Addgene pLH-sgRNA1-boxB-MS2-PP7 - Sequence Analyzer Skip to main content
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Sequence Analyzer: pLH-sgRNA1-boxB-MS2-PP7


Map View

XcmI (25) EcoRI (8127) SbfI (7961) BstXI (7848) ccdB-fwd (7832 .. 7851) BsaBI * (7744) SrfI (7731) BsrGI (7704) BstZ17I (7395) AgeI - SgrAI (7305) LKO.1 5' (7230 .. 7249) hU6-F (7059 .. 7079) KflI - PpuMI (6930) AleI (6573) MfeI (6185) NruI * (5833) SphI (5317) T3 promoter T3 (5179 .. 5199) M13 rev M13 Reverse (5144 .. 5160) lac operator M13/pUC Reverse (5125 .. 5147) lac promoter CAP binding site L4440 (4912 .. 4929) AflIII - PciI (4814) pBR322ori-F (4659 .. 4678) PfoI (67) SpeI (253) BlpI (333) AscI (342) hPGK-F (426 .. 444) BamHI (510) ZraI (622) AatII - PshAI (624) AsiSI (961) RsrII (1005) SalI (1653) KS primer AbsI (1659) pBluescriptKS (1647 .. 1663) Acc65I (1674) KpnI (1678) SV40pA-R (2087 .. 2106) EBV-rev (2141 .. 2160) SfiI (2298) StuI (2344) AvrII (2345) T7 promoter T7 (2366 .. 2385) M13 fwd M13 Forward (2395 .. 2412) M13/pUC Forward (2404 .. 2426) F1ori-R (2640 .. 2659) NgoMIV (2678) NaeI (2680) F1ori-F (2850 .. 2871) Amp-R (3357 .. 3376) pLH-sgRNA1-boxB-MS2-PP7 8337 bp

Sequence View

XcmI 60 hPGK promoter GVAPFPRQPWVCAGTRLLW t t g g g g t t g c g c c t t t t c c a a g g c a g c c c t g g g t t t g c g c a g g g a c g c g g c t g c t c t g g g a a c c c c a a c g c g g a a a a g g t t c c g t c g g g a c c c a a a c g c g t c c c t g c g c c g a c g a g a c c c

PfoI 120 hPGK promoter AWFRETQRRRPWVSHILHVR c g t g g t t c c g g g a a a c g c a g c g g c g c c g a c c c t g g g t c t c g c a c a t t c t t c a c g t c c g t t g c a c c a a g g c c c t t t g c g t c g c c g c g g c t g g g a c c c a g a g c g t g t a a g a a g t g c a g g c a a

180 hPGK promoter SQRHPDLRRYPCGPPGDASC c g c a g c g t c a c c c g g a t c t t c g c c g c t a c c c t t g t g g g c c c c c c g g c g a c g c t t c c t g c t g c g t c g c a g t g g g c c t a g a a g c g g c g a t g g g a a c a c c c g g g g g g c c g c t g c g a a g g a c g a

240 hPGK promoter SAPKSGRFLAVRGVPDVTNG c c g c c c c t a a g t c g g g a a g g t t c c t t g c g g t t c g c g g c g t g c c g g a c g t g a c a a a c g g a a g g c g g g g a t t c a g c c c t t c c a a g g a a c g c c a a g c g c c g c a c g g c c t g c a c t g t t t g c c t t

SpeI 300 hPGK promoter SRTSH* g c c g c a c g t c t c a c t a g t a c c c t c g c a g a c g g a c a g c g c c a g g g a g c a a t g g c a g c g c g c c g g c g t g c a g a g t g a t c a t g g g a g c g t c t g c c t g t c g c g g t c c c t c g t t a c c g t c g c g c g

AscIBlpI 360 hPGK promoter c g a c c g c g a t g g g c t g t g g c c a a t a g c g g c t g c t c a g c a g g g c g c g c c g a g a g c a g c g g c g c t g g c g c t a c c c g a c a c c g g t t a t c g c c g a c g a g t c g t c c c g c g c g g c t c t c g t c g c c g

420 hPGK promoter c g g g a a g g g g c g g t g c g g g a g g c g g g g t g t g g g g c g g t a g t g t g g g c c c t g t t c c t g c c c g c c c t t c c c c g c c a c g c c c t c c g c c c c a c a c c c c g c c a t c a c a c c c g g g a c a a g g a c g g g

480 hPGK promoter G T G T T C C G C A T T C T G C A A G hPGK-F g c g c g g t g t t c c g c a t t c t g c a a g c c t c c g g a g c g c a c g t c g g c a g t c g g c t c c c t c g t t c g c g c c a c a a g g c g t a a g a c g t t c g g a g g c c t c g c g t g c a g c c g t c a g c c g a g g g a g c a a

BamHI 540 hPGK promoter *AQWSP g a c c g a a t c a c c g a c c t c t c t c c c c a g g g g g a t c c a c c g g a t c a a g c t t g c c a g c t g g g g c t g g c t t a g t g g c t g g a g a g a g g g g t c c c c c t a g g t g g c c t a g t t c g a a c g g t c g a c c c c

600 1 M HygR 1 M HygR M RGRTLNPLGASRIGPPLSIH c g c c c t c t g g t a a g g t t g g g a a g c c c t g c a g a t c t g a t c c c g g g g g g c a a t g a g a t a t g a g c g g g a g a c c a t t c c a a c c c t t c g g g a c g t c t a g a c t a g g g c c c c c c g t t a c t c t a t a c t

ZraIPshAIAatII 660 5 10 15 20 KKPELTATSVEKFLIEKFDS HygR 5 10 15 20 KKPELTATSVEKFLIEKFDS HygR KKPELTATSVEKFLIEKFDS FLRFEGRRRDLLKQDFLEVA a a a a g c c t g a a c t c a c c g c g a c g t c t g t c g a g a a g t t t c t g a t c g a a a a g t t c g a c a g c g t t t t c g g a c t t g a g t g g c g c t g c a g a c a g c t c t t c a a a g a c t a g c t t t t c a a g c t g t c g c

720 25 30 35 40 VSDLMQLSEGEESRAFSFDV HygR 25 30 35 40 VSDLMQLSEGEESRAFSFDV HygR VSDLMQLSEGEESRAFSFDV DGVQHLERLAFFRTSEAEIY t c t c c g a c c t g a t g c a g c t c t c g g a g g g c g a a g a a t c t c g t g c t t t c a g c t t c g a t g t a g a g a g g c t g g a c t a c g t c g a g a g c c t c c c g c t t c t t a g a g c a c g a a a g t c g a a g c t a c a t c

780 45 50 55 60 GGRGYVLRVNSCADGFYKDR HygR 45 50 55 60 GGRGYVLRVNSCADGFYKDR HygR GGRGYVLRVNSCADGFYKDR SPTSIDQPYIAAGITEVFIT g a g g g c g t g g a t a t g t c c t g c g g g t a a a t a g c t g c g c c g a t g g t t t c t a c a a a g a t c g t t c t c c c g c a c c t a t a c a g g a c g c c c a t t t a t c g a c g c g g c t a c c a a a g a t g t t t c t a g c a a

840 65 70 75 80 YVYRHFASAALPIPEVLDIG HygR 65 70 75 80 YVYRHFASAALPIPEVLDIG HygR YVYRHFASAALPIPEVLDIG INIPVKCRGRERNRFHKVNP a t g t t t a t c g g c a c t t t g c a t c g g c c g c g c t c c c g a t t c c g g a a g t g c t t g a c a t t g g g g t a c a a a t a g c c g t g a a a c g t a g c c g g c g c g a g g g c t a a g g c c t t c a c g a a c t g t a a c c c c

900 85 90 95 100 EFSESLTYCISRRAQGVTLQ HygR 85 90 95 100 EFSESLTYCISRRAQGVTLQ HygR EFSESLTYCISRRAQGVTLQ FKALAQGIADGATCLTDRQL a a t t t a g c g a g a g c c t g a c c t a t t g c a t c t c c c g c c g t g c a c a g g g t g t c a c g t t g c a a g t t a a a t c g c t c t c g g a c t g g a t a a c g t a g a g g g c g g c a c g t g t c c c a c a g t g c a a c g t t c

960 105 110 115 120 DLPETELPAVLQPVAEAMDA HygR 105 110 115 120 DLPETELPAVLQPVAEAMDA HygR DLPETELPAVLQPVAEAMDA IQRFGFQGSNQLRDRLGHIR a t c t g c c t g a a a c c g a a c t g c c c g c t g t t c t g c a g c c g g t c g c g g a g g c c a t g g a t g c g a t a g a c g g a c t t t g g c t t g a c g g g c g a c a a g a c g t c g g c c a g c g c c t c c g g t a c c t a c g c t

RsrIIAsiSI 1020 125 130 135 140 IAAADLSQTSGFGPFGPQGI HygR 125 130 135 140 IAAADLSQTSGFGPFGPQGI HygR IAAADLSQTSGFGPFGPQGI DSRGIKALRAPEAWESRLSD t c g c t g c g g c c g a t c t t a g c c a g a c g a g c g g g t t c g g c c c a t t c g g a c c g c a a g g a a t c g a g c g a c g c c g g c t a g a a t c g g t c t g c t c g c c c a a g c c g g g t a a g c c t g g c g t t c c t t a g c

1080 145 150 155 160 GQYTTWRDFICAIADPHVYH HygR 145 150 155 160 GQYTTWRDFICAIADPHVYH HygR GQYTTWRDFICAIADPHVYH TLVSCPTIEYARNSIGMHIV g t c a a t a c a c t a c a t g g c g t g a t t t c a t a t g c g c g a t t g c t g a t c c c c a t g t g t a t c a c t c a g t t a t g t g a t g t a c c g c a c t a a a g t a t a c g c g c t a a c g a c t a g g g g t a c a c a t a g t g a

1140 165 170 175 180 WQTVMDDTVSASVAQALDEL HygR 165 170 175 180 WQTVMDDTVSASVAQALDEL HygR WQTVMDDTVSASVAQALDEL PLSHHVVGDTRGDRLSEILQ g g c a a a c t g t g a t g g a c g a c a c c g t c a g t g c g t c c g t c g c g c a g g c t c t c g a t g a g c t g a c c g t t t g a c a c t a c c t g c t g t g g c a g t c a c g c a g g c a g c g c g t c c g a g a g c t a c t c g a c t

1200 185 190 195 200 MLWAEDCPEVRHLVHADFGS HygR 185 190 195 200 MLWAEDCPEVRHLVHADFGS HygR MLWAEDCPEVRHLVHADFGS HKPGLVAGFDPVEHVRIEAG t g c t t t g g g c c g a g g a c t g c c c c g a a g t c c g g c a c c t c g t g c a c g c g g a t t t c g g c t c c a a c g a a a c c c g g c t c c t g a c g g g g c t t c a g g c c g t g g a g c a c g t g c g c c t a a a g c c g a g g t

1260 205 210 215 220 NNVLTDNGRITAVIDWSEAM HygR 205 210 215 220 NNVLTDNGRITAVIDWSEAM HygR NNVLTDNGRITAVIDWSEAM VIDQRVIAAYCRDNVPALRH a c a a t g t c c t g a c g g a c a a t g g c c g c a t a a c a g c g g t c a t t g a c t g g a g c g a g g c g a t g t t g t t a c a g g a c t g c c t g t t a c c g g c g t a t t g t c g c c a g t a a c t g a c c t c g c t c c g c t a c a

1320 225 230 235 240 FGDSQYEVANIFFWRPWLAC HygR 225 230 235 240 FGDSQYEVANIFFWRPWLAC HygR FGDSQYEVANIFFWRPWLAC EPIGLVLDGVDEEPPRPQST t c g g g g a t t c c c a a t a c g a g g t c g c c a a c a t c t t c t t c t g g a g g c c g t g g t t g g c t t g t a a g c c c c t a a g g g t t a t g c t c c a g c g g t t g t a g a a g a a g a c c t c c g g c a c c a a c c g a a c a t

1380 245 250 255 260 MEQQTRYFERRHPELAGSPR HygR 245 250 255 260 MEQQTRYFERRHPELAGSPR HygR MEQQTRYFERRHPELAGSPR HLLLRAVELPPM t g g a g c a g c a g a c g c g c t a c t t c g a g c g g a g g c a t c c g g a g c t t g c a g g a t c g c c g c g g c a c c t c g t c g t c t g c g c g a t g a a g c t c g c c t c c g t a g g c c t c g a a c g t c c t a g c g g c g c c g

1440 265 270 275 280 LRAYMLRIGLDQLYQSLVDG HygR 265 270 275 280 LRAYMLRIGLDQLYQSLVDG HygR LRAYMLRIGLDQLYQSLVDG t c c g g g c g t a t a t g c t c c g c a t t g g t c t t g a c c a a c t c t a t c a g a g c t t g g t t g a c g g c a a g g c c c g c a t a t a c g a g g c g t a a c c a g a a c t g g t t g a g a t a g t c t c g a a c c a a c t g c c g t

1500 285 290 295 300 NFDDAAWAQGRCDAIVRSGA HygR 285 290 295 300 NFDDAAWAQGRCDAIVRSGA HygR NFDDAAWAQGRCDAIVRSGA a t t t c g a t g a t g c a g c t t g g g c g c a g g g t c g a t g c g a c g c a a t c g t c c g a t c c g g a g c c g t a a a g c t a c t a c g t c g a a c c c g c g t c c c a g c t a c g c t g c g t t a g c a g g c t a g g c c t c g g c

1560 305 310 315 320 GTVGRTQIARRSAAVWTDGC HygR 305 310 315 320 GTVGRTQIARRSAAVWTDGC HygR GTVGRTQIARRSAAVWTDGC g g a c t g t c g g g c g t a c a c a a a t c g c c c g c a g a a g c g c g g c c g t c t g g a c c g a t g g c t g t g c c t g a c a g c c c g c a t g t g t t t a g c g g g c g t c t t c g c g c c g g c a g a c c t g g c t a c c g a c a c

