Tk:E. coli cut sites


 * 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