Welcome to Benchling!

You're looking at a DNA Sequence. Here are some things you can do with it:

Create an alignment

  1. Create alignments with both DNA and AA sequences.
  2. Bulk-align multiple sequences at once.
  3. Powerful visualization tool to inspect alignments in detail.

Design a primer

Create a translation

Design a CRISPR guide

Assemble and transform a sequence

Benchling is actively tested against the latest versions of Chrome, Firefox, Safari, and Edge. **It doesn't look like your current browser is supported** - for more information, [click here](/browsers).
Monospace normal
Monospace bold
working...
Advanced Settings
pU6.1-SpCas9_cloning
  • Sequence Map
Editing disabled on read-only sequence.
GTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAGCGCGCGTAATACGACTCACTATAGGGCGAATTGGAGCTCCACCGCGGTGGCGGCCGCTCTAGAACTAGTGGATCTTCTAGAAAGATCCAGCGTGTTATTTAGGACACGACGTTCCGCTAATTCAACCCATTGCGGTCCCAAAAGGGTCAGTGCTGCAACATTTTGCTGCCGGTCACTCGCGCGCATTATGCTGAGTGATATCCCGCTTAACCTCGAGGTGGCGCCACCGCCGGCGAGATCTTGATCACCTAGAAGATCTTTCTAGGTCGCACAATAAATCCTAleIBmrIEagINotISacISpeIBstXISacIIBssHIIEco53kIT7LGC_T7promM13-fwdPU6.120406080100120140160
GTCGTTTCCAAGACGaTTTTTGAACGTCAATGGGGGTaCCAGTCCCTGACGGAGATCCCACGCCCACGGGCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCAGCAAAGGTTCTGCtAAAAACTTGCAGTTACCCCCAtGGTCAGGGACTGCCTCTAGGGTGCGGGTGCCCGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGKpnIAlwNIBsmFIAcc65IPU6.1180200220240260280300320340
CCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTTCTCCCTGGAGCATTCTCTCAGCCGCCGTAAAGCAGCGGCCGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGAAGAGGGACCTCGTAAGAGAGTCGGCGGCATTTCGTCGCCGGCBpmIBsmIEagINotIPU6.1360380400420440460480500520
CCGCGAAACAGCGGAGCGGAGCGGAGCGCAGCAGAGCGGAGCAAAAGGGAACAGTGGAAGCGAAGGCTGCAAAAGCACGTTAATGTCTACACTGACTTGCTATATATACATTTAGCCTAAAAATGATACTTTGAGACGTACCATATGAACCGTCTCCGTTTTAGAGCTAGAAATAGCAGGCGCTTTGTCGCCTCGCCTCGCCTCGCGTCGTCTCGCCTCGTTTTCCCTTGTCACCTTCGCTTCCGACGTTTTCGTGCAATTACAGATGTGACTGAACGATATATATGTAAATCGGATTTTTACTATGAAACTCTGCATGGTATACTTGGCAGAGGCAAAATCTCGATCTTTATCGTAccINdeIBsmBIBsmBIEsp3IEsp3IPU6.1Cloning InsertSpCas9 scaffold540560580600620640660680700
AGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTTATCTTTCTAGAAGATCTCCTACAATATTCTCAGCTGCCATGGAAAATCGATGTTCTTCTTTTATTCTCTCAAGATTTTCAGGCTGTATATTAAAACTTATATTAAGAACTATGCTATCAATTTTATTCCGATCAGGCAATAGTTGAACTTTTTCACCGTGGCTCAGCCACGAAAAAAATAGAAAGATCTTCTAGAGGATGTTATAAGAGTCGACGGTACCTTTTAGCTACAAGAAGAAAATAAGAGAGTTCTAAAAGTCCGACATATAATTTTGAATATAATTCTTGATACGATBarIClaINcoIStyIBglIIBspDISpCas9 scaffold720740760780800820840860880
ACCACCTCATCAGGAACCGTTGTAGGTGGCGTGGGTTTTCTTGGCAATCGACTCTCATGAAAACTACGAGCTAAATATTCAATATGTTCCTCTTGACCAACTTTATTCTGCATTTTTTTTGAACGAGGTTTAGAGCAAGCTTATCGATACCGTCGACCTCGAGGGGGGGCCCGGTACCTGGTGGAGTAGTCCTTGGCAACATCCACCGCACCCAAAAGAACCGTTAGCTGAGAGTACTTTTGATGCTCGATTTATAAGTTATACAAGGAGAACTGGTTGAAATAAGACGTAAAAAAAACTTGCTCCAAATCTCGTTCGAATAGCTATGGCAGCTGGAGCTCCCCCCCGGGCCATGGAccIApaIAvaIBcgIClaIKpnISalITliIXhoIBseYIBsoBIBspDIPspXIAcc65IHincIIPaeR7IPspOMIHindIIIEcoO109I9009209409609801,0001,0201,0401,060