1620 325 330 335 340 VEVLADSGNRRPSTRPRAKE HygR 325 330 335 340 VEVLADSGNRRPSTRPRAKE HygR VEVLADSGNRRPSTRPRAKE t a g a a g t a c t c g c c g a t a g t g g a a a c c g a c g c c c c a g c a c t c g t c c g a g g g c a a a g g a a t a t c t t c a t g a g c g g c t a t c a c c t t t g g c t g c g g g g t c g t g a g c a g g c t c c c g t t t c c t t a

Acc65IKpnIAbsISalI 1680 * HygR KS primer * HygR C T A T G G C A G C T G G A G C T pBluescriptKS * a g a g t a g a t g c c g a c c g g g a t c t a t c g a t a c c g t c g a c c t c g a g g g g g g g c c c g g t a c c t t c t c a t c t a c g g c t g g c c c t a g a t a g c t a t g g c a g c t g g a g c t c c c c c c c g g g c c a t g g a

1740 t t a a g a c c a a t g a c t t a c a a g g c a g c t g t a g a t c t t a g c c a c t t t t t a a a a g a a a a g g g g a a t t c t g g t t a c t g a a t g t t c c g t c g a c a t c t a g a a t c g g t g a a a a a t t t t c t t t t c c c c

1800 3' LTR ( Δ U3) g g a c t g g a a g g g c t a a t t c a c t c c c a a c g a a g a a a a g a t c t g c t t t t t g c t t g t a c t g g g c c t g a c c t t c c c g a t t a a g t g a g g g t t g c t t c t t t t c t a g a c g a a a a a c g a a c a t g a c c c

1860 3' LTR ( Δ U3) t c t c t c t g g t t a g a c c a g a t c t g a g c c t g g g a g c t c t c t g g c t a a c t a g g g a a c c c a c t g a g a g a g a c c a a t c t g g t c t a g a c t c g g a c c c t c g a g a g a c c g a t t g a t c c c t t g g g t g a c

1920 3' LTR ( Δ U3) c t t a a g c c t c a a t a a a g c t t g c c t t g a g t g c t t c a a g t a g t g t g t g c c c g t c t g t t g t g t g a a t t c g g a g t t a t t t c g a a c g g a a c t c a c g a a g t t c a t c a c a c a c g g g c a g a c a a c a c a

1980 3' LTR ( Δ U3) g a c t c t g g t a a c t a g a g a t c c c t c a g a c c c t t t t a g t c a g t g t g g a a a a t c t c t a g c a g t c t g a g a c c a t t g a t c t c t a g g g a g t c t g g g a a a a t c a g t c a c a c c t t t t a g a g a t c g t c a

2040 a g t a g t t c a t g t c a t c t t a t t a t t c a g t a t t t a t a a c t t g c a a a g a a a t g a a t a t c a g a g t c a t c a a g t a c a g t a g a a t a a t a a g t c a t a a a t a t t g a a c g t t t c t t t a c t t a t a g t c t c

2100 SV40 poly(A) signal C G T T A T C G T A G T G T SV40pA-R a g t g a g a g g a a c t t g t t t a t t g c a g c t t a t a a t g g t t a c a a a t a a a g c a a t a g c a t c a c a t c a c t c t c c t t g a a c a a a t a a c g t c g a a t a t t a c c a a t g t t t a t t t c g t t a t c g t a g t g t

2160 SV40 poly(A) signal G T G G T T T G T C C A A A C T C A T C EBV-rev T T A A A G SV40pA-R a a t t t c a c a a a t a a a g c a t t t t t t t c a c t g c a t t c t a g t t g t g g t t t g t c c a a a c t c a t c t t a a a g t g t t t a t t t c g t a a a a a a a g t g a c g t a a g a t c a a c a c c a a a c a g g t t t g a g t a g

2220 SV40 poly(A) signal SV40 ori a a t g t a t c t t a t c a t g t c t g g c t c t a g c t a t c c c g c c c c t a a c t c c g c c c a t c c c g c c c c t t a c a t a g a a t a g t a c a g a c c g a g a t c g a t a g g g c g g g g a t t g a g g c g g g t a g g g c g g g g

2280 SV40 ori t a a c t c c g c c c a g t t c c g c c c a t t c t c c g c c c c a t g g c t g a c t a a t t t t t t t t a t t t a t g a t t g a g g c g g g t c a a g g c g g g t a a g a g g c g g g g t a c c g a c t g a t t a a a a a a a a t a a a t a c

SfiI 2340 SV40 ori c a g a g g c c g a g g c c g c c t c g g c c t c t g a g c t a t t c c a g a a g t a g t g a g g a g g c t t t t t t g g t c t c c g g c t c c g g c g g a g c c g g a g a c t c g a t a a g g t c t t c a t c a c t c c t c c g a a a a a a c

StuIAvrII 2400 SV40 ori T7 promoter M13 fwd G G G A T A T C A C T C A G C A T A A T T7 T G A C C G M13 Forward g a g g c c t a g g g a c g t a c c c a a t t c g c c c t a t a g t g a g t c g t a t t a c g c g c g c t c a c t g g c c t c c g g a t c c c t g c a t g g g t t a a g c g g g a t a t c a c t c a g c a t a a t g c g c g c g a g t g a c c g

2460 M13 fwd G C A G C A A A A T G T M13 Forward G C A A A A T G T T G C A G C A C T G A C C C M13/pUC Forward c g t c g t t t t a c a a c g t c g t g a c t g g g a a a a c c c t g g c g t t a c c c a a c t t a a t c g c c t t g c g c a g c a a a a t g t t g c a g c a c t g a c c c t t t t g g g a c c g c a a t g g g t t g a a t t a g c g g a a c g

2520 a g c a c a t c c c c c t t t c g c c a g c t g g c g t a a t a g c g a a g a g g c c c g c a c c g a t c g c c c t t c t c g t g t a g g g g g a a a g c g g t c g a c c g c a t t a t c g c t t c t c c g g g c g t g g c t a g c g g g a a g

2580 f1 ori c c a a c a g t t g c g c a g c c t g a a t g g c g a a t g g g a c g c g c c c t g t a g c g g c g c a t t a a g c g c g g t t g t c a a c g c g t c g g a c t t a c c g c t t a c c c t g c g c g g g a c a t c g c c g c g t a a t t c g c g

2640 f1 ori G F1ori-R g g c g g g t g t g g t g g t t a c g c g c a g c g t g a c c g c t a c a c t t g c c a g c g c c c t a g c g c c c g c c c g c c c a c a c c a c c a a t g c g c g t c g c a c t g g c g a t g t g a a c g g t c g c g g g a t c g c g g g c g

NgoMIVNaeI 2700 f1 ori A G G A A A G C G A A A G A A G G G A F1ori-R t c c t t t c g c t t t c t t c c c t t c c t t t c t c g c c a c g t t c g c c g g c t t t c c c c g t c a a g c t c t a g g a a a g c g a a a g a a g g g a a g g a a a g a g c g g t g c a a g c g g c c g a a a g g g g c a g t t c g a g a

2760 f1 ori a a a t c g g g g g c t c c c t t t a g g g t t c c g a t t t a g t g c t t t a c g g c a c c t c g a c c c c a a a a a t t t a g c c c c c g a g g g a a a t c c c a a g g c t a a a t c a c g a a a t g c c g t g g a g c t g g g g t t t t t

