REDUCE Suite

Hello

I'am also novice for using your great package REDUCE_Suit.
I'm interested to study the affinity profile for a vary famous gene COL1A1( I downloded COL1A1 from Ensembel database) I tried to understand the dynamic of affinity profile for a transcription factor Sp1 through its binding site for both wild and mutant COL1A1 genes .

To start my study I ran the commande :
AffinityProfile \
   -prefix=aff_ \
   -threshold=0 \
   -psam=../../Desktop/source/REDUCE-Suite-v2.2/examples/AffinityProfile/psam_001.xml \
   -sequence=sequence_COL1A1.fasta

As a Psam matrix, I used the matrix given in your example.
But then I don't understand the result.

cat seq_psam.dat
   psam_001.xml
NM_000088.3   0.0301094
####################
cat AffinityProfile.log
sequence file: sequence_COL1A1.fasta   cut-off: 0
reading in sequences from file [sequence_COL1A1.fasta]
reading in PSAM ../../Desktop/source/REDUCE-Suite-v2.2/examples/AffinityProfile/psam_001.xml [1/1]
[  1]: ../../Desktop/source/REDUCE-Suite-v2.2/examples/AffinityProfile/psam_001.xml (forward); pmax=0.025626

Time used: 00:00:00:00

#################
cat aff_psam_001.xml

NM_000088.3   0.0301094   1:2.78962e-104   2:2.8034e-101   3:2.508e-07   4:2.97891e-94   5:3.73255e-103   6:4.75891e-116   7:6.73541e-70   8:6.52039e-71   9:5.81238e-65   10:4.04049e-53   11:9.0064e-52   12:2.29734e-51   13:1.30952e-52   14:1.14509e-48   15:2.33791e-51   16:6.36074e-41   17:4.78319e-46   18:9.88362e-103   19:1.18759e-104   20:7.56195e-118   21:3.05295e-99   22:1.19914e-103   23:2.68201e-21   24:6.17375e-91   25:6.30612e-151   26:6.59257e-50   27:1.50964e-89   28:1.19137e-86   29:9.42612e-47   30:5.0609e-66   31:3.89768e-149   32:1.41179e-49   33:1.62746e-79   34:2.80803e-108   35:5.26342e-77   36:1.28883e-55   37:4.3514e-24   38:5.40903e-86   39:5.26603e-61   40:2.5533e-83   41:2.91799e-121   42:4.92685e-68   43:1.42043e-72   44:3.66844e-54   45:1.07013e-92   46:2.2805e-56   47:4.31802e-112   48:2.12206e-67   49:4.32273e-65   50:5.36831e-108   51:3.10334e-59   52:5.76347e-71   53:3.189e-74   54:1.16991e-15   55:2.31613e-120   56:4.17858e-69   57:3.11132e-70   58:6.68288e-27   59:1.72033e-105   60:7.81592e-63   61:7.91623e-64   62:9.43495e-63   63:1.05312e-74   64:9.53001e-123   65:2.04295e-66   66:5.71577e-30   67:5.90979e-108   68:8.76473e-54   69:2.51005e-73   70:2.08671e-81   71:9.14769e-38   72:5.51473e-31   73:2.33375e-44   74:1.11588e-46   75:1.80495e-39   76:3.66284e-49   77:1.52272e-44   78:4.28484e-71   79:8.19242e-23   80:7.09162e-57   81:1.31163e-58   82:7.40765e-44   83:1.63155e-65   84:6.85533e-61   85:1.67216e-60   86:3.10819e-77   87:7.99735e-26   88:2.20357e-81   89:2.67345e-53   90:7.94344e-34   91:2.97164e-83   92:5.35325e-70   93:4.00621e-67   94:9.56203e-61   95:8.90908e-50   96:2.06665e-60   97:4.78235e-53   98:2.39696e-50   99:1.73158e-52   100:4.63302e-32   101:1.96568e-84   102:9.10009e-69   103:1.6031e-73   104:8.72453e-44   105:3.37299e-88   106:5.02218e-44   107:1.70837e-107   108:6.30181e-110   109:6.10561e-89   110:6.96046e-35   111:2.86401e-101   112:2.9393e-31   113:4.69209e-129   114:2.34756e-56   115:9.01049e-68   116:3.00809e-54   ...
...
..
...
5906:9.52601e-72   5907:9.93085e-28   5908:1.0446e-76   5909:1.53848e-65   5910:6.02333e-52   5911:2.12289e-43   5912:7.00049e-71   5913:7.89907e-37   5914:8.86224e-60   5915:1.47167e-70


####################
cat   seq_psam.dat
   psam_001.xml
NM_000088.3   0.0301094


#########################

Could you please help me to understand these results ?
What is this matrix  "aff_psam_001.xml" ?
How could I obtain more details on the affinity change and dynamics of binding site ?

Thank you in advance
Best Regards

Azadeh