Tk:E. coli cut sites: Difference between revisions

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* CTAG sequences in the E. coli genome are rare.
* CTAG sequences in the E. coli genome are rare.
* SpeI cut sites in the E.coli genome: 74
* SpeI cut sites in the E.coli genome: 79
* XbaI cut sites in the E. coli genome: 40
* XbaI cut sites in the E. coli genome: 40
* Used a 300 Kb region of the E. coli genome as a sample to find the frequency of EcoRI and PstI sites.  The 300Kb is random and unimportant.  The list is partially complete. All the XbaI and SpeI sites are listed.  The # means methylation inhibited -- XbaI by dam: G(mA)TC and SpeI by EcoK: A(mA)CNNNNNNGTGC & GC(mA)CNNNNNNGTT).  For the top set, close EcoRI or PstI sites, if any (EcoRI for SpeI cut sites, and PstI for XbaI cut sites).  This task is not yet finished.




Latest revision as of 05:40, 4 March 2007

  • CTAG sequences in the E. coli genome are rare.
  • SpeI cut sites in the E.coli genome: 79
  • XbaI cut sites in the E. coli genome: 40


  • Used a 300 Kb region of the E. coli genome as a sample to find the frequency of EcoRI and PstI sites. The 300Kb is random and unimportant. The list is partially complete. All the XbaI and SpeI sites are listed. The # means methylation inhibited -- XbaI by dam: G(mA)TC and SpeI by EcoK: A(mA)CNNNNNNGTGC & GC(mA)CNNNNNNGTT). For the top set, close EcoRI or PstI sites, if any (EcoRI for SpeI cut sites, and PstI for XbaI cut sites). This task is not yet finished.


  • PstI cut sites in a 300Kbp region of the E. coli genome: 79
  • Average length of PstI fragment: 300K/79 = 3800
  • We would expect the average length of a double cut XbaI / PstI fragment to be about 1900 bp, and there to be about 40 different ones.
  • Likely there are a few with order of 100 bp length


  • EcoRI cut sites in a 300Kbp region of the E. coli genome: 42, but 18 are methylation inhibited. 24 are left actually cut.
  • Average length of EcoRI fragment: 300K/24 = 12500
  • We would expect the average length of the double cut EcoRI / SpeI to be about 6250 bp, and there to be about 79 of them.
  • Likely there are a few with order of 80 bp length


