Addgene pDM042 Sequencing Result - Sequence Analyzer Skip to main content
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Sequence Analyzer: pDM042 Sequencing Result


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EcoO109I (2997) pBRforEco (2981 .. 2999) AatII (2943) ZraI (2941) SspI (2825) XmnI (2620) Amp-R (2571 .. 2590) ScaI (2501) TsoI (2420) EaeI (2409) PvuI (2391) FspI (2243) AseI (2193) NmeAIII (2169) BpmI (2091) BsaI (2082) BmrI (2061) AhdI (2021) AlwNI (1544) PfoI (46) pGEX 3' (29 .. 51) pRS-marker (151 .. 170) NdeI (184) BstAPI (185) KasI (235) NarI (236) SfoI (237) PluTI (239) PaeR7I - XhoI (273) Eco53kI (278) BanII - SacI (280) SalI (282) AccI (283) HincII (284) BsaAI (429) BseRI (466) BstBI (586) SacII (665) NcoI - StyI (709) BbsI (711) PflMI (715) StuI (723) AflII (789) PshAI (799) AgeI (957) BspQI - SapI (1012) L4440 (1018 .. 1035) PciI (1128) pBR322ori-F (1269 .. 1288) BseYI (1432) PspFI (1436) pDM042 3008 bp

Sequence View

PfoI 60 G G A G A C T G T G T A C G T C G A G G G C C pGEX 3' t c g c g c g t t t c g g t g a t g a c g g t g a a a a c c t c t g a c a c a t g c a g c t c c c g g a g a c g g t c a a g c g c g c a a a g c c a c t a c t g c c a c t t t t g g a g a c t g t g t a c g t c g a g g g c c t c t g c c a g t

120 c a g c t t g t c t g t a a g c g g a t g c c g g g a g c a g a c a a g c c c g t c a g g g c g c g t c a g c g g g t g g t c g a a c a g a c a t t c g c c t a c g g c c c t c g t c t g t t c g g g c a g t c c c g c g c a g t c g c c c a c

180 C G G C A T C A G A G C A G A T T G T A pRS-marker t t g g c g g g t g t c g g g g c t g g c t t a a c t a t g c g g c a t c a g a g c a g a t t g t a c t g a g a g t g c a a c c g c c c a c a g c c c c g a c c g a a t t g a t a c g c c g t a g t c t c g t c t a a c a t g a c t c t c a c g

KasINarISfoIPluTINdeIBstAPI 240 MRCEIPHRCVRRKYRIRR a c c a t a t g c g g t g t g a a a t a c c g c a c a g a t g c g t a a g g a g a a a a t a c c g c a t c a g g c g c c t g g t a t a c g c c a c a c t t t a t g g c g t g t c t a c g c a t t c c t c t t t t a t g g c g t a g t c c g c g g

PaeR7IXhoIEco53kIBanIISacISalIAccIHincII 300 1 MDS mScarlet3 HSPFRLRQAAALELVDPMDS a t t c g c c a t t c a g g c t g c g c c a g g c t g c t g c t c t c g a g c t c g t c g a c c c t a t g g a c t c c a t a a g c g g t a a g t c c g a c g c g g t c c g a c g a c g a g a g c t c g a g c a g c t g g g a t a c c t g a g g t

360 5 10 15 20 TEAVIKEFMRFKVHMEGSMN mScarlet3 TEAVIKEFMRFKVHMEGSMN c c g a g g c c g t c a t c a a g g a g t t t a t g c g t t t t a a g g t t c a c a t g g a a g g t t c t a t g a a c g g g c t c c g g c a g t a g t t c c t c a a a t a c g c a a a a t t c c a a g t g t a c c t t c c a a g a t a c t t g c

420 25 30 35 40 GHEFEIEGEGEGRPYEGTQT mScarlet3 GHEFEIEGEGEGRPYEGTQT g t c a c g a g t t c g a g a t c g a g g g t g a g g g t g a g g g t c g c c c c t a c g a g g g t a c c c a g a c c g c a g t g c t c a a g c t c t a g c t c c c a c t c c c a c t c c c a g c g g g g a t g c t c c c a t g g g t c t g g c

BseRIBsaAI 480 45 50 55 60 AKLRVTKGGPLPFSWDILSP mScarlet3 AKLRVTKGGPLPFSWDILSP *REGPVDERR c c a a g t t a c g t g t t a c t a a a g g t g g t c c t t t a c c t t t c t c c t g g g a c a t c c t c t c t c c t c g g t t c a a t g c a c a a t g a t t t c c a c c a g g a a a t g g a a a g a g g a c c c t g t a g g a g a g a g g a g

540 65 70 75 80 QFMYGSRAFTKHPADIPDYW mScarlet3 QFMYGSRAFTKHPADIPDYW LEHVTGAGEGLVGSINGIIP a g t t c a t g t a c g g t t c c c g c g c c t t c a c c a a g c a c c c c g c t g a t a t t c c c g a t t a t t g g a t c a a g t a c a t g c c a a g g g c g c g g a a g t g g t t c g t g g g g c g a c t a t a a g g g c t a a t a a c c t

BstBI 600 85 90 95 100 KQSFPEGFKWERVMNFEDGG mScarlet3 KQSFPEGFKWERVMNFEDGG LLGKGLTELPLADHVEFITT a g c a g t c c t t t c c c g a g g g t t t c a a g t g g g a g c g c g t c a t g a a c t t c g a a g a t g g t g g t g t c g t c a g g a a a g g g c t c c c a a a g t t c a c c c t c g c g c a g t a c t t g a a g c t t c t a c c a c c a c

660 105 110 115 120 AVSVAQDTSLEDGTLIYKVK mScarlet3 AVSVAQDTSLEDGTLIYKVK GDRNGLISGKLVTGEDVLDL c c g t c t c t g t t g c c c a a g a t a c t t c c c t t g a g g a c g g t a c c c t c a t c t a c a a g g t c a a g c g g c a g a g a c a a c g g g t t c t a t g a a g g g a a c t c c t g c c a t g g g a g t a g a t g t t c c a g t t c g

PflMINcoIStyIBbsISacII 720 125 130 135 140 LRGTNFPPDGPVMQKKTMGW mScarlet3 LRGTNFPPDGPVMQKKTMGW EATGIKRRITGDHLLLGHTP t c c g c g g t a c c a a t t t t c c t c c t g a t g g t c c c g t c a t g c a g a a g a a g a c c a t g g g t t g g g a g g c g c c a t g g t t a a a a g g a g g a c t a c c a g g g c a g t a c g t c t t c t t c t g g t a c c c a a c c c

StuI 780 145 150 155 160 EASTERLYPEDVVLKGDIKM mScarlet3 EASTERLYPEDVVLKGDIKM LGGGFTEVRLIDNKFTVDLH a g g c c t c c a c c g a a c g t c t c t a c c c t g a g g a t g t c g t t c t t a a a g g t g a c a t c a a g a t g g t c c g g a g g t g g c t t g c a g a g a t g g g a c t c c t a c a g c a a g a a t t t c c a c t g t a g t t c t a c c

PshAIAflII 840 165 170 175 180 ALRLKDGGRYLADFKTTYRA mScarlet3 ALRLKDGGRYLADFKTTYRA GKAKLVTTAVESVELGGVTS c c c t t c g c c t t a a g g a c g g t g g t c g c t a c c t c g c t g a c t t c a a g a c c a c c t a c c g t g c t a g g g a a g c g g a a t t c c t g c c a c c a g c g a t g g a g c g a c t g a a g t t c t g g t g g a t g g c a c g a t

900 185 190 195 200 KKPVQMPGAFNIDRKLDITS mScarlet3 KKPVQMPGAFNIDRKLDITS FLGNLHRTGEVDVALEVDGG a a a a g c c c g t t c a g a t g c c t g g t g c c t t c a a c a t c g a c c g c a a g c t c g a c a t c a c c t c c c t t t t c g g g c a a g t c t a c g g a c c a c g g a a g t t g t a g c t g g c g t t c g a g c t g t a g t g g a g g g

AgeI 960 205 210 215 220 HNEDYTVVEQYERSVARHST mScarlet3 HNEDYTVVEQYERSVARHST VVLVVGDDFLILTGNSTM a c a a c g a g g a c t a c a c c g t c g t c g a a c a a t a t g a g c g t t c c g t t g c t c g t c a t t c t a c c g t g t t g c t c c t g a t g t g g c a g c a g c t t g t t a t a c t c g c a a g g c a a c g a g c a g t a a g a t g g c

