Addgene gRNA_AAVS1-T1 Sequencing Result - Sequence Analyzer Skip to main content
Addgene

Sequence Analyzer: gRNA_AAVS1-T1 Sequencing Result


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AccI (3941) SalI (3940) XmnI (3933) PstI (3892) EcoRV (3885) NotI (3866) PaeR7I - PspXI - XhoI (3860) ApaI (3846) PspOMI (3842) T7 (3816 .. 3835) M13 fwd M13 Forward (3792 .. 3809) M13/pUC Forward (3778 .. 3800) PvuI (3693) SnaBI (3661) BsiWI (3657) ccdB-fwd (3455 .. 3474) BsaI (3432) XcmI (3060) BclI * (3030) Neo-R (2931 .. 2950) PflFI - Tth111I (2756) BsrDI (2644) RsrII (2356) TsoI (2348) Neo-F (2321 .. 2340) SfiI (2006) BssHII - MauBI (1963) AatII (1961) hU6-F (1 .. 21) U6 promoter LKO.1 5' (172 .. 191) NdeI (179) SpeI (418) Eco53kI (432) SacI (434) HindIII (442) SP6 (467 .. 484) M13 rev M13 Reverse (502 .. 518) lac operator M13/pUC Reverse (515 .. 537) CAP binding site L4440 (733 .. 750) PciI (843) pBR322ori-F (984 .. 1003) DraIII (1653) FseI (1731) CsiI - SexAI * (1835) SgrAI (1885) TspMI - XmaI (1911) SmaI (1913) ZraI (1959) gRNA_AAVS1-T1 3973 bp

Sequence View

5ʹ 3ʹ 60 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 g a g g g c c t a t t t c c c a t g a t t c 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 c t c c c g g a t a a a g g g t a c t a a 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

120 U6 promoter a t a a t t a g a a t t a a t t t g a c t g 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 t a t t a a t c t t a a t t a a a c t g a c 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

NdeI 180 U6 promoter G A C T A T C A T LKO.1 5' a a g t a a t a a t t t c t t g g g t a g t 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 t t c a t t a t t a a a g a a c c c a t c a 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

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

300 U6 promoter gRNA scaffold c g a a a c a c c g t c c c c t c c a c c c c a c a g t g g t t t t a g a g c t a g a a a t a g c a a g t t a a a a t a g c t t t g t g g c a g g g g a g g t g g g g t g t c a c c a a a a t c t c g a t c t t t a t c g t t c a a t t t t a t

360 gRNA scaffold attB2 a g g c t a g t c c g t t a t c a a c t t g a a a a a g t g g c a c c g a g t c g g t g c t t t t t t t c t a g a c c c t c c g a t c a g g c a a t a g t t g a a c t t t t t c a c c g t g g c t c a g c c a c g a a a a a a a g a t c t g g g

SpeI 420 attB2 a g c t t t c t t g t a c a a a g t t g g c a t t a a a g g g c g a a t t c c a g c a c a c t g g c g g c c g t t a c t t c g a a a g a a c a t g t t t c a a c c g t a a t t t c c c g c t t a a g g t c g t g t g a c c g c c g g c a a t g a

HindIIIEco53kISacI 480 SP6 promoter G A T A T C A C A G T G G A SP6 a g t g g a t c c g a g c t c g g t a c c a a g c t t g a t g c a t a g c t t g a g t a t t c t a t a g t g t c a c c t t c a c c t a g g c t c g a g c c a t g g t t c g a a c t a c g t a t c g a a c t c a t a a g a t a t c a c a g t g g a

540 SP6 promoter M13 rev lac operator T T T A SP6 C A G T A T C G A C A A A G G A C M13 Reverse G G A C A C A C T T T A A C A A T A G G C G A M13/pUC Reverse a a a t a g c t t g g c g t a a t c a t g g t c a t a g c t g t t t c c t g t g t g a a a t t g t t a t c c g c t c a c t t t a t c g a a c c g c a t t a g t a c c a g t a t c g a c a a a g g a c a c a c t t t a a c a a t a g g c g a g t g