  • 11828 SpeI ACTAGT EcoRI site at 12890
  • 25681 XbaI TCTAGA PstI site at 23550
  • 84649 SpeI ACTAGT No close sites
  • 131428 XbaI TCTAGA PstI 127098 134707; EcoRI 131742
  • 237191 XbaI TCTAGA PstI 233863; EcoRI 237075 237338
  • 270729 XbaI TCTAGA PstI 268105 275451; EcoRI 268483 274271
  • 310919 SpeI ACTAGT PstI 308132 312819; EcoRI 310737
  • 380545 SpeI ACTAGT No close sites
  • 380557 SpeI ACTAGT PstI 381908; EcoRI 382270
  • 405554 SpeI ACTAGT PstI 404575; no close EcoRI sites
  • 445916 SpeI ACTAGT PstI 442163; EcoRI 447526
  • 570189 SpeI ACTAGT PstI 570172; EcoRI 574906
  • 594695 XbaI TCTAGA PstI 696794; no close EcoRI sites
  • 849339 XbaI TCTAGA PstI 850079; no close EcoRI sites
  • 889063 SpeI ACTAGT No close PstI sites; EcoRI 889113
  • 889173 SpeI ACTAGT No close PstI sites; EcoRI 889113
  • 921898 XbaI TCTAGA No close sites
  • 968572 SpeI ACTAGT PstI 972115; EcoRI 966871
  • 1098843 SpeI ACTAGT
  • 1184031 XbaI TCTAGA
  • 1195749 SpeI ACTAGT
  • 1196554 XbaI TCTAGA
  • 1196673 XbaI TCTAGA
  • 1198740 XbaI TCTAGA
  • 1214824 SpeI ACTAGT
  • 1219071 SpeI ACTAGT
  • 1321138 SpeI ACTAGT
  • 1321146 SpeI ACTAGT
  • 1343440 # SpeI ACTAGT
  • 1467188 SpeI ACTAGT
  • 1467200 SpeI ACTAGT
  • 1468285 XbaI TCTAGA
  • 1494788 XbaI TCTAGA
  • 1522924 SpeI ACTAGT
  • 1566793 SpeI ACTAGT
  • 1686509 SpeI ACTAGT
  • 1695103 SpeI ACTAGT
  • 1710491 SpeI ACTAGT
  • 1743206 XbaI TCTAGA
  • 1745491 SpeI ACTAGT
  • 1755429 XbaI TCTAGA
  • 1786307 SpeI ACTAGT
  • 1970292 XbaI TCTAGA
  • 2001080 SpeI ACTAGT
  • 2009992 XbaI TCTAGA
  • 2068219 SpeI ACTAGT
  • 2068231 SpeI ACTAGT
  • 2088067 SpeI ACTAGT
  • 2096253 SpeI ACTAGT
  • 2101441 SpeI ACTAGT
  • 2104050 XbaI TCTAGA
  • 2106663 SpeI ACTAGT
  • 2151995 SpeI ACTAGT
  • 2152874 XbaI TCTAGA
  • 2174649 XbaI TCTAGA
  • 2223066 XbaI TCTAGA
  • 2310221 SpeI ACTAGT
  • 2318050 SpeI ACTAGT
  • 2355074 SpeI ACTAGT
  • 2493149 SpeI ACTAGT
  • 2493548 SpeI ACTAGT
  • 2536278 SpeI ACTAGT
  • 2558074 XbaI TCTAGA
  • 2713371 XbaI TCTAGA
  • 2715691 SpeI ACTAGT
  • 2727452 XbaI TCTAGA
  • 2756439 XbaI TCTAGA
  • 2772810 SpeI ACTAGT
  • 2781697 SpeI ACTAGT
  • 2784977 XbaI TCTAGA
  • 2786429 SpeI ACTAGT
  • 2808396 SpeI ACTAGT
  • 2836247 SpeI ACTAGT
  • 2852098 SpeI ACTAGT
  • 2901546 SpeI ACTAGT
  • 2905982 SpeI ACTAGT
  • 2991253 SpeI ACTAGT
  • 2991601 XbaI TCTAGA
  • 2995637 SpeI ACTAGT
  • 2995649 SpeI ACTAGT
  • 3031463 SpeI ACTAGT
  • 3132842 SpeI ACTAGT
  • 3184179 SpeI ACTAGT
  • 3184191 SpeI ACTAGT
  • 3187097 SpeI ACTAGT
  • 3189715 SpeI ACTAGT
  • 3382752 SpeI ACTAGT
  • 3431660 XbaI TCTAGA
  • 3437163 SpeI ACTAGT
  • 3457723 SpeI ACTAGT
  • 3580870 XbaI TCTAGA
  • 3698161 XbaI TCTAGA
  • 3741621 SpeI ACTAGT
  • 3768516 SpeI ACTAGT
  • 3791883 SpeI ACTAGT
  • 3804226 XbaI TCTAGA
  • 3826538 SpeI ACTAGT
  • 3861916 # XbaI TCTAGA
  • 3922417 SpeI ACTAGT
  • 3929332 SpeI ACTAGT
  • 3941469 XbaI TCTAGA
  • 4002359 SpeI ACTAGT
  • 4166406 XbaI TCTAGA
  • 4207808 XbaI TCTAGA
  • 4308586 # XbaI TCTAGA
  • 4353824 SpeI ACTAGT
  • 4395522 SpeI ACTAGT
  • 4431187 SpeI ACTAGT
  • 4441309 SpeI ACTAGT
  • 4496265 SpeI ACTAGT
  • 4496277 SpeI ACTAGT
  • 4502621 SpeI ACTAGT
  • 4505734 XbaI TCTAGA
  • 4572269 SpeI ACTAGT
  • 4572617 XbaI TCTAGA
  • 4578672 XbaI TCTAGA
  • 4638702 SpeI ACTAGT
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