2820 f1 ori a c t t g a t t a g g g t g a t g g t t c a c g t a g t g g g c c a t c g c c c t g a t a g a c g g t t t t t c g c c c t g a a c t a a t c c c a c t a c c a a g t g c a t c a c c c g g t a g c g g g a c t a t c t g c c a a a a a g c g g g

2880 f1 ori G T G G A C T C T T G T T C C A A A C T G G F1ori-F t t t g a c g t t g g a g t c c a c g t t c t t t a a t a g t g g a c t c t t g t t c c a a a c t g g a a c a a c a c t a a a c t g c a a c c t c a g g t g c a a g a a a t t a t c a c c t g a g a a c a a g g t t t g a c c t t g t t g t g a

2940 f1 ori c a a c c c t a t c t c g g t c t a t t c t t t t g a t t t a t a a g g g a t t t t g c c g a t t t c g g c c t a t t g g t t g g g a t a g a g c c a g a t a a g a a a a c t a a a t a t t c c c t a a a a c g g c t a a a g c c g g a t a a c

3000 f1 ori g t t a a a a a a t g a g c t g a t t t a a c a a a a a t t t a a c g c g a a t t t t a a c a a a a t a t t a a c g c t c a a t t t t t t a c t c g a c t a a a t t g t t t t t a a a t t g c g c t t a a a a t t g t t t t a t a a t t g c g a

3060 f1 ori AmpR promoter t a c a a t t t a g g t g g c a c t t t t c g g g g a a a t g t g c g c g g a a c c c c t a t t t g t t t a t t t t t c a t g t t a a a t c c a c c g t g a a a a g c c c c t t t a c a c g c g c c t t g g g g a t a a a c a a a t a a a a a g

3120 AmpR promoter t a a a t a c a t t c a a a t a t g t a t c c g c t c a t g a g a c a a t a a c c c t g a t a a a t g c t t c a a t a a a t t t a t g t a a g t t t a t a c a t a g g c g a g t a c t c t g t t a t t g g g a c t a t t t a c g a a g t t a t t

3180 1 5 10 signal sequence MSIQHFRVALIPFF AmpR promoter AmpR MSIQHFRVALIPFF t a t t g a a a a a g g a a g a g t a t g a g t a t t c a a c a t t t c c g t g t c g c c c t t a t t c c c t t t t t t a t a a c t t t t t c c t t c t c a t a c t c a t a a g t t g t a a a g g c a c a g c g g g a a t a a g g g a a a a a a

3240 15 20 signal sequence AAFCLPVFA 25 30 HPETLVKVKDA AmpR AAFCLPVFAHPETLVKVKDA g c g g c a t t t t g c c t t c c t g t t t t t g c t c a c c c a g a a a c g c t g g t g a a a g t a a a a g a t g c t c g c c g t a a a a c g g a a g g a c a a a a a c g a g t g g g t c t t t g c g a c c a c t t t c a t t t t c t a c g a

3300 35 40 45 50 EDQLGARVGYIELDLNSGKI AmpR EDQLGARVGYIELDLNSGKI g a a g a t c a g t t g g g t g c a c g a g t g g g t t a c a t c g a a c t g g a t c t c a a c a g c g g t a a g a t c c t t c t a g t c a a c c c a c g t g c t c a c c c a a t g t a g c t t g a c c t a g a g t t g t c g c c a t t c t a g

3360 55 60 65 70 LESFRPEERFPMMSTFKVLL AmpR C G A T Amp-R LESFRPEERFPMMSTFKVLL c t t g a g a g t t t t c g c c c c g a a g a a c g t t t t c c a a t g a t g a g c a c t t t t a a a g t t c t g c t a g a a c t c t c a a a a g c g g g g c t t c t t g c a a a a g g t t a c t a c t c g t g a a a a t t t c a a g a c g a t

3420 75 80 85 90 CGAVLSRIDAGQEQLGRRIH AmpR A C A C C G C G C C A T A A T A Amp-R CGAVLSRIDAGQEQLGRRIH t g t g g c g c g g t a t t a t c c c g t a t t g a c g c c g g g c a a g a g c a a c t c g g t c g c c g c a t a c a c a c a c c g c g c c a t a a t a g g g c a t a a c t g c g g c c c g t t c t c g t t g a g c c a g c g g c g t a t g t g

3480 95 100 105 110 YSQNDLVEYSPVTEKHLTDG AmpR YSQNDLVEYSPVTEKHLTDG t a t t c t c a g a a t g a c t t g g t t g a g t a c t c a c c a g t c a c a g a a a a g c a t c t t a c g g a t g g c a t a a g a g t c t t a c t g a a c c a a c t c a t g a g t g g t c a g t g t c t t t t c g t a g a a t g c c t a c c g

3540 115 120 125 130 MTVRELCSAAITMSDNTAAN AmpR MTVRELCSAAITMSDNTAAN a t g a c a g t a a g a g a a t t a t g c a g t g c t g c c a t a a c c a t g a g t g a t a a c a c t g c g g c c a a c t a c t g t c a t t c t c t t a a t a c g t c a c g a c g g t a t t g g t a c t c a c t a t t g t g a c g c c g g t t g

3600 135 140 145 150 LLLTTIGGPKELTAFLHNMG AmpR LLLTTIGGPKELTAFLHNMG t t a c t t c t g a c a a c g a t c g g a g g a c c g a a g g a g c t a a c c g c t t t t t t g c a c a a c a t g g g g a a t g a a g a c t g t t g c t a g c c t c c t g g c t t c c t c g a t t g g c g a a a a a a c g t g t t g t a c c c c

3660 155 160 165 170 DHVTRLDRWEPELNEAIPND AmpR DHVTRLDRWEPELNEAIPND g a t c a t g t a a c t c g c c t t g a t c g t t g g g a a c c g g a g c t g a a t g a a g c c a t a c c a a a c g a c c t a g t a c a t t g a g c g g a a c t a g c a a c c c t t g g c c t c g a c t t a c t t c g g t a t g g t t t g c t g

3720 175 180 185 190 ERDTTMPVAMATTLRKLLTG AmpR ERDTTMPVAMATTLRKLLTG g a g c g t g a c a c c a c g a t g c c t g t a g c a a t g g c a a c a a c g t t g c g c a a a c t a t t a a c t g g c c t c g c a c t g t g g t g c t a c g g a c a t c g t t a c c g t t g t t g c a a c g c g t t t g a t a a t t g a c c g

3780 195 200 205 210 ELLTLASRQQLIDWMEADKV AmpR ELLTLASRQQLIDWMEADKV g a a c t a c t t a c t c t a g c t t c c c g g c a a c a a t t a a t a g a c t g g a t g g a g g c g g a t a a a g t t c t t g a t g a a t g a g a t c g a a g g g c c g t t g t t a a t t a t c t g a c c t a c c t c c g c c t a t t t c a a

3840 215 220 225 230 AGPLLRSALPAGWFIADKSG AmpR AGPLLRSALPAGWFIADKSG g c a g g a c c a c t t c t g c g c t c g g c c c t t c c g g c t g g c t g g t t t a t t g c t g a t a a a t c t g g a c g t c c t g g t g a a g a c g c g a g c c g g g a a g g c c g a c c g a c c a a a t a a c g a c t a t t t a g a c c t