600 -10 -35 lac operator lac promoter CAP binding site a a t t c c a c a c a a c a t a c g a g c c g g a a g c a t a a a g t g t a a a g c c t g g g g t g c c t a a t g a g t t t a a g g t g t g t t g t a t g c t c g g c c t t c g t a t t t c a c a t t t c g g a c c c c a c g g a t t a c t c a

660 CAP binding site g a g c t a a c t c a c a t t a a t t g c g t t g c g c t c a c t g c c c g c t t t c c a g t c g g g a a a c c t g t c c t c g a t t g a g t g t a a t t a a c g c a a c g c g a g t g a c g g g c g a a a g g t c a g c c c t t t g g a c a g

720 g t g c c a g c t g c a t t a a t g a a t c g g c c a a c g c g c g g 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 a c g g t c g a c g t a a t t a c t t a g c c g g t t g c g c g c c 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

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

840 a t c a g c t c a c t c a a a 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 t a g t c g a g t g a g t t t 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

PciI 900 g a a c a t g t g a g c a a a 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 c t t g t a c a c t c g t t 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

960 ori g t t t t t c c a t a g g c t 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 c a a a a a g g t a t c c g a 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

1020 ori T T T C T A T G G T C C G C A A A G G G pBR322ori-F g t g g c g a a a c c c g a c 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 c a c c g c t t t g g g c t g 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

1080 ori g c g c t c t c c t g t t c c 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 c g c g a g a g g a c a a g g 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

1140 ori a a g c g t g g c g c t t t c 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 t t c g c a c c g c g a a a 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

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

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

1320 ori t g g t a a c a g g a t t a g 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 a c c a t t g t c c t a a t c 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

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

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

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

1560 t t t g a t c t t t t c t a c 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 a a a c t a g a a a a g a t g 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

1620 *ILFSTK g g t c a t g a g a t t a t c 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 c c a g t a c t c t a a t 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

DraIII 1680 125 120 115 110 *DQEEAVFHVCNGAPDR BleoR ARTLGAGRGRLARLQRGPRA t a g c a c g t g t c a g t c c t g c t c c t c g g c c a c g a a g t g c a c g c a g t t g c c g g c c g g g t c g c g a t c g t g c a c a g t c a g g a c g a g g a g c c g g t g c t t c a c g t g c g t c a a c g g c c g g c c c a g c g c

FseI 1740 105 100 95 90 LAFERGWPQEGIETMAPGSA BleoR PRVGAGVAARRDRDHGARLR c a g g g c g a a c t c c c g c c c c c a c g g c t g c t c g c c g a t c t c g g t c a t g g c c g g c c c g g a g g c g t c c c g c t t g a g g g c g g g g g t g c c g a c g a g c g g c t a g a g c c a g t a c c g g c c g g g c c t c c g

1800 85 80 75 70 DRFNTSVVESWEAYLEDLGR BleoR GPLEHVRGGVVRRVARGPRA g t c c c g g a a g t t c g t g g a c a c g a c c t c c g a c c a c t c g g c g t a c a g c t c g t c c a g g c c g c g c a g g g c c t t c a a g c a c c t g t g c t g g a g g c t g g t g a g c c g c a t g t c g a g c a g g t c c g g c g c

SexAI*CsiI 1860 65 60 55 50 VWVWALTNDPVVQDQVASIF BleoR GVGLGPHQGAGGPGPGRQHV c a c c c a c a c c c a g g c c a g g g t g t t g t c c g g c a c c a c c t g g t c c t g g a c c g c g c t g a t g a a g t g g g t g t g g g t c c g g t c c c a c a a c a g g c c g t g g t g g a c c a g g a c c t g g c g c g a c t a c t t

