* scan 3.42
* 2006/10/26 01:15:47, 2006/10/26 01:15:47, furoligos

define "Fur-M9-24" " w" "  " "  " -9.0 9.0

ribl "Fur-M9-24"
* Ri 2.77
*
* Ri(b,l) table is from:
** rseq 5.41 rsequence calculated from encoded sequences from:
** encode 1.41; encoding of sequences in
** * 2006/08/28 17:47:40, 2004/10/11 17:24:49, fur sites version - 1.01 of Fur-M9-24.inst 2006 Aug 28
*
* BOOK/INST sequences are from:
* 2006/08/28 17:47:40, 2004/10/11 17:24:49, fur sites version - 1.01 of Fur-M9-24.inst 2006 Aug 28
* title 'fur sites version - 1.01 of Fur-M9-24.inst 2006 Aug 28';
*
* PARAMETERS FOR Ri:
* -9 9 from-to
* 1 column of value file
* -2147483647.000000 2147483647.000000 lowest to highest Ri selected
* -2147483647.000000 2147483647.000000 lowest to highest Value selected
* not printing sequences to sequ
*     printing sequences to rixyin
* -: whole line printed when partial site
*  using Staden's Method: when f(b,l) = 0, replace with f(b,l) = 1/(n+t), t = 2
* 
* i alignmenttype first, book, instructions
*    Ri(a,l)    Ri(c,l)    Ri(g,l)    Ri(t,l)        l        a        c        g        t
      -9        9 frombase, tobase
    1.539033  -3.689786  -3.630893  -0.171461       -9       36        0        1       11
    1.578561  -3.689786  -2.045930  -0.630893       -8       37        0        3        8
   -2.045930  -2.045930  -3.630893   1.726660       -7        3        3        1       41
   -0.630893  -3.630893   1.654510  -3.689786       -6        8        1       39        0
    1.726660  -2.045930  -3.630893  -2.045930       -5       41        3        1        3
   -0.630893  -3.689786  -0.630893   1.369107       -4        8        0        8       32
    1.860961  -3.689786  -3.689786  -2.045930       -3       45        0        0        3
    1.617035  -1.630893  -2.630893  -1.630893       -2       38        4        2        4
   -3.689786  -0.630893  -3.630893   1.654510       -1        0        8        1       39
   -0.308964   0.176462   0.176462  -0.308964        0       10       14       14       10
    1.654510  -3.630893  -0.630893  -3.689786        1       39        1        8        0
   -1.630893  -2.630893  -1.630893   1.617035        2        4        2        4       38
   -2.045930  -3.689786  -3.689786   1.860961        3        3        0        0       45
    1.369107  -0.630893  -3.689786  -0.630893        4       32        8        0        8
   -2.045930  -3.630893  -2.045930   1.726660        5        3        1        3       41
   -3.689786   1.654510  -3.630893  -0.630893        6        0       39        1        8
    1.726660  -3.630893  -2.045930  -2.045930        7       41        1        3        3
   -0.630893  -2.045930  -3.689786   1.578561        8        8        3        0       37
   -0.171461  -3.630893  -3.689786   1.539033        9       11        1        0       36
*
 19.684195 bits = mean (Rsequence of selected region)
  4.628724 bits = standard deviation
*
 29.630532 bits = Ri of consensus sequence from -9 to 9
-64.371754 bits = Ri of anticonsensus sequence from -9 to 9
*
-25.441307 bits = average Ri for random sequence from -9 to 9
*
48 n, number of sequences used to create the matrix
*
odd symmetry of the matrix
*
-5000.000000 Ri bound: lower bound on Ri
100.000000 Z bound: lower bound on Z
  1.000000 P bound: upper probability
*
l  extreme: char; h or l, the high or low extreme to be defined
 0.0  wavelocation: real; the location in bases of the extreme
 1.0  wavebit: real; the location in bits of the extreme
 0.5  waveamplitude: real; the amplitude of the wave in bits
10.6  wavelength: real; the wave length of the wave in bases
 0.2  0.2  0.0 dashon, dashoff, dashoffset (in bases)
 0.0  thickness: real; the thickness of the cosine wave.  <=0 means default
.

