NBA: Near-optimal Block Alignment

Please Input the First Sequence: S1=

e.g. bacddb
(Class Type: Characters of Set Symbol.)

Please Input the Second Sequence: S2=

e.g. abdcd
(Class Type: Characters of Set Symbol.)

Please Input the Symbols that Are Used in S1,S2: Symbol=

e.g. abcd
(Class Type: English Alphabets.)

Please Input the Score Matrix: Score Matrix=

e.g.
 - a b c d
- -10000 -1 -1 -1 -1
a 4 1 0 2
b 3 0 -2
c 2 1
d 1
= -10000,-1,-1,-1,-1,4,1,0,2,3,0,-2,2,1,1
(Class Type: Matrix of Integers with size |Symbol+1|X|Symbol+1|, Upper Triangle Only.)

Please Input the Threshold of the Near-optimal: Near=

e.g. 2
(Class Type: Integers that Equal or Greater Than 0. )

Please Input the Threshold when Judging Blocks: Tau=

e.g. 0
(Class Type: Float Numbers.)

Block Color Setting:
Red Orange Yellow Green Blue Indigo Violet White

 > Tau

 = Tau

 < Tau


Reference:

Just Copy and paste them to respective fields. Compositional problems can be ignored.

Symbol Set of of Proteins

ACDEFGHIKLMNPQRSTVWY

PAM250 Score Matrix

-99999-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2-2
 2-200-41-1-1-1-2-1010-2110-6-3
  12-5-5-4-3-3-2-5-6-5-4-3-5-40-2-2-80
   43-611-20-4-32-12-100-2-7-4
    4-501-20-3-21-12-100-2-7-4
     9-5-21-520-4-5-5-4-3-3-107
      5-2-3-2-4-30-1-1-310-1-7-5
       6-20-2-22032-1-1-2-30
        5-222-2-2-2-2-104-5-1
         5-301-11300-2-3-4
          64-3-3-2-3-3-22-2-1
           6-2-2-10-2-12-4-2
            2-11010-2-4-2
             60010-1-6-5
              41-1-1-2-5-4
               60-1-22-4
                21-1-2-3
                 30-5-3
                  4-6-2
                   170
                    10