3900 235 240 245 250 AGERGSRGIIAALGPDGKPS AmpR AGERGSRGIIAALGPDGKPS g c c g g t g a g c g t g g g t c t c g c g g t a t c a t t g c a g c a c t g g g g c c a g a t g g t a a g c c c t c c c g g c c a c t c g c a c c c a g a g c g c c a t a g t a a c g t c g t g a c c c c g g t c t a c c a t t c g g g a g g

3960 255 260 265 270 RIVVIYTTGSQATMDERNRQ AmpR RIVVIYTTGSQATMDERNRQ c g t a t c g t a g t t a t c t a c a c g a c g g g g a g t c a g g c a a c t a t g g a t g a a c g a a a t a g a c a g g c a t a g c a t c a a t a g a t g t g c t g c c c c t c a g t c c g t t g a t a c c t a c t t g c t t t a t c t g t c

4020 275 280 285 IAEIGASLIKHW* AmpR IAEIGASLIKHW* a t c g c t g a g a t a g g t g c c t c a c t g a t t a a g c a t t g g t a a c t g t c a g a c c a a g t t t a c t c a t a g c g a c t c t a t c c a c g g a g t g a c t a a t t c g t a a c c a t t g a c a g t c t g g t t c a a a t g a g t

4080 t a t a t a c t t t a g a t t g a t t t a a a a c t t c a t t t t t a a t t t a a a a g g a t c t a g g t g a a g a t c a t a t a t g a a a t c t a a c t a a a t t t t g a a g t a a a a a t t a a a t t t t c c t a g a t c c a c t t c t a g

4140 c t t t t t g a t a a t c t c a t g a c c a a a a t c c c t t a a c g t g a g t t t t c g t t c c a c t g a g c g t c a g a a a a a c t a t t a g a g t a c t g g t t t t a g g g a a t t g c a c t c a a a a g c a a g g t g a c t c g c a g t

4200 ori g a c c c c g t a g a a a a g a t c a a a g g a t c t t c t t g a g a t c c t t t t t t t c t g c g c g t a a t c t g c c t g g g g c a t c t t t t c t a g t t t c c t a g a a g a a c t c t a g g a a a a a a a g a c g c g c a t t a g a c g

4260 ori t g c t t g c a a a c a a a a a a a c c a c c g c t a c c a g c g g t g g t t t g t t t g c c g g a t c a a g a g c t a a c g a a c g t t t g t t t t t t t g g t g g c g a t g g t c g c c a c c a a a c a a a c g g c c t a g t t c t c g a t

4320 ori c c a a c t c t t t t t c c g a a g g t a a c t g g c t t c a g c a g a g c g c a g a t a c c a a a t a c t g t t c t t g g t t g a g a a a a a g g c t t c c a t t g a c c g a a g t c g t c t c g c g t c t a t g g t t t a t g a c a a g a a

4380 ori c t a g t g t a g c c g t a g t t a g g c c a c c a c t t c a a g a a c t c t g t a g c a c c g c c t a c a t a c c t c g a t c a c a t c g g c a t c a a t c c g g t g g t g a a g t t c t t g a g a c a t c g t g g c g g a t g t a t g g a g

4440 ori g c t c t g c t a a t c c t g t t a c c a g t g g c t g c t g c c a g t g g c g a t a a g t c g t g t c t t a c c g g g c g a g a c g a t t a g g a c a a t g g t c a c c g a c g a c g g t c a c c g c t a t t c a g c a c a g a a t g g c c c

4500 ori t t g g a c t c a a g a c g a t a g t t a c c g g a t a a g g c g c a g c g g t c g g g c t g a a c g g g g g g t t c g a a c c t g a g t t c t g c t a t c a a t g g c c t a t t c c g c g t c g c c a g c c c g a c t t g c c c c c c a a g c

4560 ori t g c a c a c a g c c c a g c t t g g a g c g a a c g a c c t a c a c c g a a c t g a g a t a c c t a c a g c g t g a g a c g t g t g t c g g g t c g a a c c t c g c t t g c t g g a t g t g g c t t g a c t c t a t g g a t g t c g c a c t c

4620 ori c t a t g a g a a a g c g c c a c g c t t c c c g a a g g g a g a a a g g c g g a c a g g t a t c c g g t a a g c g g c g a t a c t c t t t c g c g g t g c g a a g g g c t t c c c t c t t t c c g c c t g t c c a t a g g c c a t t c g c c g

4680 ori G G G A A A C G C C T G G T A T C T T T pBR322ori-F a g g g t c g g a a c a g g a g a g c g c a c g a g g g a g c t t c c a g g g g g a a a c g c c t g g t a t c t t t a t t c c c a g c c t t g t c c t c t c g c g t g c t c c c t c g a a g g t c c c c c t t t g c g g a c c a t a g a a a t a

4740 ori a g t c c t g t c g g g t t t c g c c a c c t c t g a c t t g a g c g t c g a t t t t t g t g a t g c t c g t c a g g g t c a g g a c a g c c c a a a g c g g t g g a g a c t g a a c t c g c a g c t a a a a a c a c t a c g a g c a g t c c c

4800 ori g g g c g g a g c c t a t g g a a a a a c g c c a g c a a c g c g g c c t t t t t a c g g t t c c t g g c c t t t t g c c c c g c c t c g g a t a c c t t t t t g c g g t c g t t g c g c c g g a a a a a t g c c a a g g a c c g g a a a a c g

AflIIIPciI 4860 t g g c c t t t t g c t c a c a t g t t c t t t c c t g c g t t a t c c c c t g a t t c t g t g g a t a a c c g t a t t a c c g g a a a a c g a g t g t a c a a g a a a g g a c g c a a t a g g g g a c t a a g a c a c c t a t t g g c a t a a

4920 A G C G A G T C A L4440 a c c g c c t t t g a g t g a g c t g a t a c c g c t c g c c g c a g c c g a a c g a c c g a g c g c a g c g a g t c a t g g c g g a a a c t c a c t c g a c t a t g g c g a g c g g c g t c g g c t t g c t g g c t c g c g t c g c t c a g t

4980 G T G A G C G A G L4440 g t g a g c g a g g a a g c g g a a g a g c g c c c a a t a c g c a a a c c g c c t c t c c c c g c g c g t t g g c c g c a c t c g c t c c t t c g c c t t c t c g c g g g t t a t g c g t t t g g c g g a g a g g g g c g c g c a a c c g g c

5040 a t t c a t t a a t g c a g c t g g c a c g a c a g g t t t c c c g a c t g g a a a g c g g g c a g t g a g c g c a a c t a a g t a a t t a c g t c g a c c g t g c t g t c c a a a g g g c t g a c c t t t c g c c c g t c a c t c g c g t t g

5100 -35 CAP binding site lac promoter g c a a t t a a t g t g a g t t a g c t c a c t c a t t a g g c a c c c c a g g c t t t a c a c t t t a t g c t t c c g c g t t a a t t a c a c t c a a t c g a g t g a g t a a t c c g t g g g g t c c g a a a t g t g a a a t a c g a a g g c

5160 -10 lac promoter lac operator M13 rev A G C G G A T A A C A A T T T C A C A C A G G M13/pUC Reverse C A G G A A A C A G C T A T G A C M13 Reverse g c t c g t a t g t t g t g t g g a a t t g t g a g c g g a t a a c a a t t t c a c a c a g g a a a c a g c t a t g a c c g a g c a t a c a a c a c a c c t t a a c a c t c g c c t a t t g t t a a a g t g t g t c c t t t g t c g a t a c t g

5220 T3 promoter G C A A T T A A C C C T C A C T A A A G G T3 c a t g a t t a c g c c a a g c g c g c a a t t a a c c c t c a c t a a a g g g a a c a a a a g c t g g a g c t g c a a g t a c t a a t g c g g t t c g c g c g t t a a t t g g g a g t g a t t t c c c t t g t t t t c g a c c t c g a c g t t

5280 RSV promoter g c t t a a t g t a g t c t t a t g c a a t a c t c t t g t a g t c t t g c a a c a t g g t a a c g a t g a g t t a g c c g a a t t a c a t c a g a a t a c g t t a t g a g a a c a t c a g a a c g t t g t a c c a t t g c t a c t c a a t c g

SphI 5340 RSV promoter a a c a t g c c t t a c a a g g a g a g a a a a a g c a c c g t g c a t g c c g a t t g g t g g a a g t a a g g t g g t t t g t a c g g a a t g t t c c t c t c t t t t t c g t g g c a c g t a c g g c t a a c c a c c t t c a t t c c a c c a

5400 RSV promoter a c g a t c g t g c c t t a t t a g g a a g g c a a c a g a c g g g t c t g a c a t g g a t t g g a c g a a c c a c t g t g c t a g c a c g g a a t a a t c c t t c c g t t g t c t g c c c a g a c t g t a c c t a a c c t g c t t g g t g a c

5460 RSV promoter 5' LTR (truncated) a a t t g c c g c a t t g c a g a g a t a t t g t a t t t a a g t g c c t a g c t c g a t a c a t a a a c g g g t c t c t t a a c g g c g t a a c g t c t c t a t a a c a t a a a t t c a c g g a t c g a g c t a t g t a t t t g c c c a g a g

5520 5' LTR (truncated) t c t g g t t a g a c c a g a t c t g a g c c t g g g a g c t c t c t g g c t a a c t a g g g a a c c c a c t g c t t a a g a c c a a t c t g g t c t a g a c t c g g a c c c t c g a g a g a c c g a t t g a t c c c t t g g g t g a c g a a t

5580 5' LTR (truncated) a g c c t c a a t a a a g c t t g c c t t g a g t g c t t c a a g t a g t g t g t g c c c g t c t g t t g t g t g a c t t c g g a g t t a t t t c g a a c g g a a c t c a c g a a g t t c a t c a c a c a c g g g c a g a c a a c a c a c t g a

5640 5' LTR (truncated) c t g g t a a c t a g a g a t c c c t c a g a c c c t t t t a g t c a g t g t g g a a a a t c t c t a g c a g t g g c g g a c c a t t g a t c t c t a g g g a g t c t g g g a a a a t c a g t c a c a c c t t t t a g a g a t c g t c a c c g c

5700 HIV-1 Ψ c c c g a a c a g g g a c t t g a a a g c g a a a g g g a a a c c a g a g g a g c t c t c t c g a c g c a g g a c t c g g g g c t t g t c c c t g a a c t t t c g c t t t c c c t t t g g t c t c c t c g a g a g a g c t g c g t c c t g a g c

5760 HIV-1 Ψ g c t t g c t g a a g c g c g c a c g g c a a g a g g c g a g g g g c g g c g a c t g g t g a g t a c g c c a a a a a t c g a a c g a c t t c g c g c g t g c c g t t c t c c g c t c c c c g c c g c t g a c c a c t c a t g c g g t t t t t a

5820 HIV-1 Ψ t t t g a c t a g c g g a g g c t a g a a g g a g a g a g a t g g g t g c g a g a g c g t c a g t a t t a a g c g g g g a a a c t g a t c g c c t c c g a t c t t c c t c t c t c t a c c c a c g c t c t c g c a g t c a t a a t t c g c c c c

NruI* 5880 g a g a a t t a g a t c g c g a t g g g a a a a a a t t c g g t t a a g g c c a g g g g g a a a g a a a a a a t a t a a c t c t t a a t c t a g c g c t a c c c t t t t t t a a g c c a a t t c c g g t c c c c c t t t c t t t t t t a t a t t

5940 a t t a a a a c a t a t a g t a t g g g c a a g c a g g g a g c t a g a a c g a t t c g c a g t t a a t c c t g g c c t t a a t t t t g t a t a t c a t a c c c g t t c g t c c c t c g a t c t t g c t a a g c g t c a a t t a g g a c c g g a

6000 g t t a g a a a c a t c a g a a g g c t g t a g a c a a a t a c t g g g a c a g c t a c a a c c a t c c c t t c a g a c c a a t c t t t g t a g t c t t c c g a c a t c t g t t t a t g a c c c t g t c g a t g t t g g t a g g g a a g t c t g

6060 a g g a t c a g a a g a a c t t a g a t c a t t a t a t a a t a c a g t a g c a a c c c t c t a t t g t g t g c a t c a t c c t a g t c t t c t t g a a t c t a g t a a t a t a t t a t g t c a t c g t t g g g a g a t a a c a c a c g t a g t

6120 a a g g a t a g a g a t a a a a g a c a c c a a g g a a g c t t t a g a c a a g a t a g a g g a a g a g c a a a a c a a t t c c t a t c t c t a t t t t c t g t g g t t c c t t c g a a a t c t g t t c t a t c t c c t t c t c g t t t t g t t

6180 M a a g t a a g a c c a c c g c a c a g c a a g c g g c c g c t g a t c t t c a g a c c t g g a g g a g g a g a t a t g a t t c a t t c t g g t g g c g t g t c g t t c g c c g g c g a c t a g a a g t c t g g a c c t c c t c c t c t a t a c t

MfeI 6240 RDNWRSELYKYKVVKIEPLG g g g a c a a t t g g a g a a g t g a a t t a t a t a a a t a t a a a g t a g t a a a a a t t g a a c c a t t a g g a g c c c t g t t a a c c t c t t c a c t t a a t a t a t t t a t a t t t c a t c a t t t t t a a c t t g g t a a t c c t c

6300 RRE VAPTKAKRRVVQREKRAVGI t a g c a c c c a c c a a g g c a a a g a g a a g a g t g g t g c a g a g a g a a a a a a g a g c a g t g g g a a t a g a t c g t g g g t g g t t c c g t t t c t c t t c t c a c c a c g t c t c t c t t t t t t c t c g t c a c c c t t a t c

6360 RRE GALFLGFLGAAGSTMGAASM g a g c t t t g t t c c t t g g g t t c t t g g g a g c a g c a g g a a g c a c t a t g g g c g c a g c g t c a a t g a c t c g a a a c a a g g a a c c c a a g a a c c c t c g t c g t c c t t c g t g a t a c c c g c g t c g c a g t t a c t