BspQISapI 1020 225 GGSGGS * mScarlet3 G A G L4440 GGSGGS* g t g g t t c t g g t g g t t c c t a a g g a g a g g c g g t t t g c g t a t t g g g c g c t c t t c c g c t t c c t c c a c c a a g a c c a c c a a g g a t t c c t c t c c g c c a a a c g c a t a a c c c g c g a g a a g g c g a a g g a g

1080 C G A G T G A C T G A G C G A L4440 g c t c a c t g a c t c g c t g c g c t c g g t c g t t c g g c t g c g g c g a g c g g t a t c a g c t c a c t c a a a c g a g t g a c t g a g c g a c g c g a g c c a g c a a g c c g a c g c c g c t c g c c a t a g t c g a g t g a g t t t

PciI 1140 g g c g g t a a t a c g g t t a t c c a c a g a a t c a g g g g a t a a c g c a g g a a a g a a c a t g t g a g c a a a c c g c c a t t a t g c c a a t a g g t g t c t t a g t c c c c t a t t g c g t c c t t t c t t g t a c a c t c g t t t

1200 ori a g g c c a g c a a a a g g c c a g g a a c c g t a a a a a g g c c g c g t t g c t g g c g t t t t t c c a t a g g c t t c c g g t c g t t t t c c g g t c c t t g g c a t t t t t c c g g c g c a a c g a c c g c a a a a a g g t a t c c g a

1260 ori c c g c c c c c c t g a c g a g c a t c a c a a a a a t c g a c g c t c a a g t c a g a g g t g g c g a a a c c c g a c g g c g g g g g g a c t g c t c g t a g t g t t t t t a g c t g c g a g t t c a g t c t c c a c c g c t t t g g g c t g

1320 ori T T T C T A T G G T C C G C A A A G G G pBR322ori-F a g g a c t a t a a a g a t a c c a g g c g t t t c c c c c t g g a a g c t c c c t c g t g c g c t c t c c t g t t c c t c c t g a t a t t t c t a t g g t c c g c a a a g g g g g a c c t t c g a g g g a g c a c g c g a g a g g a c a a g g

1380 ori g a c c c t g c c g c t t a c c g g a t a c c t g t c c g c c t t t c t c c c t t c g g g a a g c g t g g c g c t t t c c t g g g a c g g c g a a t g g c c t a t g g a c a g g c g g a a a g a g g g a a g c c c t t c g c a c c g c g a a a g

BseYIPspFI 1440 ori t c a t a g c t c a c g c t g t a g g t a t c t c a g t t c g g t g t a g g t c g t t c g c t c c a a g c t g g g c t g a g t a t c g a g t g c g a c a t c c a t a g a g t c a a g c c a c a t c c a g c a a g c g a g g t t c g a c c c g a c

1500 ori t g t g c a c g a a c c c c c c g t t c a g c c c g a c c g c t g c g c c t t a t c c g g t a a c t a t c g t c t t g a a c a c g t g c t t g g g g g g c a a g t c g g g c t g g c g a c g c g g a a t a g g c c a t t g a t a g c a g a a c t

AlwNI 1560 ori g t c c a a c c c g g t a a g a c a c g a c t t a t c g c c a c t g g c a g c a g c c a c t g g t a a c a g g a t t a g c a g g t t g g g c c a t t c t g t g c t g a a t a g c g g t g a c c g t c g t c g g t g a c c a t t g t c c t a a t c

1620 ori c a g a g c g a g g t a t g t a g g c g g t g c t a c a g a g t t c t t g a a g t g g t g g c c t a a c t a c g g c t a g t c t c g c t c c a t a c a t c c g c c a c g a t g t c t c a a g a a c t t c a c c a c c g g a t t g a t g c c g a t

1680 ori c a c t a g a a g a a c a g t a t t t g g t a t c t g c g c t c t g c t g a a g c c a g t t a c c t t c g g a a a a a g g t g a t c t t c t t g t c a t a a a c c a t a g a c g c g a g a c g a c t t c g g t c a a t g g a a g c c t t t t t c

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

1800 ori c a a g c a g c a g a t t a c g c g c a g a a a a a a a g g a t c t c a a g a a g a t c c t t t g a t c t t t t c t a c g t t c g t c g t c t a a t g c g c g t c t t t t t t t c c t a g a g t t c t t c t a g g a a a c t a g a a a a g a t g