TspMIXmaISmaISgrAI 1920 45 40 35 30 LTVDDRVVGAFDDEVFDRSF BleoR PDRRGPGCRRLRGGRLGPLV c a g g g t c a c g t c g t c c c g g a c c a c a c c g g c g a a g t c g t c c t c c a c g a a g t c c c g g g a g a a g t c c c a g t g c a g c a g g g c c t g g t g t g g c c g c t t c a g c a g g a g g t g c t t c a g g g c c c t c t t

ZraIAatIIBssHIIMauBI 1980 25 20 15 10 GLRDTWFEVAGAVDRATLVP BleoR RAPRDLVRGSRRRRARHAGS c c c g a g c c g g t c g g t c c a g a a c t c g a c c g c t c c g g c g a c g t c g c g c g c g g t g a g c a c c g g g g g c t c g g c c a g c c a g g t c t t g a g c t g g c g a g g c c g c t g c a g c g c g c g c c a c t c g t g g c c

SfiI 2040 5 1 VASTLKAM BleoR Kozak sequence RCQDVQGHHGEERAIISANI a a c g g c a c t g g t c a a c t t g g c c a t g g t g g c c c t c c t c a c g t g c t a t t a t t g a a g c a t t t a t t g c c g t g a c c a g t t g a a c c g g t a c c a c c g g g a g g a g t g c a c g a t a a t a a c t t c g t a a a t

2100 LTITEHASVYKFTNLFIFLY 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 t a t t t a g a a a a a t a a a c 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 a t a a a t c t t t t t a t t t g t t t a

2160 PNRACKGSFHWRIRHSIGCL 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 t g c g g t g t g a a a t a c c g c a c 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 a c g c c a c a c t t t a t g g c g t g t

2220 265 *FFE NeoR/KanR 265 *FFE NeoR/KanR MRKEKIPHQEIVSVNNSEEL HTLLFYRM*FFE 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 a a a t t g t a a g c g t t a a t a a t t c a g a a g a a c 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 t t t a a c a t t c g c a a t t a t t a a g t c t t c t t g a

2280 260 255 250 245 DLLRYFAIRQSDPAAIGYLV NeoR/KanR 260 255 250 245 DLLRYFAIRQSDPAAIGYLV NeoR/KanR VKKAIEGDALRIGSGDTVKH DLLRYFAIRQSDPAAIGYLV c g t c a a g a a g g c g a t a g a a g g c g a t g c g c t g c g a a t c g g g a g c g g c g a t a c c g t a a a g c a g c a g t t c t t c c g c t a t c t t c c g c t a c g c g a c g c t t a g c c c t c g c c g c t a t g g c a t t t c g t

2340 240 235 230 225 LFRDAWEGGLEEAIDRTALA NeoR/KanR 240 235 230 225 LFRDAWEGGLEEAIDRTALA NeoR/KanR T T A T A G T G C C C A T C G G T T G C Neo-F EEAVSPFAAKLFSNITGSQR LFRDAWEGGLEEAIDRTALA c g a g g a a g c g g t c a g c c c a t t c g c c g c c a a g c t c t t c a g c a a t a t c a c g g g t a g c c a a c g g c t c c t t c g c c a g t c g g g t a a g c g g c g g t t c g a g a a g t c g t t a t a g t g c c c a t c g g t t g c

RsrIITsoI 2400 220 215 210 205 IDQYRDAVGLRGCDIFGSFR NeoR/KanR 220 215 210 205 IDQYRDAVGLRGCDIFGSFR NeoR/KanR YVLIAVRHTQPATVDESRKA IDQYRDAVGLRGCDIFGSFR c t a t g t c c t g a t a g c g g t c c g c c a c a c c c a g c c g g c c a c a g t c g a t g a a t c c a g a a a a g c g a t a c a g g a c t a t c g c c a g g c g g t g t g g g t c g g c c g g t g t c a g c t a c t t a g g t c t t t t c g

