MSA on Complete Sequences

                 ***  Heuristic Multiple Alignment  ***

***********************************************************231   **********
APRSVDWREKGYVTPVKDQGQCGSCWAFSTTGALEGQHFRTKGKLVSLSEQNLVDCSRPE-GNQGCNGGLMDQAF
LPDSMDWREKGCVTEVKYQGACGSCWAFSAVGALEAQVKLKTGKLVSLSAQNLVDCSTAKYGNKGCNGGFMTEAF
YPQSIDWRAKGAVTPVKNQGACGSCWAFSTIATVEGINKIVTGNLLELSEQELVDCDKHSY---GCKGGYQTTSL

***123  ***************2******123 ***********************12****************
QYVQDNGGIDSEESYPYTAKDDEDCRYKAEYNA-ANDTGFVDIPQGHERALMKAVASVGPVSVAIDAGHSSFQFY
QYIIDNNGIDSEASYPYKAMDGK-CQYDVKNRA-ATCSRYIELPFGSEEALKEAVANKGPVSVGIDASHSSFFLY
QYV-ANNGVHTSKVYPYQAKQYK-CRATDKPGPKVKITGYKRVPSNCETSFLGALANQ-PLSVLVEAGGKPFQLY

*****123 **231*****************************************123   ***123
QSGIYYEPDCSSEDLDHGVLVVGYGFEGGKKYWIVKNSWGEKWGDKGYIYMAKDRKN---HCGIATAASYPLV--
KTGVYYDPSCT-QNVNHGVLVVGYGNLDGKDYWLVKNSWGLHFGDQGYIRMARNSGN---HCGIANYPSYPEI--
KSGVF-DGPCG-TKLDHAVTAVGYGTSDGKNYIIIKNSWGPNWGEKGYMRLKRQSGNSQGTCGVYKSSYYPFKGF

-
-
A
                  ***  Optimal Multiple Alignment  ***

APRSVDWREKGYVTPVKDQGQCGSCWAFSTTGALEGQHFRTKGKLVSLSEQNLVDCSRPE-GNQGCNGGLMDQAF
LPDSMDWREKGCVTEVKYQGACGSCWAFSAVGALEAQVKLKTGKLVSLSAQNLVDCSTAKYGNKGCNGGFMTEAF
YPQSIDWRAKGAVTPVKNQGACGSCWAFSTIATVEGINKIVTGNLLELSEQELVDCDKHSY---GCKGGYQTTSL

QYVQDNGGIDSEESYPYTAKDDEDCRYKAEYNA-ANDTGFVDIPQGHERALMKAVASVGPVSVAIDAGHSSFQFY
QYIIDNNGIDSEASYPYKAMDGK-CQYDVKNRA-ATCSRYIELPFGSEEALKEAVANKGPVSVGIDASHSSFFLY
QYV-ANNGVHTSKVYPYQAKQYK-CRATDKPGPKVKITGYKRVPSNCETSFLGALANQ-PLSVLVEAGGKPFQLY

QSGIYYEPDCSSEDLDHGVLVVGYGFEGGKKYWIVKNSWGEKWGDKGYIYMAKDRKNH---CGIATAASYPLV--
KTGVYYDPSCT-QNVNHGVLVVGYGNLDGKDYWLVKNSWGLHFGDQGYIRMARNSGNH---CGIANYPSYPEI--
KSGV-FDGPCG-TKLDHAVTAVGYGTSDGKNYIIIKNSWGPNWGEKGYMRLKRQSGNSQGTCGVYKSSYYPFKGF

-
-
A

End gaps not penalized.
Costfile:                   pam250
Alignment cost:    9454     Lower bound:    9429
Delta:               25     Max. Delta:       30

Sequences  Proj. Cost  Pair. Cost  Epsilon  Max. Epsi.  Weight  Weight*Cost
  1   2        3013        3013        0         5         1        3013
  1   3        3235        3217       18        18         1        3235
  2   3        3206        3199        7         7         1        3206
Elapsed time =   1.450