C:\Users\matt\Desktop\SW_Perl>perl SW_full.pl AAUGCCAUUGACGG CAGCCUCGCUUAG

SEQUENCE 1 : AAUGCCAUUGACGG     LENGTH: 14
SEQUENCE 2 : CAGCCUCGCUUAG      LENGTH: 13

DYNAMIC PROGRAMMING MATRICES:

I) Scores:

    A   A   U   G   C   C   A   U   U   G   A   C   G   G

C  0.0 0.0 0.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0
A  1.0 1.0 0.0 0.0 0.0 0.7 2.0 0.7 0.0 0.0 1.0 0.0 0.7 0.0
G  0.0 0.7 0.7 1.0 0.0 0.0 0.7 1.7 0.3 1.0 0.0 0.7 1.0 1.7
C  0.0 0.0 0.3 0.3 2.0 1.0 0.0 0.3 1.3 0.0 0.7 1.0 0.3 0.7
C  0.0 0.0 0.0 0.0 1.3 3.0 1.7 0.3 0.0 1.0 0.0 1.7 0.7 0.0
U  0.0 0.0 1.0 0.0 0.0 1.7 2.7 2.7 1.3 0.0 0.7 0.3 1.3 0.3
C  0.0 0.0 0.0 0.7 1.0 1.0 1.3 2.3 2.3 1.0 0.0 1.7 0.3 1.0
G  0.0 0.0 0.0 1.0 0.3 0.7 0.7 1.0 2.0 3.3 2.0 0.7 2.7 1.3
C  0.0 0.0 0.0 0.0 2.0 1.3 0.3 0.3 0.7 2.0 3.0 3.0 1.7 2.3
U  0.0 0.0 1.0 0.0 0.7 1.7 1.0 1.3 1.3 0.7 1.7 2.7 2.7 1.3
U  0.0 0.0 1.0 0.7 0.0 0.3 1.3 2.0 2.3 1.0 0.3 1.3 2.3 2.3
A  1.0 1.0 0.0 0.7 0.3 0.0 1.3 1.0 1.7 2.0 2.0 0.7 1.0 2.0
G  0.0 0.7 0.7 1.0 0.3 0.0 0.0 1.0 0.7 2.7 1.7 1.7 1.7 2.0

II) Pointers:

    A   A   U   G   C   C   A   U   U   G   A   C   G   G

C   *   *   *   *   d   d   *   *   *   *   *   d   *   *
A   d   d   *   *   *   d   d   l   *   *   d   *   d   *
G   *   d   d   d   *   *   u   d   l   d   *   d   d   d
C   *   *   d   d   d   d   *   u   d   l   d   d   d   d
C   *   *   *   d   d   d   l   l   u   d   *   d   d   d
U   *   *   d   *   u   u   d   d   l   l   d   u   d   d
C   *   *   *   d   d   d   d   d   d   d   *   d   l   d
G   *   *   *   d   d   d   d   d   d   d   l   l   d   d
C   *   *   *   *   d   d   d   d   d   u   d   d   l   d
U   *   *   d   *   u   d   d   d   d   u   d   d   d   d
U   *   *   d   d   *   u   d   d   d   d   u   d   d   d
A   d   d   *   d   d   *   d   d   d   d   d   l   d   d
G   *   d   d   d   d   d   u   d   d   d   d   d   d   d


Max score = 3.3 column: 10 (G)  row: 8 (G)

Alignment:

GCCAUUG
||| |.|
GCC-UCG