Markers + reference

Hechtia

14 species · Bromeliaceae · Poales

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Species 14
Genome length 155–160 kb
Candidate markers 279
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF SSC 651 0.0120 1.00 59.4 yes View details
rpl32-trnL-UAG SSC 790 0.0098 1.00 69.0 yes View details
ndhF SSC 32 0.0000 0.97 22.5 no View details
trnS-GCU-trnG-UCC LSC 1363 0.0105 0.97 65.3 yes View details
psaA-ycf3 LSC 668 0.0087 1.00 62.1 yes View details
rps4-trnT-UGU LSC 342 0.0101 0.98 48.8 yes View details
ndhC-trnV-UAC LSC 1052 0.0084 1.00 72.2 yes View details
accD-psaI LSC 847 0.0084 1.00 70.9 yes View details
petA-psbJ LSC 1127 0.0188 1.00 77.6 yes View details
rpl22 LSC 387 0.0065 1.00 37.0 yes View details
rpoB-trnC-GCA LSC 1372 0.0064 1.00 71.5 yes View details
rps19-psbA LSC 137 0.0342 1.00 70.1 yes View details
atpH-atpI LSC 937 0.0059 0.99 70.1 yes View details
rps16-trnQ-UUG LSC 1506 0.0058 1.00 68.3 yes View details
rps3-rpl22 LSC 40 0.0326 1.00 67.9 yes View details
trnC-GCA-petN LSC 1035 0.0073 1.00 66.0 yes View details
trnT-UGU-trnL-UAA LSC 788 0.0095 1.00 65.8 yes View details
rpl22-rps19 IRa 102 0.0294 1.00 65.5 yes View details
ndhD SSC 1523 0.0056 1.00 65.4 yes View details
petN-psbM LSC 1209 0.0056 1.00 65.1 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
ndhF_p1 ndhF AACCAAAATCCCCTACACGA TTTTAATACTTCTATGCTGGGA 172–176 0.857 41.1
ndhF_p2 ndhF TCGAGCAAATCCCGAAATTCT TTTTAATACTTCTATGCTGGGA 236–240 0.857 39.3
ndhF_p3 ndhF TCGAGCAAATCCCGAAATTCT TTTTTAATACTTCTATGCTGGGA 237–241 0.857 39.3
ndhF_p4 ndhF TCGAGCAAATCCCGAAATTCT TTAATACTTCTATGCTGGGATT 234–238 0.857 39.3
ndhF_p5 ndhF TCGAGCAAATCCCGAAATTCT TTTAATACTTCTATGCTGGGAT 235–239 0.857 39.3
rpl32-trnL-UAG_p1 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT AGCGTGTCTACCGATTTCAC 847–878 1.000 82.2
rpl32-trnL-UAG_p2 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT CAGCGTGTCTACCGATTTCA 848–879 1.000 82.2
rpl32-trnL-UAG_p3 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT TTTAGAAGATGCCGCCACTC 907–938 1.000 81.7
rpl32-trnL-UAG_p4 rpl32-trnL-UAG TTCCACCGGGCATTCAAAAA AGCGTGTCTACCGATTTCAC 850–881 1.000 81.7
rpl32-trnL-UAG_p5 rpl32-trnL-UAG TTTCCACCGGGCATTCAAAA AGCGTGTCTACCGATTTCAC 851–882 1.000 81.6
ndhD_p1 ndhD AAGACTTTCCTTCCGTCTCA TTTTGAGGACGGGCTTTTCT 1437–1586 1.000 68.2
ndhD_p2 ndhD AAGACTTTCCTTCCGTCTCA TTTGAGGACGGGCTTTTCTG 1436–1585 1.000 67.9
ndhD_p3 ndhD AAGACTTTCCTTCCGTCTCA TCTTTACCGACAAAAGCCCG 1476–1625 1.000 67.1
ndhD_p4 ndhD AGACTTTCCTTCCGTCTCAT TTTTGAGGACGGGCTTTTCT 1436–1585 1.000 66.3
ndhD_p5 ndhD AGACTTTCCTTCCGTCTCAT TTTGAGGACGGGCTTTTCTG 1435–1584 1.000 66.0
rps19-psbA_p1 rps19-psbA TCTGACTTTCGCGAGACATG CCTCTAGACCTAGCTGCTGT 230–237 1.000 84.9
rps19-psbA_p2 rps19-psbA TCTGACTTTCGCGAGACATG TTCCCTCTAGACCTAGCTGC 233–240 1.000 84.7
rps19-psbA_p3 rps19-psbA CCTACTCTGACTTTCGCGAG CCTCTAGACCTAGCTGCTGT 235–242 1.000 83.4
rps19-psbA_p4 rps19-psbA CCTACTCTGACTTTCGCGAG TTCCCTCTAGACCTAGCTGC 238–245 1.000 83.3
rps19-psbA_p5 rps19-psbA CTCTGACTTTCGCGAGACAT CCTCTAGACCTAGCTGCTGT 231–238 1.000 82.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAAATCAAAATGGGGCGTGG 1612–1677 1.000 85.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAAATCAAAATGGGGCGTGG 1610–1675 1.000 85.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAAATCAAAATGGGGCGTGG 1618–1683 1.000 85.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1554–1619 1.000 85.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1552–1617 1.000 85.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GAGAAAGCGGAAAGAGAGGG AACCGATGGACCCCTTAACT 1441–1557 1.000 84.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACCGATGGACCCCTTAACT 1386–1502 1.000 84.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GAGAAAGCGGAAAGAGAGGG AAACCGATGGACCCCTTAAC 1442–1558 1.000 83.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AAACCGATGGACCCCTTAAC 1387–1503 1.000 83.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GAGAAAGCGGAAAGAGAGGG ACCGATGGACCCCTTAACTA 1440–1556 1.000 83.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Hechtia aquamarina NC_080290.1 155133 View on NCBI ↗
Hechtia colossa NC_080291.1 157929 View on NCBI ↗
Hechtia confusa NC_080292.1 157118 View on NCBI ↗
Hechtia elliptica NC_080294.1 159395 View on NCBI ↗
Hechtia iltisii NC_080295.1 157935 View on NCBI ↗
Hechtia matudae NC_080296.1 159490 View on NCBI ↗
Hechtia michoacana NC_080297.1 158255 View on NCBI ↗
Hechtia mooreana NC_080298.1 155203 View on NCBI ↗
Hechtia myriantha NC_080299.1 159657 View on NCBI ↗
Hechtia podantha NC_080300.1 158441 View on NCBI ↗
Hechtia pringlei NC_080301.1 156758 View on NCBI ↗
Hechtia rosea NC_080302.1 158828 View on NCBI ↗
Hechtia schottii NC_080303.1 159488 View on NCBI ↗
Hechtia stenopetala NC_080304.1 155173 View on NCBI ↗