6420 RRE TLTVQARQLLSGIVQQQNNL c g c t g a c g g t a c a g g c c a g a c a a t t a t t g t c t g g t a t a g t g c a g c a g c a g a a c a a t t t g c g c g a c t g c c a t g t c c g g t c t g t t a a t a a c a g a c c a t a t c a c g t c g t c g t c t t g t t a a a c g

6480 RRE LRAIEAQQHLLQLTVWGIKQ t g a g g g c t a t t g a g g c g c a a c a g c a t c t g t t g c a a c t c a c a g t c t g g g g c a t c a a g c a g c a c t c c c g a t a a c t c c g c g t t g t c g t a g a c a a c g t t g a g t g t c a g a c c c c g t a g t t c g t c g

6540 RRE LQARILAVERYLKDQQLLGI t c c a g g c a a g a a t c c t g g c t g t g g a a a g a t a c c t a a a g g a t c a a c a g c t c c t g g g g a t t t a g g t c c g t t c t t a g g a c c g a c a c c t t t c t a t g g a t t t c c t a g t t g t c g a g g a c c c c t a a a

AleI 6600 WGCSGKLICTTAVPWNASWS g g g g t t g c t c t g g a a a a c t c a t t t g c a c c a c t g c t g t g c c t t g g a a t g c t a g t t g g a g t a c c c c a a c g a g a c c t t t t g a g t a a a c g t g g t g a c g a c a c g g a a c c t t a c g a t c a a c c t c a t

6660 NKSLEQIWNHTTWMEWDREI a t a a a t c t c t g g a a c a g a t t t g g a a t c a c a c g a c c t g g a t g g a g t g g g a c a g a g a a a t t a t a t t t a g a g a c c t t g t c t a a a c c t t a g t g t g c t g g a c c t a c c t c a c c c t g t c t c t t t a a t

6720 1 K gp41 peptide NNYTSLIHSLIEESQNQQEK a c a a t t a c a c a a g c t t a a t a c a c t c c t t a a t t g a a g a a t c g c a a a a c c a g c a a g a a a a g a t g t t a a t g t g t t c g a a t t a t g t g a g g a a t t a a c t t c t t a g c g t t t t g g t c g t t c t t t t c t

6780 5 10 15 NEQELLELDKWASL (in frame with gp41 peptide) WNWFNI gp41 peptide NEQELLELDKWASLWNWFNI a t g a a c a a g a a t t a t t g g a a t t a g a t a a a t g g g c a a g t t t g t g g a a t t g g t t t a a c a t a a t a c t t g t t c t t a a t a a c c t t a a t c t a t t t a c c c g t t c a a a c a c c t t a a c c a a a t t g t a t t

6840 (in frame with gp41 peptide) TNWLWYIKLFIMIVGGLVGL TNWLWYIKLFIMIVGGLVGL c a a a t t g g c t g t g g t a t a t a a a a t t a t t c a t a a t g a t a g t a g g a g g c t t g g t a g g t t t a a g t t t a a c c g a c a c c a t a t a t t t t a a t a a g t a t t a c t a t c a t c c t c c g a a c c a t c c a a a t t

6900 (in frame with gp41 peptide) RIVFAVLSIVNRVRQGYSPL RIVFAVLSIVNRVRQGYSPL g a a t a g t t t t t g c t g t a c t t t c t a t a g t g a a t a g a g t t a g g c a g g g a t a t t c a c c a t t a t c t t a t c a a a a a c g a c a t g a a a g a t a t c a c t t a t c t c a a t c c g t c c c t a t a a g t g g t a a t a

PpuMIKflI 6960 (in frame with gp41 peptide) SFQTHLPTPRGPDRPEGIEE SFQTHLPTPRGPDRPEGIEE c g t t t c a g a c c c a c c t c c c a a c c c c g a g g g g a c c c g a c a g g c c c g a a g g a a t a g a a g a a g g c a a a g t c t g g g t g g a g g g t t g g g g c t c c c c t g g g c t g t c c g g g c t t c c t t a t c t t c t t c

7020 (in frame with gp41 peptide) EGGERDRDRSIRLVNGSRRY EGGERDRDRSIRLVNGSRRY a a g g t g g a g a g a g a g a c a g a g a c a g a t c c a t t c g a t t a g t g a a c g g a t c t c g a c g g t a t c t t c c a c c t c t c t c t c t g t c t c t g t c t a g g t a a g c t a a t c a c t t g c c t a g a g c t g c c a t a g

7080 RSRD* U6 promoter G A G G G C C T A T T T C C C A T G A T T hU6-F RSRD* g a t c a c g a g a c t a g c c t c g a g c g g c c g c c c c c t t c a c c g a g g g c c t a t t t c c c a t g a t t c c t a g t g c t c t g a t c g g a g c t c g c c g g c g g g g g a a g t g g c t c c c g g a t a a a g g g t a c t a a g

7140 U6 promoter c t t c a t a t t t g c a t a t a c g a t a c a a g g c t g t t a g a g a g a t a a t t g g a a t t a a t t t g a c t g g a a g t a t a a a c g t a t a t g c t a t g t t c c g a c a a t c t c t c t a t t a a c c t t a a t t a a a c t g a c

7200 U6 promoter t a a a c a c a a a g a t a t t a g t a c a a a a t a c g t g a c g t a g a a a g t a a t a a t t t c t t g g g t a g t a t t t g t g t t t c t a t a a t c a t g t t t t a t g c a c t g c a t c t t t c a t t a t t a a a g a a c c c a t c a

7260 U6 promoter G A C T A T C A T A T G C T T A C C G T LKO.1 5' t t g c a g t t t t a a a a t t a t g t t t t a a a a t g g a c t a t c a t a t g c t t a c c g t a a c t t g a a a g t a a c g t c a a a a t t t t a a t a c a a a a t t t t a c c t g a t a g t a t a c g a a t g g c a t t g a a c t t t c a

SgrAIAgeI 7320 U6 promoter a t t t c g a t t t c t t g g c t t t a t a t a t c t t g t g g a a a g g a c g a a a c a c c g g t g t c t t c g a g g t a a a g c t a a a g a a c c g a a a t a t a t a g a a c a c c t t t c c t g c t t t g t g g c c a c a g a a g c t c c

7380 c t t a c t a a a a g c c a g a t a a c a g t a t g c g t a t t t g c g c g c t g a t t t t t g c g g t a t a a g a a t g a a t g a t t t t c g g t c t a t t g t c a t a c g c a t a a a c g c g c g a c t a a a a a c g c c a t a t t c t t a

BstZ17I 7440 a t a t a c t g a t a t g t a t a c c c g a a g t a t g t c a a a a a g a g g t g t g c t a t g a a g c a g c g t a t t t a t a t g a c t a t a c a t a t g g g c t t c a t a c a g t t t t t c t c c a c a c g a t a c t t c g t c g c a t a a

7500 a c a g t g a c a g t t g a c a g c g a c a g c t a t c a g t t g c t c a a g g c a t a t a t g a t g t c a a t a t c t t g t c a c t g t c a a c t g t c g c t g t c g a t a g t c a a c g a g t t c c g t a t a t a c t a c a g t t a t a g a