@ yoeA 19.0 +1 "Fur-M9-24" " 5.3 bits"   5.300838  -3.107413   0.000944
@ yoeA 25.0 +1 "Fur-M9-24" "27.1 bits"  27.145110   1.611873   0.053495
@ yoeA 28.0 +1 "Fur-M9-24" " 4.7 bits"   4.746056  -3.227269   0.000625
@ yoeA 31.0 +1 "Fur-M9-24" " 7.3 bits"   7.253309  -2.685597   0.003620
@ yoeA 37.0 +1 "Fur-M9-24" " 9.8 bits"   9.764625  -2.143046   0.016055
@ yoeA 43.0 +1 "Fur-M9-24" " 4.8 bits"   4.822012  -3.210860   0.000662
@ yoeA 85.0 +1 "Fur-M9-24" " 4.8 bits"   4.822012  -3.210860   0.000662
@ yoeA 91.0 +1 "Fur-M9-24" " 9.8 bits"   9.764625  -2.143046   0.016055
@ yoeA 97.0 +1 "Fur-M9-24" " 7.3 bits"   7.253309  -2.685597   0.003620
@ yoeA 100.0 +1 "Fur-M9-24" " 4.7 bits"   4.746056  -3.227269   0.000625
@ yoeA 103.0 +1 "Fur-M9-24" "27.1 bits"  27.145110   1.611873   0.053495
@ yoeA 109.0 +1 "Fur-M9-24" " 5.3 bits"   5.300838  -3.107413   0.000944
@ fepD-entS 25.0 +1 "Fur-M9-24" " 9.9 bits"   9.902602  -2.113237   0.017290
@ fepD-entS 31.0 +1 "Fur-M9-24" "20.1 bits"  20.124592   0.095144   0.462100
@ fepD-entS 37.0 +1 "Fur-M9-24" "13.0 bits"  12.961341  -1.452421   0.073192
@ fepD-entS 43.0 +1 "Fur-M9-24" " 3.6 bits"   3.551461  -3.485352   0.000246
@ fepD-entS 85.0 +1 "Fur-M9-24" " 3.6 bits"   3.551461  -3.485352   0.000246
@ fepD-entS 91.0 +1 "Fur-M9-24" "13.0 bits"  12.961341  -1.452421   0.073192
@ fepD-entS 97.0 +1 "Fur-M9-24" "20.1 bits"  20.124592   0.095144   0.462100
@ fepD-entS 103.0 +1 "Fur-M9-24" " 9.9 bits"   9.902602  -2.113237   0.017290
@ gpmA 19.0 +1 "Fur-M9-24" " 5.8 bits"   5.844609  -2.989935   0.001395
@ gpmA 22.0 +1 "Fur-M9-24" " 6.9 bits"   6.857734  -2.771058   0.002794
@ gpmA 25.0 +1 "Fur-M9-24" "27.1 bits"  27.145110   1.611873   0.053495
@ gpmA 31.0 +1 "Fur-M9-24" " 4.3 bits"   4.283622  -3.327175   0.000439
@ gpmA 73.0 +1 "Fur-M9-24" " 4.3 bits"   4.283622  -3.327175   0.000439
@ gpmA 79.0 +1 "Fur-M9-24" "27.1 bits"  27.145110   1.611873   0.053495
@ gpmA 82.0 +1 "Fur-M9-24" " 6.9 bits"   6.857734  -2.771058   0.002794
@ gpmA 85.0 +1 "Fur-M9-24" " 5.8 bits"   5.844609  -2.989935   0.001395
@ ryhB 19.0 +1 "Fur-M9-24" " 7.6 bits"   7.553426  -2.620759   0.004387
@ ryhB 25.0 +1 "Fur-M9-24" "25.3 bits"  25.345133   1.223002   0.110664
@ ryhB 31.0 +1 "Fur-M9-24" " 7.8 bits"   7.793233  -2.568950   0.005100
@ ryhB 73.0 +1 "Fur-M9-24" " 7.8 bits"   7.793233  -2.568950   0.005100
@ ryhB 79.0 +1 "Fur-M9-24" "25.3 bits"  25.345133   1.223002   0.110664
@ ryhB 85.0 +1 "Fur-M9-24" " 7.6 bits"   7.553426  -2.620759   0.004387
@ fhuA 25.0 +1 "Fur-M9-24" "10.6 bits"  10.562841  -1.970598   0.024385
@ fhuA 31.0 +1 "Fur-M9-24" "19.9 bits"  19.862049   0.038424   0.484675
@ fhuA 37.0 +1 "Fur-M9-24" " 5.4 bits"   5.359731  -3.094690   0.000985
@ fhuA 79.0 +1 "Fur-M9-24" " 5.4 bits"   5.359731  -3.094690   0.000985
@ fhuA 85.0 +1 "Fur-M9-24" "19.9 bits"  19.862049   0.038424   0.484675
@ fhuA 91.0 +1 "Fur-M9-24" "10.6 bits"  10.562841  -1.970598   0.024385
@ nohA 19.0 +1 "Fur-M9-24" "12.7 bits"  12.689814  -1.511082   0.065384
@ nohA 25.0 +1 "Fur-M9-24" "20.8 bits"  20.836119   0.248864   0.401733
@ nohA 79.0 +1 "Fur-M9-24" "20.8 bits"  20.836119   0.248864   0.401733
@ nohA 85.0 +1 "Fur-M9-24" "12.7 bits"  12.689814  -1.511082   0.065384
@ oppA 25.0 +1 "Fur-M9-24" " 9.6 bits"   9.564414  -2.186300   0.014397
@ oppA 31.0 +1 "Fur-M9-24" "21.2 bits"  21.163066   0.319499   0.374674
@ oppA 85.0 +1 "Fur-M9-24" "21.2 bits"  21.163066   0.319499   0.374674
@ oppA 91.0 +1 "Fur-M9-24" " 9.6 bits"   9.564414  -2.186300   0.014397
@ gspC 22.0 +1 "Fur-M9-24" " 3.5 bits"   3.519678  -3.492219   0.000240
@ gspC 28.0 +1 "Fur-M9-24" "14.3 bits"  14.304473  -1.162247   0.122568
@ gspC 76.0 +1 "Fur-M9-24" "14.3 bits"  14.304473  -1.162247   0.122568
@ gspC 82.0 +1 "Fur-M9-24" " 3.5 bits"   3.519678  -3.492219   0.000240
@ yhaU 22.0 +1 "Fur-M9-24" " 8.6 bits"   8.567583  -2.401658   0.008160
@ yhaU 25.0 +1 "Fur-M9-24" "11.0 bits"  11.041513  -1.867185   0.030938
@ yhaU 28.0 +1 "Fur-M9-24" "14.3 bits"  14.266622  -1.170425   0.120915
@ yhaU 31.0 +1 "Fur-M9-24" " 6.6 bits"   6.570278  -2.833160   0.002305
@ yhaU 79.0 +1 "Fur-M9-24" " 6.6 bits"   6.570278  -2.833160   0.002305
@ yhaU 82.0 +1 "Fur-M9-24" "14.3 bits"  14.266622  -1.170425   0.120915
@ yhaU 85.0 +1 "Fur-M9-24" "11.0 bits"  11.041513  -1.867185   0.030938
@ yhaU 88.0 +1 "Fur-M9-24" " 8.6 bits"   8.567583  -2.401658   0.008160
@ yahA 25.0 +1 "Fur-M9-24" "14.3 bits"  14.330667  -1.156588   0.123720
@ yahA 31.0 +1 "Fur-M9-24" "16.6 bits"  16.588191  -0.668868   0.251790
@ yahA 85.0 +1 "Fur-M9-24" "16.6 bits"  16.588191  -0.668868   0.251790
@ yahA 91.0 +1 "Fur-M9-24" "14.3 bits"  14.330667  -1.156588   0.123720
@ fadD 19.0 +1 "Fur-M9-24" " 3.8 bits"   3.779920  -3.435996   0.000295
@ fadD 25.0 +1 "Fur-M9-24" "23.0 bits"  22.961620   0.708062   0.239453
@ fadD 79.0 +1 "Fur-M9-24" "23.0 bits"  22.961620   0.708062   0.239453
@ fadD 85.0 +1 "Fur-M9-24" " 3.8 bits"   3.779920  -3.435996   0.000295
@ exbB 24.0 +1 "Fur-M9-24" "18.9 bits"  18.887751  -0.172066   0.431693
@ exbB 36.0 +1 "Fur-M9-24" " 3.2 bits"   3.205488  -3.560097   0.000185
@ exbB 76.0 +1 "Fur-M9-24" " 3.2 bits"   3.205488  -3.560097   0.000185
@ exbB 88.0 +1 "Fur-M9-24" "18.9 bits"  18.887751  -0.172066   0.431693
@ fhuF 16.0 +1 "Fur-M9-24" "22.1 bits"  22.090320   0.519825   0.301593
@ fhuF 33.0 +1 "Fur-M9-24" "22.4 bits"  22.386711   0.583858   0.279658
@ fhuF 39.0 +1 "Fur-M9-24" "15.9 bits"  15.947184  -0.807352   0.209732
@ fhuF 75.0 +1 "Fur-M9-24" "15.9 bits"  15.947184  -0.807352   0.209732
@ fhuF 81.0 +1 "Fur-M9-24" "22.4 bits"  22.386711   0.583858   0.279658
@ fhuF 98.0 +1 "Fur-M9-24" "22.1 bits"  22.090320   0.519825   0.301593