Markers + reference

Prosopis

2 species · Fabaceae · Fabales

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Species 2
Genome length 163–164 kb
Candidate markers 265
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 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 392 0.1096 0.95 79.9 yes View details
trnQ-UUG-psbK LSC 733 0.0792 0.86 80.0 yes View details
psbI-trnS-GCU LSC 262 0.1098 0.97 76.2 yes View details
trnS-GCU-trnR-UCU LSC 2320 0.0478 0.96 80.9 yes View details
atpH-atpI LSC 1457 0.0447 0.97 76.1 yes View details
rpoB-trnC-GCA LSC 1244 0.0562 0.97 75.8 yes View details
trnC-GCA-petN LSC 1296 0.0803 0.94 81.8 yes View details
trnT-UGU-trnL-UAA LSC 1376 0.0714 0.95 82.5 yes View details
trnL-UAA-trnF-GAA LSC 410 0.1953 0.92 86.4 yes View details
psbE-petL LSC 1331 0.0550 0.98 89.6 yes View details
atpF-atpH LSC 601 0.0594 0.95 91.2 yes View details
petA-psbJ LSC 1328 0.0451 0.97 87.2 yes View details
trnF-GAA-ndhJ LSC 700 0.0441 0.97 82.1 yes View details
psaA-ycf3 LSC 841 0.0470 0.99 80.9 yes View details
trnS-GGA-rps4 LSC 292 0.0563 0.97 80.7 yes View details
psbZ-trnG-UCC LSC 626 0.0615 0.96 80.5 yes View details
accD-psaI LSC 636 0.0583 0.89 79.2 yes View details
rps12-clpP LSC 202 0.0697 1.00 78.7 yes View details
rpl33-rps18 LSC 346 0.0737 0.98 76.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGTATCTGGTTTACCGCGTT 633–634 1.000 86.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GGTATCTGGTTTACCGCGTT 647–648 1.000 86.4
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTTCTCGCTACCTATGGCT GGTATCTGGTTTACCGCGTT 951 0.500 59.3
trnH-GUG-psbA_p4 trnH-GUG-psbA TCACGGTACCTATGATGGCT GGTATCTGGTTTACCGCGTT 1163 0.500 59.2
trnH-GUG-psbA_p5 trnH-GUG-psbA TATGATGGCTGTGACTGGGA GGTATCTGGTTTACCGCGTT 1153 0.500 58.9
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA ACAGACCAAACTAAAGATATTAAGCA 716–798 1.000 49.3
trnQ-UUG-psbK_p2 trnQ-UUG-psbK ACCAAAACCCGTTGCCTTAC ACAGACCAAACTAAAGATATTAAGCA 715–797 1.000 49.3
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA ACAAATACAGACCAAACTAAAGA 722–804 1.000 49.2
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GAATAGCGGGACCAAAACCC ACAGACCAAACTAAAGATATTAAGCA 725–807 1.000 49.2
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GAATAGCGGGACCAAAACCC ACAAATACAGACCAAACTAAAGA 731–813 1.000 49.2
psbI-trnS-GCU_p1 psbI-trnS-GCU CTTTTGTTTGGCAAGCTGCT TGGACTAAAGCGTCGGATTG 656–661 1.000 84.3
psbI-trnS-GCU_p2 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 651–656 1.000 84.3
psbI-trnS-GCU_p3 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG GTGGACTAAAGCGTCGGATT 652–657 1.000 84.3
psbI-trnS-GCU_p4 psbI-trnS-GCU CTTTTGTTTGGCAAGCTGCT GTGGACTAAAGCGTCGGATT 657–662 1.000 84.2
psbI-trnS-GCU_p5 psbI-trnS-GCU CTTTTGTTTGGCAAGCTGCT GCCCTTTTCAATTGGGGAGA 686–691 1.000 83.6
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 2317–2391 1.000 70.7
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 2316–2390 1.000 70.7
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 2323–2397 1.000 70.0
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 2322–2396 1.000 70.0
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA AGAAGACCTCTGTCCTATCCA 2371–2445 1.000 69.4
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGGCTGGTTGTAGCATTAG 717–719 1.000 82.7
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG AGGCAGAGGGAAAAATACGG 784–786 1.000 82.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCAGAGGGAAAAATACGGGG 782–784 1.000 80.6
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCAGAGGGAAAAATACGGG 783–785 1.000 80.6
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CCGAGGCAGAGGGAAAAATA 787–789 1.000 79.8
atpH-atpI_p1 atpH-atpI GCGGCAGAAATCAGTGGATT TTTTGCAACTTTAGCTGCGG 1524–1535 1.000 77.6
atpH-atpI_p2 atpH-atpI CGGCAGAAATCAGTGGATTC TTTTGCAACTTTAGCTGCGG 1523–1534 1.000 75.8
atpH-atpI_p3 atpH-atpI CCCAGCAGCAATAACCGAA TTTTGCAACTTTAGCTGCGG 1543–1554 1.000 75.7
atpH-atpI_p4 atpH-atpI GCGGCAGAAATCAGTGGAT TTTTGCAACTTTAGCTGCGG 1524–1535 1.000 75.1
atpH-atpI_p5 atpH-atpI CCCAGCAGCAATAACCGAAG TTTTGCAACTTTAGCTGCGG 1543–1554 1.000 74.6

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
Prosopis cineraria NC_049133.1 163677 View on NCBI ↗
Prosopis farcta NC_061227.1 162900 View on NCBI ↗