Protein-DNA interface analysis program output:
number of chains= 3, chain IDs:  ABC
 number of bases/residues= 63 11 11
          number of atoms= 513 220 225

chain ID, number of bases, ifdna(0/1): A       0     0
KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLRV
chain ID, number of bases, ifdna(0/1): B      11     1
TAGCCGCCAGC
chain ID, number of bases, ifdna(0/1): C      11     1
GCTGGCGGCTA

chain, chain ID and number of paired bases:  1  A     0
chain, chain ID and number of paired bases:  2  B    11
chain, chain ID and number of paired bases:  3  C    11


chain, chain ID and number of bases contacting protein  2  B     7
B0003 B0004 B0005 B0006 B0007 B0008 B0009 
C0024 C0024 C0022 C0021 C0020 C0019 C0018 

chain, chain ID and number of bases contacting protein  3  C     8
C0015 C0016 C0017 C0018 C0019 C0020 C0021 C0022 
B0012 B0011 B0010 B0009 B0008 B0007 B0006 B0005 

 Detected binding site
 chain, range of basepairs contacting protein, length
 2:   3 ->   12  length: 10
 B0003 C0024 ->  B0012 C0015

Binding sequence:
TAGCCGCCAG

Sequence vs. energy
Full energy model
Calculated PWM (download in TransFac format)
AC  M3D000
P0      A      C      G      T         195.3
01     33    960      1      5      C     71
02      0    556     79    363      Y     70
03      0      0    999      0      G    105
04      0    999      0      0      C    144
05      0   1000      0      0      C    207
06      0      0    999      0      G    106
07    854    126     14      4      A     67
08      0    787      0    212      C     82
09      1    990      8      0      C     78
10    459    113    411     15      R     65
XX

Sequence logo: