCCTTCCGTC 1128–1171 1.000 70.4
rps16-trnQ(UUG)_p3 rps16-trnQ(UUG) TGCTTTCTACCACATCGTTTC GAGGTTCGAATCCTTCCGTC 1129–1172 1.000 70.4
rps16-trnQ(UUG)_p4 rps16-trnQ(UUG) TGCTTTCTACCACATCGTTT GAGGTTCGAATCCTTCCGTC 1129–1172 1.000 68.3
rps16-trnQ(UUG)_p5 rps16-trnQ(UUG) GCTTTCTACCACATCGTTTCAA GAGGTTCGAATCCTTCCGTC 1128–1171 1.000 68.0
rpoB-trnC(GCA)_p1 rpoB-trnC(GCA) CGAGCCCATATCCTTGCTTT CCGAGGAAGAATTCTGCGAA 1812–1857 1.000 87.1
rpoB-trnC(GCA)_p2 rpoB-trnC(GCA) TGCCAAACCCCAATCAATGA CGCTTCTACCGTGGATTCAA 1584 0.333 53.1
rpoB-trnC(GCA)_p3 rpoB-trnC(GCA) TGCCAAACCCCAATCAATGA CCGAGGAAGAATTCTGCGAA 1441 0.333 53.1
rpoB-trnC(GCA)_p4 rpoB-trnC(GCA) CGAGCCCATATCCTTGCTTT CGCTTCTACCGTGGATTCAA 2000 0.333 53.1
rpoB-trnC(GCA)_p5 rpoB-trnC(GCA) TGCCAAACCCCAATCAATGA ACAAAGCATCAACGACCTGT 1485 0.333 52.9
trnC(GCA)-petN_p1 trnC(GCA)-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCGAGATTTACT 946–959 1.000 89.1
trnC(GCA)-petN_p2 trnC(GCA)-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 999–1012 1.000 88.9
trnC(GCA)-petN_p3 trnC(GCA)-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 997–1010 1.000 88.9
trnC(GCA)-petN_p4 trnC(GCA)-petN TTTCCCCAGTTCAAATCCGG AGGTCCGGTTTTCCTCACTA 1329–1352 0.667 73.9
trnC(GCA)-petN_p5 trnC(GCA)-petN TTTCCCCAGTTCAAATCCGG AAAGGTCCGGTTTTCCTCAC 1331–1354 0.667 73.9
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA TCATTCTAGTTCCTACCGCCT 1092–1110 1.000 79.4
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACCGCCT 1090–1108 1.000 79.4
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA TCTAGTTCCTACCGCCTTTCT 1088–1106 1.000 78.9
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT TCTAGTTCCTACCGCCTTTCT 1086–1104 1.000 78.9
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG TCATTCTAGTTCCTACCGCCT 1089–1107 1.000 78.8
trnD(GUC)-trnY(GUA)_p1 trnD(GUC)-trnY(GUA) CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 150–158 1.000 79.4
trnD(GUC)-trnY(GUA)_p2 trnD(GUC)-trnY(GUA) CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 149–157 1.000 79.4
trnD(GUC)-trnY(GUA)_p3 trnD(GUC)-trnY(GUA) CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 171–179 1.000 77.9
trnD(GUC)-trnY(GUA)_p4 trnD(GUC)-trnY(GUA) CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 170–178 1.000 77.7
trnD(GUC)-trnY(GUA)_p5 trnD(GUC)-trnY(GUA) CGGTGCTCTGACCAATTGAA CGGACTGTAAATTCGTTGGC 166–174 1.000 76.7
trnE(UUC)-trnT(GGU)_p1 trnE(UUC)-trnT(GGU) CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 719–741 1.000 85.0
trnE(UUC)-trnT(GGU)_p2 trnE(UUC)-trnT(GGU) CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 698–720 1.000 84.8
trnE(UUC)-trnT(GGU)_p3 trnE(UUC)-trnT(GGU) CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 695–717 1.000 84.6
trnE(UUC)-trnT(GGU)_p4 trnE(UUC)-trnT(GGU) CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 716–738 1.000 83.9
trnE(UUC)-trnT(GGU)_p5 trnE(UUC)-trnT(GGU) CGTTGCCTCCTTGAAAGAGA TTGAACCGATGACTTACGCC 721–743 1.000 82.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Echinacanthus attenuatus NC_039762.1 152672 View on NCBI ↗
Echinacanthus longipes NC_039761.1 152644 View on NCBI ↗
Echinacanthus longzhouensis NC_039678.1 152385 View on NCBI ↗