2460 200 195 190 185 GNEVMINPLCADGHTVVLDE NeoR/KanR 200 195 190 185 GNEVMINPLCADGHTVVLDE NeoR/KanR AIFHHDIRQAGIAMGHDEIL GNEVMINPLCADGHTVVLDE g g c c a t t t t c c a c c a t g a t a t t c g g c a a g c a g g c a t c g c c a t g g g t c a c g a c g a g a t c c t c c g g t a a a a g g t g g t a c t a t a a g c c g t t c g t c c g t a g c g g t a c c c a g t g c t g c t c t a g g a

2520 180 175 170 165 GDPMSAKLRAFLEAPALGQH NeoR/KanR 180 175 170 165 GDPMSAKLRAFLEAPALGQH NeoR/KanR AVGHARLEPGEQFGWREPLM GDPMSAKLRAFLEAPALGQH c g c c g t c g g g c a t g c t c g c c t t g a g c c t g g c g a a c a g t t c g g c t g g c g c g a g c c c c t g a t g c g g c a g c c c g t a c g a g c g g a a c t c g g a c c g c t t g t c a a g c c g a c c g c g c t c g g g g a c t a

2580 160 155 150 145 EEDLDDQDVLGAEMRTRARE NeoR/KanR 160 155 150 145 EEDLDDQDVLGAEMRTRARE NeoR/KanR LFVQIILIDKTGFHPSTCSL EEDLDDQDVLGAEMRTRARE g c t c t t c g t c c a g a t c a t c c t g a t c g a c a a g a c c g g c t t c c a t c c g a g t a c g t g c t c g c t c g a g a a g c a g g t c t a g t a g g a c t a g c t g t t c t g g c c g a a g g t a g g c t c a t g c a c g a g c g a

2640 140 135 130 125 IRHKAQHDFPCTAPDLTHLR NeoR/KanR 140 135 130 125 IRHKAQHDFPCTAPDLTHLR NeoR/KanR DAMFRLVVEWAGSRIKRMQP IRHKAQHDFPCTAPDLTHLR c g a t g c g a t g t t t c g c t t g g t g g t c g a a t g g g c a g g t a g c c g g a t c a a g c g t a t g c a g c c g c t a c g c t a c a a a g c g a a c c a c c a g c t t a c c c g t c c a t c g g c c t a g t t c g c a t a c g t c g g

BsrDI 2700 120 115 110 105 RMADAMISVKEAPALHSSLL NeoR/KanR 120 115 110 105 RMADAMISVKEAPALHSSLL NeoR/KanR PHCISHDGYFLGRSKVR* RMADAMISVKEAPALHSSLL g c c g c a t t g c a t c a g c c a t g a t g g a t a c t t t c t c g g c a g g a g c a a g g t g a g a t g a c a g g a c g g c g t a a c g t a g t c g g t a c t a c c t a t g a a a g a g c c g t c c t c g t t c c a c t c t a c t g t c c t

Tth111IPflFI 2760 100 95 90 85 DQGPVEGLLLWDRGAETVVD NeoR/KanR 100 95 90 85 DQGPVEGLLLWDRGAETVVD NeoR/KanR DQGPVEGLLLWDRGAETVVD g a t c c t g c c c c g g c a c t t c g c c c a a t a g c a g c c a g t c c c t t c c c g c t t c a g t g a c a a c g t c t a g g a c g g g g c c g t g a a g c g g g t t a t c g t c g g t c a g g g a a g g g c g a a g t c a c t g t t g c a

2820 80 75 70 65 LVAACPVGTTALWSLRAAED NeoR/KanR 80 75 70 65 LVAACPVGTTALWSLRAAED NeoR/KanR LVAACPVGTTALWSLRAAED c g a g c a c a g c t g c g c a a g g a a c g c c c g t c g t g g c c a g c c a c g a t a g c c g c g c t g c c t c g t g c t c g t g t c g a c g c g t t c c t t g c g g g c a g c a c c g g t c g g t g c t a t c g g c g c g a c g g a g c a

2880 60 55 50 45 QLENLAGSLDTKVFLVPRGQ NeoR/KanR 60 55 50 45 QLENLAGSLDTKVFLVPRGQ NeoR/KanR QLENLAGSLDTKVFLVPRGQ c t t g c a g t t c a t t c a g g g c a c c g g a c a g g t c g g t c t t g a c a a a a a g a a c c g g g c g c c c c t g a a c g t c a a g t a a g t c c c g t g g c c t g t c c a g c c a g a a c t g t t t t t c t t g g c c c g c g g g g a

2940 40 35 30 25 ASLRFVAADSCGITQQAWDY NeoR/KanR 40 35 30 25 ASLRFVAADSCGITQQAWDY NeoR/KanR G C C C A G T C A T Neo-R ASLRFVAADSCGITQQAWDY g c g c t g a c a g c c g g a a c a c g g c g g c a t c a g a g c a g c c g a t t g t c t g t t g t g c c c a g t c a t c g c g a c t g t c g g c c t t g t g c c g c c g t a g t c t c g t c g g c t a a c a g a c a a c a c g g g t c a g t a

3000 20 15 10 5 GFLREVWAAPSGAHLGDQEI NeoR/KanR 20 15 10 5 GFLREVWAAPSGAHLGDQEI NeoR/KanR A G C C G A A T A G Neo-R GFLREVWAAPSGAHLGDQEI a g c c g a a t a g c c t c t c c a c c c a a g c g g c c g g a g a a c c t g c g t g c a a t c c a t c t t g t t c a a t c g g c t t a t c g g a g a g g t g g g t t c g c c g g c c t c t t g g a c g c a c g t t a g g t a g a a c a a g t t

XcmIBclI* 3060 1 M NeoR/KanR 1 M NeoR/KanR M t c a t g c g a a a c g a t c c t c a t c c t g t c t c t t g a t c a g a g c t t g a t c c c c t g c g c c a t c a g a a g t a c g c t t t g c t a g g a g t a g g a c a g a g a a c t a g t c t c g a a c t a g g g g a c g c g g t a g t c t

3120 t c c t t g g c g g c a a g a a a g c c a t c c a g t t t a c t t t g c a g g g c t t c c c a a c c t t a c c a g a g g a g g a a c c g c c g t t c t t t c g g t a g g t c a a a t g a a a c g t c c c g a a g g g t t g g a a t g g t c t c c

3180 g c g c c c c a g c t g g c a a t t c c g g t t c g c t t g c t g t c c a t a a a a c c g c c c a g t c t a g c t a t c c g c g g g g t c g a c c g t t a a g g c c a a g c g a a c g a c a g g t a t t t t g g c g g g t c a g a t c g a t a g

3240 g c c a t g t a a g c c c a c t g c a a g c t a c c t g c t t t c t c t t t g c g c t t g c g t t t t c c c t t g t c c c g g t a c a t t c g g g t g a c g t t c g a t g g a c g a a a g a g a a a c g c g a a c g c a a a a g g g a a c a g g

3300 a g a t a g c c c a g t a g c t g a c a t t c a t c c g g g g t c a g c a c c g t t t c t g c g g a c t g g c t t t c t t c t a t c g g g t c a t c g a c t g t a a g t a g g c c c c a g t c g t g g c a a a g a c g c c t g a c c g a a a g a

3360 100 *IG ccdB a c g t g a a a a g g a t c t a g g t g a a g a t c c t t t t t g a t a a t c t c a t g c c t g a c a t t t a t a t t c t g c a c t t t t c c t a g a t c c a c t t c t a g g a a a a a c t a t t a g a g t a c g g a c t g t a a a t a t a a g