CAGCTTTTGTTCCCTTTAGTGAGGGTTAATTTCGAGCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAATTGCGTTGCGCGTCGAAAACAAGGGAAATCACTCCCAATTAAAGCTCGAACCGCATTAGTACCAGTATCGACAAAGGACACACTTTAACAATAGGCGAGTGTTAAGGTGTGTTGTATGCTCGGCCTTCGTATTTCACATTTCGGACCCCACGGATTACTCACTCGATTGAGTGTAATTAACGCAACGCGlac promoterLacOM13-revT3LGC_T3T3 promoter1,0801,1001,1201,1401,1601,1801,2001,2201,240
TCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACAGTGACGGGCGAAAGGTCAGCCCTTTGGACAGCACGGTCGACGTAATTACTTAGCCGGTTGCGCGCCCCTCTCCGCCAAACGCATAACCCGCGAGAAGGCGAAGGAGCGAGTGACTGAGCGACGCGAGCCAGCAAGCCGACGCCGCTCGCCATAGTCGAGTGAGTTTCCGCCATTATGSapITfiIBsaXIBspQI1,2601,2801,3001,3201,3401,3601,3801,4001,420
GGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATACCAATAGGTGTCTTAGTCCCCTATTGCGTCCTTTCTTGTACACTCGTTTTCCGGTCGTTTTCCGGTCCTTGGCATTTTTCCGGCGCAACGACCGCAAAAAGGTATCCGAGGCGGGGGGACTGCTCGTAGTGTTTTTAGCTGCGAGTTCAGTCTCCACCGCTTTGGGCTGTCCTGATATDrdINspIPciITfiIAflIIIColE1 origin1,4401,4601,4801,5001,5201,5401,5601,5801,600
AAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACTTCTATGGTCCGCAAAGGGGGACCTTCGAGGGAGCACGCGAGAGGACAAGGCTGGGACGGCGAATGGCCTATGGACAGGCGGAAAGAGGGAAGCCCTTCGCACCGCGAAAGAGTATCGAGTGCGACATCCATAGAGTCAAGCCACATCCAGCAAGCGAGGTTCGACCCGACACACGTGApaLIBciVIBseYIBssSIBssSαIColE1 origin1,6201,6401,6601,6801,7001,7201,7401,7601,780
GAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTACTTGGGGGGCAAGTCGGGCTGGCGACGCGGAATAGGCCATTGATAGCAGAACTCAGGTTGGGCCATTCTGTGCTGAATAGCGGTGACCGTCGTCGGTGACCATTGTCCTAATCGTCTCGCTCCATACATCCGCCACGATGTCTCAAGAACTTCACCACCGGATTGATGCCGATGTGATAlwNIColE1 origin1,8001,8201,8401,8601,8801,9001,9201,940
GAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGCTTCCTGTCATAAACCATAGACGCGAGACGACTTCGGTCAATGGAAGCCTTTTTCTCAACCATCGAGAACTAGGCCGTTTGTTTGGTGGCGACCATCGCCACCAAAAAAACAAACGTTCGTCGTCTAATGCGCGTCTTTTTTTCCTAGAGTTCTTCTAGGAAACTAGAAAAGATGCCCAcuIColE1 origin1,9601,9802,0002,0202,0402,0602,0802,1002,120
GTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCACAGACTGCGAGTCACCTTGCTTTTGAGTGCAATTCCCTAAAACCAGTACTCTAATAGTTTTTCCTAGAAGTGGATCTAGGAAAATTTAATTTTTACTTCAAAATTTAGTTAGATTTCATATATACTCATTTGAACCAGACTGTCAATGGTTACGAATTAGTCACTCCGTGGATAGAGTColE1 originAmpR2,1402,1602,1802,2002,2202,2402,2602,2802,300
GCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGCGCTAGACAGATAAAGCAAGTAGGTATCAACGGACTGAGGGGCAGCACATCTATTGATGCTATGCCCTCCCGAATGGTAGACCGGGGTCACGACGTTACTATGGCGCTCTGGGTGCGAGTGGCCGAGGTCTAAATAGTCGTTATTTGGTCGGTCGGCCTTCCCGGCTCGCGTCTTCACAhdIBglIBmrIBpmIBsaIBsrDIBsrFIAmpR2,3202,3402,3602,3802,4002,4202,4402,4602,480
GTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTCAGGACGTTGAAATAGGCGGAGGTAGGTCAGATAATTAACAACGGCCCTTCGATCTCATTCATCAAGCGGTCAATTATCAAACGCGTTGCAACAACGGTAACGATGTCCGTAGCACCACAGTGCGAGCAGCAAACCATACCGAAGTAAGTCGAGGCCAAGGGTTGCTAGTTCCGCTCAAclIFspIAvaIIBsrDINmeAIIIAmpR2,5002,5202,5402,5602,5802,6002,6202,6402,660
TACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCAATGTACTAGGGGGTACAACACGTTTTTTCGCCAATCGAGGAAGCCAGGAGGCTAGCAACAGTCTTCATTCAACCGGCGTCACAATAGTGAGTACCAATACCGTCGTGACGTATTAAGAGAATGACAGTACGGTAGGCATTCTACGAAAAGACACTGACCACTCATGAGTTGGTTCAGTPvuIScaITatIAvaIIAmpR2,6802,7002,7202,7402,7602,7802,8002,8202,840
TTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACAAGACTCTTATCACATACGCCGCTGGCTCAACGAGAACGGGCCGCAGTTATGCCCTATTATGGCGCGGTGTATCGTCTTGAAATTTTCACGAGTAGTAACCTTTTGCAAGAAGCCCCGCTTTTGAGAGTTCCTAGAATGGCGACAACTCTAGGTCAAGCTACATTGGGTGAGCACGTGAclIAcuIBcgIXmnIApaLIBsaHIBssSIBssSαIAmpR2,8602,8802,9002,9202,9402,9602,9803,0003,020
CCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATGGTTGACTAGAAGTCGTAGAAAATGAAAGTGGTCGCAAAGACCCACTCGTTTTTGTCCTTCCGTTTTACGGCGTTTTTTCCCTTATTCCCGCTGTGCCTTTACAACTTATGAGTATGAGAAGGAAAAAGTTATAATAACTTCGTAAATAGTCCCAATAACAGAGTACTCGCCTATGTABciVI3,0403,0603,0803,1003,1203,1403,1603,1803,200
ATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTAAATTGTAAGCGTTAATATTTTGTTAAAATTCGCGTTAAATTTTTGTTAAATCAGCTCATTTTTTAACCAATAGGCCGAAATCGGCAAAATCCCTTATAAATCAAAAGAATTAAACTTACATAAATCTTTTTATTTGTTTATCCCCAAGGCGCGTGTAAAGGGGCTTTTCACGGTGGATTTAACATTCGCAATTATAAAACAATTTTAAGCGCAATTTAAAAACAATTTAGTCGAGTAAAAAATTGGTTATCCGGCTTTAGCCGTTTTAGGGAATATTTAGTTTTCTTAApoIApoIPsiICspCI3,2203,2403,2603,2803,3003,3203,3403,3603,380
AGACCGAGATAGGGTTGAGTGTTGTTCCAGTTTGGAACAAGAGTCCACTATTAAAGAACGTGGACTCCAACGTCAAAGGGCGAAAAACCGTCTATCAGGGCGATGGCCCACTACGTGAACCATCACCCTAATCAAGTTTTTTGGGGTCGAGGTGCCGTAAAGCACTAAATCGGAACCCTCTGGCTCTATCCCAACTCACAACAAGGTCAAACCTTGTTCTCAGGTGATAATTTCTTGCACCTGAGGTTGCAGTTTCCCGCTTTTTGGCAGATAGTCCCGCTACCGGGTGATGCACTTGGTAGTGGGATTAGTTCAAAAAACCCCAGCTCCACGGCATTTCGTGATTTAGCCTTGGGAloIDrdIBsaAIBsaXIBtgZIDraIIIF1 ori3,4003,4203,4403,4603,4803,5003,5203,5403,560
TAAAGGGAGCCCCCGATTTAGAGCTTGACGGGGAAAGCCGGCGAACGTGGCGAGAAAGGAAGGGAAGAAAGCGAAAGGAGCGGGCGCTAGGGCGCTGGCAAGTGTAGCGGTCACGCTGCGCGTAACCACCACACCCGCCGCGCTTAATGCGCCGCTACAGGGCGCGTCCCATTCGCCAATTTCCCTCGGGGGCTAAATCTCGAACTGCCCCTTTCGGCCGCTTGCACCGCTCTTTCCTTCCCTTCTTTCGCTTTCCTCGCCCGCGATCCCGCGACCGTTCACATCGCCAGTGCGACGCGCATTGGTGGTGTGGGCGGCGCGAATTACGCGGCGATGTCCCGCGCAGGGTAAGCGGTNaeIBsmFIBsrFINgoMIVF1 ori010 Hs...s: 0)La...a3,5803,6003,6203,6403,6603,6803,7003,720
TTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATAAGTCCGACGCGTTGACAACCCTTCCCGCTAGCCACGCCCGGAGAAGCGATAATGCGGTCGACCGCTTTCCCCCTABglIFspIPvuILacZ alpha643 NIA1p...ches: 0)3,7403,7603,7803,800
  • Plasmid
Editing disabled on read-only sequence.
3814 bp2750300032503500250500750AmpRSpCas9 scaffoldmut

Welcome to Benchling!

Sign in to view data.

New digest

Saved digests

Enzyme AatII
Enzyme lists
Cut sites visible on maps
Find enzyme
Name Cuts
Selected Color
Show enzymes that cut

Primers

Version history

 Show full history
Change User Timestamp

Sequence Alignments

Saved alignments

Sequence Info

Tags

Name
Parent version
Folder
Topology
Start index
Locked
Created
--
Length
--
Export data
Split Workspace
Bases
3814