1860 g g g g t c t g a c g c t c a g t g g a a c g a a a a c t c a c g t t a a g g g a t t t t g g t c a t g a g a t t a t c c c c c a g a c t g c g a g t c a c c t t g c t t t t g a g t g c a a t t c c c t a a a a c c a g t a c t c t a a t a g

1920 a a a a a g g a t c t t c a c c t a g a t c c t t t t a a a t t a a a a a t g a a g t t t t a a a t c a a t c t a a a g t t t t t c c t a g a a g t g g a t c t a g g a a a a t t t a a t t t t t a c t t c a a a a t t t a g t t a g a t t t c

1980 285 280 *WHKILSAGIE AmpR *WHKILSAGIE t a t a t a t g a g t a a a c t t g g t c t g a c a g t t a c c a a t g c t t a a t c a g t g a g g c a c c t a t c t c a t a t a t a c t c a t t t g a a c c a g a c t g t c a a t g g t t a c g a a t t a g t c a c t c c g t g g a t a g a g

AhdI 2040 275 270 265 260 AIQRNREDMTAQSGTTYIVV AmpR AIQRNREDMTAQSGTTYIVV a g c g a t c t g t c t a t t t c g t t c a t c c a t a g t t g c c t g a c t c c c c g t c g t g t a g a t a a c t a c t c g c t a g a c a g a t a a a g c a a g t a g g t a t c a a c g g a c t g a g g g g c a g c a c a t c t a t t g a t g

BpmIBsaIBmrI 2100 255 250 245 240 IRSPKGDPGLAAIIGRSGRE AmpR IRSPKGDPGLAAIIGRSGRE g a t a c g g g a g g g c t t a c c a t c t g g c c c c a g t g c t g c a a t g a t a c c g c g a g a c c c a c g c t c c t a t g c c c t c c c g a a t g g t a g a c c g g g g t c a c g a c g t t a c t a t g g c g c t c t g g g t g c g a g

2160 235 230 225 220 GAGSKDAIFWGAPLASRLLP AmpR GAGSKDAIFWGAPLASRLLP a c c g g c t c c a g a t t t a t c a g c a a t a a a c c a g c c a g c c g g a a g g g c c g a g c g c a g a a g t g g t g g c c g a g g t c t a a a t a g t c g t t a t t t g g t c g g t c g g c c t t c c c g g c t c g c g t c t t c a c c

AseINmeAIII 2220 215 210 205 200 GAVKDAEMWDILQQRSALTL AmpR GAVKDAEMWDILQQRSALTL t c c t g c a a c t t t a t c c g c c t c c a t c c a g t c t a t t a a t t g t t g c c g g g a a g c t a g a g t a a g a g g a c g t t g a a a t a g g c g g a g g t a g g t c a g a t a a t t a a c a a c g g c c c t t c g a t c t c a t t c

FspI 2280 195 190 185 180 LEGTLLKRLTTAMAVPMTTD AmpR LEGTLLKRLTTAMAVPMTTD t a g t t c g c c a g t t a a t a g t t t g c g c a a c g t t g t t g c c a t t g c t a c a g g c a t c g t g g t g t c a t c a a g c g g t c a a t t a t c a a a c g c g t t g c a a c a a c g g t a a c g a t g t c c g t a g c a c c a c a g

2340 175 170 165 160 REDNPIAENLEPEWRDLRTV AmpR REDNPIAENLEPEWRDLRTV a c g c t c g t c g t t t g g t a t g g c t t c a t t c a g c t c c g g t t c c c a a c g a t c a a g g c g a g t t a c t g c g a g c a g c a a a c c a t a c c g a a g t a a g t c g a g g c c a a g g g t t g c t a g t t c c g c t c a a t g

PvuI 2400 155 150 145 140 HDGMNHLFATLEKPGGITTL AmpR HDGMNHLFATLEKPGGITTL a t g a t c c c c c a t g t t g t g c a a a a a a g c g g t t a g c t c c t t c g g t c c t c c g a t c g t t g t c a g t a c t a g g g g g t a c a a c a c g t t t t t t c g c c a a t c g a g g a a g c c a g g a g g c t a g c a a c a g t c

