Motif    Start   End  Length   Motif
Motif1    2      4      3      [ST][C][C]
Motif2    9      12     4      [GA][R][NS][CN]
Motif3    26     28     3      [C][A][NT]


Motif marked on the alignment

           ***    ****             ***                                
d1bhpa  : KSCCKSTLGRNCYNLCRA-RGAQKLCANVCRCKLTSGLSCPKDFPK
d3nira  : TTCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN