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Table 5 List of primers and edition of sequences

From: Multilocus analysis of introgression between two sand fly vectors of leishmaniasis

locus primers Removed gap sitesa NR blocksb Removed sequences from NR blocksc
Ca1D 5LWIca1D
5'-CAGGATATAATGATGGATTG-3'
3LWIca1D
5'-CACGAACAAGTTGATAAT-3'
159–160; 162–169; 183 1–176 IAFCa_A12; IAFCa_F09; WAFCa_B12; WAFCa_C09; WAFCa_H11; WAFCa_H12
Cac 5Llcac
5'-GTGGCCGAACATAATGTTAG-3'
3Llcac
5'-CCACGAACAAGTTCAACATC-3'
10; 19; 124–126; 129–132; 150; 170; 180; 182 122–172 IAFcac_H05; WAFcac_F01; WAFcac_H07
Per 5llper2
5'-AGCATCCTTTTGTAGCAAAC-3'
3llper2
5'-TCAGATGAACTCTTGCTGTC-3'
154–157; 167–169; 204 125–210 IAFPER16; WAFPER05
Rp49 5RP49semideg1
5'-TTCATYCGYCAYCAGWSBGA-3'
3llRP49exp2
5'-GGGCGATCTCAGCACAGTAT-3'
29–36; 46–49; 55–56; 59; 65–69; 72; 74; 87 1–237 IAFrp49_B08; IAFrp49_C08; IAFrp49_E05; IAFrp49_E08; IAFrp49_G08; IAFrp49_H06; WAFrp49_D11
RpL17A 5LLrpL17A
5'-TCAATTGCGCCGACAATAC-3'
3LLrpL17A
5'-GCTGATCCTTTCATTTCGCC-3'
90–91; 101–102; 109–110; 131; 135; 144; 147–148; 153–154 1–114 IAFr17a_D10; IAFr17a_E10; IAFr17a_F10; IAFr17a_G11
RpL36 5LWIrpL36
5'-GTTCCTCACGCTTCCTCTTG-3'
3LWIrpL36
5'-AAAGTGAAAGGACTCCGCCC-3'
26–29; 46; 52; 65; 77; 215–217; 226; 238–253; 267; 270; 274; 289–294; 362 126–238 IAFr36_D07; IAFr36_H11
RpS19a 5LWrpS19
5'-TGATCAACACAAGATTGTCCG-3'
3LWrpS19
5'-ACACCATTCCTCTTACGACC-3'
174 77–193 IAF19_G01; IAF19_H02; WAF19_B08; WAF19_F079
TfIIA-L 5LLTfIIA-L
5'-GATAATGATCCAGACGATGCC-3'
3LLTfIIA-L
5'-GAAAACATAGTCCTTCCCACC-3'
162; 173–179; 201–259; 277; 284–319; 341; 345–346; 369–370; 386–387 1–254 -
Up 5LLup
5'-GCAACAAGTCCAAAGAGCAG-3'
3LLup
5'-TCATAGGAGCGGGTGTCAAC-3'
189–191; 224; 351–355; 360–361; 368–369; 396–397 1–354 -
zetacop 5LLzetacop
5'-GGATGCAGATCCTTCATCCG-3'
3LLzetacop
5'-CGACCACTTCAGTTGTTCTC-3'
115; 131–134; 149–150; 168; 181; 195; 224; 234–235; 240–242 1–230 IAFztp_H07; WAFztp_C06
  1. a Sites with indels or ambiguous alignment removed before the analyses.
  2. b Fragment positions of the non-recombining blocks used in the analyses.
  3. c Recombining sequences removed before the analyses using the non-recombining blocks.