7560 c c g g t c t g g t a a g c a c a a c c a t g c a g a a t g a a g c c c g t c g t c t g c g t g c c g a a c g c t g g a g g c c a g a c c a t t c g t g t t g g t a c g t c t t a c t t c g g g c a g c a g a c g c a c g g c t t g c g a c c t

7620 a a g c g g a a a a t c a g g a a g g g a t g g c t g a g g t c g c c c g g t t t a t t g a a a t g a a c g g c t c t t t t c g c c t t t t a g t c c t t c c c t a c c g a c t c c a g c g g g c c a a a t a a c t t t a c t t g c c g a g a a

7680 1 5 10 MQFKVYTYKRE ccdB t t g c t g a c g a g a a c a g g g a c t g g t g a a a t g c a g t t t a a g g t t t a c a c c t a t a a a a g a g a g a a c g a c t g c t c t t g t c c c t g a c c a c t t t a c g t c a a a t t c c a a a t g t g g a t a t t t t c t c t c

SrfIBsrGI 7740 15 20 25 30 SRYRLFVDVQSDIIDTPGRR ccdB a g c c g t t a t c g t c t g t t t g t g g a t g t a c a g a g t g a t a t t a t t g a c a c g c c c g g g c g a c g g t c g g c a a t a g c a g a c a a a c a c c t a c a t g t c t c a c t a t a a t a a c t g t g c g g g c c c g c t g c c

BsaBI* 7800 35 40 45 50 MVIPLASARLLSDKVSRELY ccdB a t g g t g a t c c c c c t g g c c a g t g c a c g t c t g c t g t c a g a t a a a g t c t c c c g t g a a c t t t a c t a c c a c t a g g g g g a c c g g t c a c g t g c a g a c g a c a g t c t a t t t c a g a g g g c a c t t g a a a t g

BstXI 7860 55 60 65 70 PVVHIGDESWRMMTTDMASV ccdB G C A T G A T G A C C A C C G A T A T G ccdB-fwd c c g g t g g t g c a t a t c g g g g a t g a a a g c t g g c g c a t g a t g a c c a c c g a t a t g g c c a g t g t g g g c c a c c a c g t a t a g c c c c t a c t t t c g a c c g c g t a c t a c t g g t g g c t a t a c c g g t c a c a c

7920 75 80 85 90 PVSVIGEEVADLSHRENDIK ccdB c c g g t c t c c g t t a t c g g g g a a g a a g t g g c t g a t c t c a g c c a c c g c g a a a a t g a c a t c a a a g g c c a g a g g c a a t a g c c c c t t c t t c a c c g a c t a g a g t c g g t g g c g c t t t t a c t g t a g t t t

SbfI 7980 95 100 NAINLMFWGI* ccdB a a c g c c a t t a a c c t g a t g t t c t g g g g a a t a t a a a c c c t g c a g g a c g a a g a c c c g t t t g a g t t g c g g t a a t t g g a c t a c a a g a c c c c t t a t a t t t g g g a c g t c c t g c t t c t g g g c a a a c t c

8040 boxB a g c t a g g g c c c t g a a g a a g g g c c c t a g c a a g t t c a a a t a a g g c t a g t c c g t t a t c a a c t t t c g a t c c c g g g a c t t c t t c c c g g g a t c g t t c a a g t t t a t t c c g a t c a g g c a a t a g t t g a a

8100 MS2 stem loop MSAGPSGTESVRS g g c c a a c a t g a g g a t c a c c c a t g t c t g c a g g g c c a a g t g g c a c c g a g t c g g t g c g g a g c a c c g g t t g t a c t c c t a g t g g g t a c a g a c g t c c c g g t t c a c c g t g g c t c a g c c a c g c c t c g t

EcoRI 8160 RRYGVAPFFEFSTSRQMAVF g a c g a t a t g g c g t c g c t c c t t t t t t t g a a t t c t c g a c c t c g a g a c a a a t g g c a g t a t t c a c t g c t a t a c c g c a g c g a g g a a a a a a a c t t a a g a g c t g g a g c t c t g t t t a c c g t c a t a a g t

8220 cPPT/CTS IHNFKRKGGIGGYSAGERIV t c c a c a a t t t t a a a a g a a a a g g g g g g a t t g g g g g g t a c a g t g c a g g g g a a a g a a t a g t a g a g g t g t t a a a a t t t t c t t t t c c c c c c t a a c c c c c c a t g t c a c g t c c c c t t t c t t a t c a t c

8280 cPPT/CTS DIIATDIQTKELQKQITKIQ a c a t a a t a g c a a c a g a c a t a c a a a c t a a a g a a t t a c a a a a a c a a a t t a c a a a a a t t c a a a t g t a t t a t c g t t g t c t g t a t g t t t g a t t t c t t a a t g t t t t t g t t t a a t g t t t t t a a g t t t

8337 cPPT/CTS hPGK promoter NFRVYYRDSRDPLWPRLEG a t t t t c g g g t t t a t t a c a g g g a c a g c a g a g a t c c a c t t t g g c c g c g g c t c g a g g g g g t a a a a g c c c a a a t a a t g t c c c t g t c g t c t c t a g g t g a a a c c g g c g c c g a g c t c c c c c

Restriction Enzymes

Instructions: By default, all cutters are shown. Filter on number of cut sites or search by enzyme name.

Filter

Features

Primers

BLAST

BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. Click on the buttons below to submit a BLAST search to NCBI. The results will appear in a new window. See your recent BLAST results on NCBI's website.

  • Nucleotide-Nucleotide BLAST (BLASTN)

  • Translated Nucleotide-Protein BLAST (BLASTX)

  • Sequence alignment using BLAST (BLAST2)

Sequence Analyzer Guide

Map

Displays a graphical map based on nucleotide sequence data labeled with restriction enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. Hovering over data labels will display additional information (e.g. cut site)

To select a portion of sequence, click one location on the plasmid and then a second location to display the sequence between the two locations.

Sequence

Displays both strands of base paired nucleotide sequences with annotated enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. Hovering over data labels will display additional information (e.g. cut site).

To select a portion of sequence, click one location on the sequence and then a second location to display the sequence between the two locations.

Enzymes

List of restriction enzymes that can cut a given nucleotide sequence. Table lists enzyme name and the sequence location of the cut.

Features

List of common features detected in a given nucleotide sequence. Table lists feature name, location, size, color used to indicate its position on the map, and direction (if relevant).

Primers

List of commonly used primers detected in a given nucleotide sequence. Table lists primer name, sequence, length, binding site location, and direction.

BLAST

Use Basic Local Alignment Search Tool (BLAST) via the NCBI website to determine similarity between a given sequence and nucleotide (BLASTN) or protein (BLASTX) sequence databases. Additionally, align a custom nucleotide sequence against a given sequence using BLAST2.

File Downloads

GenBank

File contains the nucleotide sequence and annotated features in GenBank flat file format. Open the file with a text editor or plasmid mapping software to view the sequence.

SnapGene

File contains the nucleotide sequence and enhanced annotations from SnapGene Server. Open the file with SnapGene software or the free Viewer to view the plasmid map, sequence, and perform additional sequence analysis.