title "version = 1.25 of inst.soxs 1999 May 18";
(* 1.25: correction: switch names of sodA_1 and sodA_2 *)
(* 1.24: correction fur should be fldA *)
(* origin before 1996 June 19 *)

(* lines with the word "REMOVE"
can be REMOVED to get single pieces for scanning *)

organism E.coli;
chromosome E.coli;
piece U00096;

(* Li.Demple1996 proven by gel shift *)
name "araI1";
(* piece D10483; *)
(* get from 69804 +150 to same -150 direction -; *)
(* a much better candidate is at 69857! *)
(*
  "gccatag#catttttatccataagat"
  "atcttatggataaaaatgctatggc"
                    ^ 69804 *
*)
get from 70144 +150 to same -150 direction -;

(* Zheng, Doan, Schneider, Storz personal communication, 1999 April 7 *)
name "fldA";
get from 710801 -150 to same +150 direction +;

name "pqi-5";
(* piece X81561; *)
(* get from 470 -150 to same +150 direction +; *)
get from 1010841 -150 to same +150 direction +;


(* Wolf *)
name "mar";
(* piece M96235; *)
(* get from 1362 +150 to same -150 direction -; *)
(* old: get from 1364 -150 to same +150 direction +; *)
get from 1617060 +150 to same -150 direction -;

(* Wolf *)
name "fumC";
(* piece X04065; *)
get from 1684719 +150 to same -150 direction -;

(* Wolf *)
name "zwf_3";
(* get from 642 -150 to same +150 direction +; (* REMOVE *)
get from 1934404 +150 to same -150 direction -; (* REMOVE *)

(* Wolf *)
name "zwf_1";
(* piece M55005; *)
(* get from 589 -150 to same +150 direction +; *)
get from 1934457 +150 to same -150 direction -;

(* Li.Demple1996 *) (* REMOVE *)
name "zwf_2"; (* REMOVE *)
(* piece M55005; (* REMOVE *)
(* get from 569 +150 to same -150 direction -; (* REMOVE *)
get from 1934477 -150 to same +150 direction +; (* REMOVE *)

(* Wolf *)
name "nfo";
(* piece U00007; *)
(* get from 58507 -150 to same +150 direction +; *)
get from 2248782 -150 to same +150 direction +;

(* Li.Demple1996 *) (* REMOVE *)
name "micF_2"; (* REMOVE *)
(* piece K00541; (* REMOVE *)
(* get from 268 +150 to same -150 direction -; (* REMOVE *)
get from 2310992 -150 to same +150 direction +; (* REMOVE *)

(* Wolf *)
name "micF_1";
(* piece K00541; *)
(* get from 203 +150 to same -150 direction -; *)
get from 2311057 -150 to same +150 direction +;

name "ompR";
(*
* Fawcett footprinted SoxS on ompR.  In accession number J01656, 
* the footprint extends from position 51 through position 69.
(That's the thesis.)
*)
(* piece J01656; *)
(* get from 57 -150 to same +150 direction +; *)
get from 3534416 +150 to same -150 direction -;

(* Li.Demple1996 proven by gel shift *)
name "oriC";
(* piece K01789; *)
(* get from 277 -150 to same +150 direction +; *)
(*
  "gtagatcgcacgatctgtatacttat"
           ^ 277 *
*)
get from 3923626 -150 to same +150 direction +;

(* Li.Demple1996 *) (* REMOVE *)
name "sodA_2"; (* REMOVE *)
(* piece M94879; (* REMOVE *)
(* get from 836 -150 to same +150 direction +; (* REMOVE *)
get from 4098256 -150 to same +150 direction +; (* REMOVE *)

(* Wolf *)
name "sodA_1";
(* piece M94879; *)
(* get from 874 -150 to same +150 direction +; *)
get from 4098294 -150 to same +150 direction +;

(* Wolf *)
name "fpr";
(* piece Z11767; *)
(* get from 1169 +150 to same -150 direction -; *)
get from 4112131 -150 to same +150 direction +;

(* Li.Demple1996 *)
name "soxS";
(* piece U00006; *)
(* get from 142729 -150 to same +150 direction +; *)
(*
  "ttaccccgcattaaagcgctg"
           ^ 142729 *
*)
get from 4275068 -150 to same +150 direction +;

(******************************************************************************)

(******************************************************************************)

(* Wolf Fawcett  1996 June 11
>       1.  In addition to the primary footprint site in fpr, Fawcett
> also found protection at positions 1012 -1047 in Z11767.  Deletion of
> this upstream site has no effect on SoxS activation of fpr in vivo.
This region is outside the range I scanned.  I changed the delila 
instructions to include it and found that there is a 3.9 bit site with zero
base at 1019.   
before adding the site: 
Rs total is  9.44150 +/-  0.55625 bits in the range from -5 to 15 
after adding the site:
% Rs total is  8.13918 +/-  0.51985 bits in the range from -5 to 15 
The site itself goes up to 4.2 bits but a LARGE number of other sites now 
appear.  I think something is wrong with it, though it is not clear what.  I
am also suspicious about this site because of its unusual length (35
bases!).  It seems best to leave it out but I'm not really sure that is the
right thing to do.
 *)
(* name "fpr 2"; REMOVE *)
(* piece Z11767; REMOVE *)
(* get from 1019 +150 to same -150 direction -; REMOVE *)

(*
SoxS sites from Rick Wolf 1996 May 29
        micF    K00541  209-186 (compl strand)
        nfo     M22591  GT plus 1-23
        sodA    M94879  865-891
        fumC    X04065  51-72
        fpr     Z11767  1151-1179
        zwf     M55005  583-606
        pqi-5   X81561  466-487 (guess)
        mar     M96235  1349-1364 (MarA footprint)
*)

(*
From wolf@umbc.edu Tue Jun 18 11:42 EDT 1996
A few days ago I faxed Dr. Roe (Seoul National University) a
request for the coordinates of the footprint of SoxS on pqi-5 that she
reported at a transcription meeting that my student, Kam, attended.  I
told her that you and I were carrying out an analysis of SoxS binding
sites based on information theory and that if a publication resulted from
the analysis their contribution would be acknowledged and proper
references would be cited.  I also asked whether she could provide the
SoxS.  Today, I received her reply that the coordinates are positions
463-494 in X81561.  These are close to the positions that I had guessed
preliminary at this point.
 *)