Multiple Sequence Alignment Output

Here is the Input Data File

>Seq 1
MAALRMLWMGLVLLGLLGFPQTPAQGHDTVQPNFQQDKFLGRWYSAGLASNSSWFREKKAVLYMCKTVVA%0APSTEGGLNLTSTFLRKNQCETKIMVLQPAGAPGHYTYSSPHSGSIHSVSVVEANYDEYALLFSRGTKGPG%0AQDFRMATLYSRTQTLKDELKEKFTTFSKAQGLTEEDIVFLPQPDKCIQE%0A
>Seq 2
APEAQVSVQPNFQPDKFLGRWFSAGLASNSSWLQEKKAALSMCKSVVAPAADGGFNLTSTFLRKNQCETR%0ATMLLQPGDSLGSYSYRSPHWGSTYSVSVVETDYDHYALLYSQGSKGPGEDFRMATLYSRTQTPRAELKEK%0AFTAFCKAQGFTEDSIVFLPQTDKCMTEQ%0A
>Seq 3
MATHHTLWMGLALLGVLGDLQAAPEAQVSVQPNFQQDKFLGRWFSAGLASNSSWLREKKAALSMCKSVVA%0APATDGGLNLTSTFLRKNQCETRTMLLQPAGSLGSYSYRSPHWGSTYSVSVVETDYDQYALLYSQGSKGPG%0AEDFRMATLYSRTQTPRAELKEKFTAFCKAQGFTEDTIVFLPQTDKCMTEQ%0A

Here is the Output from the Run

---------------- Tree given from ancestor ----------------
On the left:   Internal Node  Distance to parent =   21.50
On the left:   Leaf #1        Distance to parent =  256.50
On the right:  Leaf #2        Distance to parent =   93.50
On the right:  Leaf #3        Distance to parent =    0.00


                 ***  Heuristic Multiple Alignment  ***

123                   ************************************************1****
MAALRMLWMGLVLLGLLGFPQTPAQGHDTVQPNFQQDKFLGRWYSAGLASNSSWFREKKAVLYMCKTVVAAPSTE
----------------------APEAQVSVQPNFQPDKFLGRWFSAGLASNSSWLQEKKAALSMCKSVVA-PAAD
MATHHTLWMGLALLGVLGDLQAAPEAQVSVQPNFQQDKFLGRWFSAGLASNSSWLREKKAALSMCKSVVAAPATD

******************1************************************************1*******
GGLNLTSTFLRKNQCETK-IMVLQPAGAPGHYTYSSPHSGSIHSVSVVEANYDEYALLFSRGTKGPGAQDFRMAT
GGFNLTSTFLRKNQCETRATMLLQPGDSLGSYSYRSPHWGSTYSVSVVETDYDHYALLYSQGSKGPG-EDFRMAT
GGLNLTSTFLRKNQCETR-TMLLQPAGSLGSYSYRSPHWGSTYSVSVVETDYDQYALLYSQGSKGPGAEDFRMAT

***************1****************************2
LYSRTQTLKDELKEK-FTTFSKAQGLTEEDIVFLPQPDKCIQEA-
LYSRTQTPRAELKEKAFTAFCKAQGFTEDSIVFLPQTDKCMTEQA
LYSRTQTPRAELKEK-FTAFCKAQGFTEDTIVFLPQTDKCMTEQA


                  ***  Optimal Multiple Alignment  ***

MAALRMLWMGLVLLGLLGFPQTPAQGHDTVQPNFQQDKFLGRWYSAGLASNSSWFREKKAVLYMCKTVVAAPSTE
----------------------APEAQVSVQPNFQPDKFLGRWFSAGLASNSSWLQEKKAALSMCKSVV-APAAD
MATHHTLWMGLALLGVLGDLQAAPEAQVSVQPNFQQDKFLGRWFSAGLASNSSWLREKKAALSMCKSVVAAPATD

GGLNLTSTFLRKNQCETK-IMVLQPAGAPGHYTYSSPHSGSIHSVSVVEANYDEYALLFSRGTKGPGAQDFRMAT
GGFNLTSTFLRKNQCETRATMLLQPGDSLGSYSYRSPHWGSTYSVSVVETDYDHYALLYSQGSKGPG-EDFRMAT
GGLNLTSTFLRKNQCETR-TMLLQPAGSLGSYSYRSPHWGSTYSVSVVETDYDQYALLYSQGSKGPGAEDFRMAT

LYSRTQTLKDELKEK-FTTFSKAQGLTEEDIVFLPQPDKCIQEA-
LYSRTQTPRAELKEKAFTAFCKAQGFTEDSIVFLPQTDKCMTEQA
LYSRTQTPRAELKEK-FTAFCKAQGFTEDTIVFLPQTDKCMTEQA

End gaps not penalized.
Costfile:                   pam250
Alignment cost:    7484     Lower bound:    7484
Delta:                0     Max. Delta:       15

Sequences  Proj. Cost  Pair. Cost  Epsilon  Max. Epsi.  Weight  Weight*Cost
  1   2        2559        2559        0         5         1        2559
  1   3        2524        2524        0         5         1        2524
  2   3        2401        2401        0         5         1        2401
Elapsed time =   1.077