TsoIEaeI 2460 135 130 125 120 LLNAATNDSMTIAASCLERV AmpR LLNAATNDSMTIAASCLERV a a g t a a g t t g g c c g c a g t g t t a t c a c t c a t g g t t a t g g c a g c a c t g c a t a a t t c t c t t a c t t c a t t c a a c c g g c g t c a c a a t a g t g a g t a c c a a t a c c g t c g t g a c g t a t t a a g a g a a t g

ScaI 2520 115 110 105 100 TMGDTLHKETVPSYEVLDNQ AmpR TMGDTLHKETVPSYEVLDNQ t g t c a t g c c a t c c g t a a g a t g c t t t t c t g t g a c t g g t g a g t a c t c a a c c a a g t c a t t c t g a c a g t a c g g t a g g c a t t c t a c g a a a a g a c a c t g a c c a c t c a t g a g t t g g t t c a g t a a g a c

2580 95 90 85 80 SYHIRRGLQEQGADIRSLVA AmpR A T A A T A C C G C Amp-R SYHIRRGLQEQGADIRSLVA a g a a t a g t g t a t g c g g c g a c c g a g t t g c t c t t g c c c g g c g t c a a t a c g g g a t a a t a c c g c t c t t a t c a c a t a c g c c g c t g g c t c a a c g a g a a c g g g c c g c a g t t a t g c c c t a t t a t g g c g

XmnI 2640 75 70 65 60 GCLLVKFTSMMPFREEPRFS AmpR G C C A C A T A G C Amp-R GCLLVKFTSMMPFREEPRFS g c c a c a t a g c a g a a c t t t a a a a g t g c t c a t c a t t g g a a a a c g t t c t t c g g g g c g a a a a c t c g g t g t a t c g t c t t g a a a t t t t c a c g a g t a g t a a c c t t t t g c a a g a a g c c c c g c t t t t g a

2700 55 50 45 40 ELIKGSNLDLEIYGVRAGLQ AmpR ELIKGSNLDLEIYGVRAGLQ c t c a a g g a t c t t a c c g c t g t t g a g a t c c a g t t c g a t g t a a c c c a c t c g t g c a c c c a a c t g g a g t t c c t a g a a t g g c g a c a a c t c t a g g t c a a g c t a c a t t g g g t g a g c a c g t g g g t t g a c

2760 35 30 25 DEADKVKVLTEPH 20 signal sequence AFVPLCF AmpR DEADKVKVLTEPHAFVPLCF a t c t t c a g c a t c t t t t a c t t t c a c c a g c g t t t c t g g g t g a g c a a a a a c a g g a a g g c a a a a t a g a a g t c g t a g a a a a t g a a a g t g g t c g c a a a g a c c c a c t c g t t t t t g t c c t t c c g t t t t

2820 15 10 5 1 signal sequence AAFFPILAVRFHQISM AmpR AmpR promoter AAFFPILAVRFHQISM t g c c g c a a a a a a g g g a a t a a g g g c g a c a c g g a a a t g t t g a a t a c t c a t a c t c t t c c t t t t a c g g c g t t t t t t c c c t t a t t c c c g c t g t g c c t t t a c a a c t t a t g a g t a t g a g a a g g a a a a

SspI 2880 AmpR promoter t c a a t a t t a t t g a a g c a t t t a t c a g g g t t a t t g t c t c a t g a g c g g a t a c a t a t t t g a a t g a g t t a t a a t a a c t t c g t a a a t a g t c c c a a t a a c a g a g t a c t c g c c t a t g t a t a a a c t t a c

2940 AmpR promoter t a t t t a g a a a a a t a a a c a a a t a g g g g t t c c g c g c a c a t t t c c c c g a a a a g t g c c a c c t g a a t a a a t c t t t t t a t t t g t t t a t c c c c a a g g c g c g t g t a a a g g g g c t t t t c a c g g t g g a c t

EcoO109IZraIAatII 3000 A A T A G G C G T A T C A C G A G G C pBRforEco c g t c t a a g a a a c c a t t a t t a t c a t g a c a t t a a c c t a t a a a a a t a g g c g t a t c a c g a g g c c g c a g a t t c t t t g g t a a t a a t a g t a c t g t a a t t g g a t a t t t t t a t c c g c a t a g t g c t c c g g

3008 c t t t c g t c g a a a g c a g

Restriction Enzymes

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

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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)

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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.