3420 95 90 85 80 WFMLNIANKIDNERHSLDAV ccdB c c c a g a a c a t c a g g t t a a t g g c g t t t t t g a t g t c a t t t t c g c g g t g g c t g a g a t c a g c c a g g g t c t t g t a g t c c a a t t a c c g c a a a a a c t a c a g t a a a a g c g c c a c c g a c t c t a g t c g g t

BsaI 3480 75 70 65 60 EEGIVSVPVSAMDTTMMRWS ccdB G T A T A G C C A C C A G T A G T A C G ccdB-fwd c t t c t t c c c c g a t a a c g g a g a c c g g c a c a c t g g c c a t a t c g g t g g t c a t c a t g c g c c a g c g a a g a a g g g g c t a t t g c c t c t g g c c g t g t g a c c g g t a t a g c c a c c a g t a g t a c g c g g t c g

3540 55 50 45 40 EDGIHVVPYLERSVKDSLLR ccdB t t t c a t c c c c g a t a t g c a c c a c c g g g t a a a g t t c a c g g g a g a c t t t a t c t g a c a g c a g a c a a a g t a g g g g c t a t a c g t g g t g g c c c a t t t c a a g t g c c c t c t g a a a t a g a c t g t c g t c t g

3600 35 30 25 20 ASALPIVMRRGPTDIIDSQV ccdB g t g c a c t g g c c a g g g g g a t c a c c a t c c g t c g c c c c g g c g t g t c a a t a a t a t c a c t c t g t a c a c g t g a c c g g t c c c c c t a g t g g t a g g c a g c g g g g c c g c a c a g t t a t t a t a g t g a g a c a t

BsiWI 3660 15 10 5 DVFLRYRSERKYTYVKFQ ccdB c a t c c a c a a a c a g a c g a t a a c g g c t c t c t c t t t t a t a g g t g t a a a c c t t a a a c t g c c g t a g t a g g t g t t t g t c t g c t a t t g c c g a g a g a g a a a a t a t c c a c a t t t g g a a t t t g a c g g c a t

PvuISnaBI 3720 c g t a t a g g c t g c g c a a c t g t t g g g a a g g g c g a t c g g t g c g g g c c t c t t c g c t a t t a c g c c g c a t a t c c g a c g c g t t g a c a a c c c t t c c c g c t a g c c a c g c c c g g a g a a g c g a t a a t g c g g

3780 C C C M13/pUC Forward a g c t g g c g a a a g g g g g a t g t g c t g c a a g g c g a t t a a g t t g g g t a a c g c c a g g g t t t t c c c t c g a c c g c t t t c c c c c t a c a c g a c g t t c c g c t a a t t c a a c c c a t t g c g g t c c c a a a a g g g

3840 M13 fwd T7 promoter A G T C A C G A C G T T G T A A A A C G M13/pUC Forward T G T A A A A C G A C G G C C A G T M13 Forward T A A T A C G A C T C A C T A T A G G G T7 a g t c a c g a c g t t g t a a a a c g a c g g c c a g t g a a t t g t a a t a c g a c t c a c t a t a g g g c g a a t t c a g t g c t g c a a c a t t t t g c t g c c g g t c a c t t a a c a t t a t g c t g a g t g a t a t c c c g c t t a

PstIEcoRVNotIPaeR7IPspXIXhoIPspOMIApaI 3900 t g g g c c c t c t a g a t g c a t g c t c g a g c g g c c g c c a g t g t g a t g g a t a t c t g c a g a a t t c g c a c c c g g g a g a t c t a c g t a c g a g c t c g c c g g c g g t c a c a c t a c c t a t a g a c g t c t t a a g c g

SalIAccIXmnI 3960 c c t t t g t a c a a a a a a g c a g g c t t t a a a g g a a c c a a t t c a g t c g a c t g g a t c c g g t a c c a a g g a a a c a t g t t t t t t c g t c c g a a a t t t c c t t g g t t a a g t c a g c t g a c c t a g g c c a t g g t t

3ʹ 5ʹ 3973 g g t c g g g c a g g a a c c a g c c c g t c c t t

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.