Tk:E. coli cut sites

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  • 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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