Hotspot

rps4-trnT-UGU

LSC · 45660-46032 · 373 bp

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Pi 0.0302
MarkerSeek score 71.10
Primer available yes
Label rps4-trnT-UGU

Feature Metadata

label_name
rps4-trnT-UGU
feature_type
igs
region
LSC
length_bp
373
variable_sites
38
pi
0.0302
unique_haplotype_count
16
primer_available
yes
alignment_reliability
0.94
markerseek_score
71.10

Pi Curve

Alignment Viewer

                         1                                                                                                   
Salvia_aethiopis_1       AAAATAAAGACTCCTTGATTCTTATTTAGAATTCATTTCATTC--------TTTTTTTCTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_amarissima_2      AAAATAAAGACTCCTTAATTCTTATTTAGAATTCATTTCATTC----TTTTTTTTTTTTTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_chinensis_3       AAAATAAAGACTCCTTAATTCTTATTTAGAATTCATTTCATTCTTTTTTTTTTTTTTTATTTGATTTTACAGAATAAATCGAAACTCAAACTGAACTAAA
Salvia_dorrii_4          AAAATAAAGACTCCTTAATTCTTATTTAGAATTCATTTCATTC-----TTTTTTTTTGATTTGATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_eremostachya_5    AAAATAAAGACTCCTTAATTCTTATTTAGAATTCATTTCATTC-----TTTTTTTTTGATTTGATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_fruticosa_6       AAAATAAAGACTCCTTGATTCTTATTTAGAATTCATTTCATTC--------TTTTTTTCTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_huberi_7          AAAATAAAGACTCCTTGATTCTTATTTAGAATTCATTTCATTC--------TTTTTTTCTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_kronenburgii_8    AAAATAAAGACTCCTTGATTCTTATTTAGAATTCATTTCATTC--------TTTTTTTCTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_limbata_9         AAAATAAAGACTCCTTGATTCTTATTTAGAATTCATTTCATTC--------TTTTTTTCTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_mohavensis_10     AAAATAAAGACTCCTTAATTCTTATTTAGAATTCATTTCATTC-----TTTTTTTTTGATTTGATTTTACAGAATAAATCGAAACTCAAACTGAACTAAA
Salvia_officinalis_subsp AAAATAAAGACTCCTTGATTCTTATTTAGAATTCATTTCATTC--------TTTTTTTCTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_pachyphylla_12    AAAATAAAGACTCCTTAATTCTTATTTAGAATTCATTTCATTC----TTTTTTTTTTGATTTGATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_pratensis_13      AAAATAAAGACTCCTTGATTCTTATTTAGAATTCATTTCATTC--------TTTTTTTCTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_saccardiana_14    AAAATAAAGACTCCTTGATTCTTATTTAGAATTCATTTCATTC--------TTTTTTTCTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_sonomensis_15     AAAATAAAGACTCCTTAATTCTTATTTAGAATTCATTTCATTC-----TTTTTTTTTGATTTGATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_spathacea_16      AAAATAAAGACTCCTTAATTCTTATTTAGAATTCATTTCATTC-----TTTTTTTTTGATTTGATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_verbenaca_17      AAAATAAAGACTCCTTGATTCTTATTTAGAATTCATTTCATTC--------TTTTTTTCTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
Salvia_xanthocheila_18   AAAATAAAGACTCCTTGATTCTTATTTAGAATTCATTTCATTC--------TTTTTTTCTTTTATTTTACAGAATAAATCTAAACTCAAACTGAACTAAA
                         101                                                                                                 
Salvia_aethiopis_1       TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATT----------
Salvia_amarissima_2      TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACAATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTATAT------
Salvia_chinensis_3       TGAAGCGAAGTTTGCTGAAGTAGTGTACTTCTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTAATATCTATTATT
Salvia_dorrii_4          TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTATATATATAT
Salvia_eremostachya_5    TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGAGAAATTGGATAAATAGTCAAACTTTCTATTATTAT--------
Salvia_fruticosa_6       TGAAGCGAAGTTTACTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATT----------
Salvia_huberi_7          TGAAGCGAAGTTTACTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTATATATAATA
Salvia_kronenburgii_8    TGAAGCGAAGTTTACTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTATATATAATA
Salvia_limbata_9         TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTATATATAATA
Salvia_mohavensis_10     TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTAT--------
Salvia_officinalis_subsp TGAAGCGAAGTTTACTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTATATAT----
Salvia_pachyphylla_12    TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTAT--------
Salvia_pratensis_13      TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATT----------
Salvia_saccardiana_14    TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATT----------
Salvia_sonomensis_15     TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTAT--------
Salvia_spathacea_16      TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTATATATATAT
Salvia_verbenaca_17      TGAAGCGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATT----------
Salvia_xanthocheila_18   TGAAGTGAAGTTTGCTGAAGTAGTGTACTTGTACTATTACTATACAGAAGAATGAGATAAATTGGATAAATAGTCAAACTTTCTATTATTATATAT-ATA
                         201                                                                                                 
Salvia_aethiopis_1       ATATATATAATAATATATAAGATCCTTTTCCTGACATAGTCAGGAGTTCCCCCTATAACTT-----ATTCATGGATTTTGGAAAGAGGGGAAGACACTTT
Salvia_amarissima_2      ------------ATATATAAGATCCTTTTCCTGTCATAGTCATGCGTTCCCCCTATAACTTAATAAATTCATGGATTTTGGAAAGAGGGGAAGACACTTT
Salvia_chinensis_3       ATATATATAATAATAGATAAGATCCTTTTCCTGGCATAGTCATGAGTTCCCCCTAGAACTTCCAAAATTCATGGATTTTGGAAAGGGGGGAAGACACTTT
Salvia_dorrii_4          ATATATATAAGAATATATAAGATCCTTTTCCTGGCATAGTAATGAGTTCCCCCTATAACTTAATAAATTCATGGATTTTGGAAAGAGGGGAAGGCACTTT
Salvia_eremostachya_5    ATATATATAAGAATATATAAGATCCTTTTCCTGGCATAGTCATGAGTTCCCCCTATAACTTAATAAATTCATGGATTTTGGAAAGAGGGGAAGGCACTTT
Salvia_fruticosa_6       ---------ATAATATATAAGATCCTTTTCCTGACATAGTCAGGAGTTCCCCCTATAACTT-----ATTCATGGATTTTGGAAAG-GGGGAAGACACTTT
Salvia_huberi_7          TAATATAATATAATATATAAGATCCTTTTCCTGACATAGTCAGGAGTTCCCCCTATAACTT-----ATTCATGGATTTTGGAAAG-GGGGAAGACACTTT
Salvia_kronenburgii_8    TTATATA--ATAATATATAAGATCCTTTTCCTGACATAGTCAGGAGTTCCCCCTATAACTT-----ATTCATGGATTTTGGAAAG-GGGGAAGACACTTT
Salvia_limbata_9         ATATATATAATAATATATAAGATCCTTTTCCTGACATAGTCAGGAGTTCCCCCTATAACTT-----ATTCATGGATTTTGGAAAGAGGGGAAGACACTTT
Salvia_mohavensis_10     ATATATATAAGAATATATAAGATCCTTTTCCTGGCATAGTAATGAGTTCCCCCTATAACTTAATAAATTCATGGATTTTGGAAAGAGGGGAAGGCACTTT
Salvia_officinalis_subsp ---------ATAATATATAAGATCCTTTTCCTGACATAGTCAGGAGTTCCCCCTATAACTT-----ATTCATGGATTTTGGAAAG-GGGGAAGACACTTT
Salvia_pachyphylla_12    ATATATATAAGAATATATAAGATCCTTTTCCTGGCATAGTAATGAGTTCCCCCTATAACTTAATAAATTCATGGATTTTGGAAAGAGGGGAAGGCACTTT
Salvia_pratensis_13      ATATATATAATAATATATAAGATCCTTTTCCTGACATAGTCAGGAGTTCCCCCTATAACTT-----ATTCATGGATTTTGGAAAGAGGGGAAGACACTTT
Salvia_saccardiana_14    ATATATATAATAATATATAAGATCCTTTTCCTGACATAGTCAGGAGTTCCCCCTATAACTT-----ATTCATGGATTTTGGAAAGAGGGGAAGACACTTT
Salvia_sonomensis_15     ATATATATAAGAATATATAAGATCCTTTTCCTGGCATAGTAATGAGTTCCCCCTATAACTTAATAAATTCATGGATTTTGGAAAGAGGGGAAGGCACTTT
Salvia_spathacea_16      ATATATATAAGAATATATAAGATCCTTTTCCTGGCATAGTAATGAGTTCCCCCTATAACTTAATAAATTCATGGATTTTGGAAAGAGGGGAAGGCACTTT
Salvia_verbenaca_17      ATATATATAATAATATATAATATCCTTTTCCTGACATAGTCAGGAGTTCCCCCTATAACTT-----ATTCATGGATTTTGGAAAGAGGGGAAGACACTTT
Salvia_xanthocheila_18   ATATATATAATAATATATAAGATCCTTTTCCTGACATAGTCAGGAGTTCCCCCTATAACTT-----ATTCATGGATTTTGGAAAGAGGGGAAGACACTTT
                         301                                                                      
Salvia_aethiopis_1       TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTGGAAAAATGGAATAAAAAAATGAAAAATAGAAAAA
Salvia_amarissima_2      TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATCAAAAAATGAAAAATAGAAAAA
Salvia_chinensis_3       TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTGAAAAATGGAATAAAAAAATGAAAAATATAAAAA
Salvia_dorrii_4          TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATAAAAAAATGAAAAATATAAAAA
Salvia_eremostachya_5    TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATAAAAAAATGAAAAATATAAAAA
Salvia_fruticosa_6       TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATAAAAAAATGAAAAATAGAAAAA
Salvia_huberi_7          TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATAAAAAAATGAAAAATAGAAAAA
Salvia_kronenburgii_8    TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATAAAAAAATGAAAAATAGAAAAA
Salvia_limbata_9         TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCCAAAATGGAATAAAAAAATGAAAAATAGAAAAA
Salvia_mohavensis_10     TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATAAAAAAATGAAAAATATAAAAA
Salvia_officinalis_subsp TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATAAAAAAATGAAAAATAGAAAAA
Salvia_pachyphylla_12    TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATAAAAAAATGAAAAATATAAAAA
Salvia_pratensis_13      TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTGAAAAATGGAATAAAAAAATGAAAAATAGAAAAA
Salvia_saccardiana_14    TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTGAAAAATGGAATAAAAAAATGAAAAATAGAAAAA
Salvia_sonomensis_15     TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATAAAAAAATGAAAAATATAAAAA
Salvia_spathacea_16      TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTCAAAAATGGAATAAAAAAATGAAAAATATAAAAA
Salvia_verbenaca_17      TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTTGAAAAATGGAATAAAAAAATGAAAAATAGAAAAA
Salvia_xanthocheila_18   TCAATATTCTTTGATTTCAAAGGAAGATTCTCCATTTTGGAAAAATGGAATAAAAAAATGAAAAATAGAAAAA

Haplotype Network

Species Separation

Primer Ranking

Primer ID fwd_seq rev_seq fwd_gc rev_gc fwd_tm rev_tm amplicon_size cross_species_success_rate primer_score
rps4-trnT-UGU_p1 GTTAGTCCTGGTAAAGCCCC CTCAGAGGTTAGAGCATCGC 55.0 55.0 57.6 57.9 469-501 bp 0.944444 83.5
rps4-trnT-UGU_p2 GTTAGTCCTGGTAAAGCCCC ATGGTCATCGGTTCGATTCC 55.0 50.0 57.6 57.8 437-469 bp 0.944444 83.1
rps4-trnT-UGU_p3 TTAGTCCTGGTAAAGCCCCC CTCAGAGGTTAGAGCATCGC 55.0 55.0 58.7 57.9 468-500 bp 0.944444 81.2
rps4-trnT-UGU_p4 GTTAGTCCTGGTAAAGCCCC ATAATATGGGCCCGCTTAGC 55.0 50.0 57.6 57.6 488-520 bp 0.944444 81.1
rps4-trnT-UGU_p5 GTTAGTCCTGGTAAAGCCCC CCGCTTAGCTCAGAGGTTAG 55.0 55.0 57.6 57.5 477-509 bp 0.944444 80.5

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