The "one base extra" problem I metioned is in this page:

	exon26.html

I cut/paste a part of the page here:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                |                                                    |
                   R  A  A  K  E  A  N  I  H  A  F  I  E  S  L  P  N  K
 P  W  M  R  *  *  L  A  A  K  A  A  N  I  H  S  F  I  E  G  L  P  Q  V  A 
  H  G  *  D  S  S  L  L  L  K  Q  P  T  S  T  A  S  S  K  G  C  L  R  *  R
CCATGGATGAGATAGTAGCTTGCTGCTAAAGCAGCCAACATCCACAGCTTCATCGAAGGGCTGCCTCAGGTAGCGG
     22970     22980     22990     23000     23010     23020     23030
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
The 2 vertical bars "|" at the top indicated the exon which was not found
by the GeneFinder program. I picked it up manually based on the clustalw
alignment. The 1st line under the bar "RAAKEANIHAFIESLPNK" is the AA
fragment from MDR1_HUMAN. All other MDRs have this conserved fragment. 

You may see this in the page: 

	align-aa4.html

I cut/paste a part of this page:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                     |                |
MDR1_FUGU_  SRSVSMDEIVAAAKAANIHSFIEGLPQRYDTQAGDKGTQLSGGQKQRVAIARAIIRNPKL
MSR3_FUGU_  SRSVSMDEI------------------RYDTQAGDKGTQLSGGQKQRVAIARAIIRNPKL
MDR1_HUMAN  SRVVSQEEIVRAAKEANIHAFIESLPNKYSTKVGDKGTQLSGGQKQRIAIARALVRQPHI
MDR1_LEIEN  G--ATDEEVEEAARLAHIHHEIIKWTDGYDTEVGYKGRALSGGQKQRIAIARGLLRRPRL
MDR1_MOUSE  SRAVSHEEIVRAAKEANIHQFIDSLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHI
MDR1_RAT_   SRVVSHEEIVRAAREANIHQFIDSLPEKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHI
MDR1_CRIGR  SRVVSQDEIERAAKEANIHQFIESLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHI
MDR1_CAEEL  PSSVTMAQVEEAARLANIHNFIAELPEGFETRVGDRGTQLSGGQKQRIAIARALVRNPKI
MDR3_HUMAN  SRVVSQDEIVSAAKAANIHPFIETLPHKYETRVGDKGTQLSGGQKQRIAIARALIRQPQI
MDR3_MOUSE  SRVVSYEEIVRAAKEANIHQFIDSLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHI
MDR3_CRIGR  SRVVSQDEIVRAAKAANIHPFIETLPQKYKTRVGDKGTQLSGGQKQRLAIRRALIRQPRV
MDR3_CAEEL  N--ITQDQVEKAATLANIHTFVMGLPDGYDTSVGASGGRLSGGQKQRVAIARAIVRDPKI
                .  ..                   . *  *  *  ********.** * ..* *..
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 

You can see clearly that a fragment of 18 AAs was missed there. 

I picked the DNA segment 22951-23040 out and removed the extra base G at 
the position 22982 (low case). 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
 TCGCTCCGTGTCCATGGATGAGATAGTAgCTTGCTGCTAAAGCAGCCAACATCCACAGCTTCATCGAAGGGCTGCCTCAGGTAGCGGCTGT
                          ^^^^
                             |
                           22982

   R  S  V  S  M  D  E  I  V  L  A  A  K  A  A  N  I  H  S  F  I  E  G  L  P  Q  V  A  A  V
 TCGCTCCGTGTCCATGGATGAGATAGTACTTGCTGCTAAAGCAGCCAACATCCACAGCTTCATCGAAGGGCTGCCTCAGGTAGCGGCTGT
                          ^^^
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 

Then did a translation. The original 1st reading frame now continues with 
the 2nd reading frame and the missed AA fragment was picked out. 

Put the AA fragment at the top of the aligmnet, you can see how nice it 
aligns with all the MDR1 and MDR3 as well as the other gene of FUGU 
(MDR1_FUGU) in the contig: 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                     |                |
             RSVSMDEIVLAAKAANIHSFIEGLPQVAAV
MDR1_FUGU_  SRSVSMDEIVAAAKAANIHSFIEGLPQRYDTQAGDKGTQLSGGQKQRVAIARAIIRNPKL
MSR3_FUGU_  SRSVSMDEI------------------RYDTQAGDKGTQLSGGQKQRVAIARAIIRNPKL
MDR1_HUMAN  SRVVSQEEIVRAAKEANIHAFIESLPNKYSTKVGDKGTQLSGGQKQRIAIARALVRQPHI
MDR1_LEIEN  G--ATDEEVEEAARLAHIHHEIIKWTDGYDTEVGYKGRALSGGQKQRIAIARGLLRRPRL
MDR1_MOUSE  SRAVSHEEIVRAAKEANIHQFIDSLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHI
MDR1_RAT_   SRVVSHEEIVRAAREANIHQFIDSLPEKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHI
MDR1_CRIGR  SRVVSQDEIERAAKEANIHQFIESLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHI
MDR1_CAEEL  PSSVTMAQVEEAARLANIHNFIAELPEGFETRVGDRGTQLSGGQKQRIAIARALVRNPKI
MDR3_HUMAN  SRVVSQDEIVSAAKAANIHPFIETLPHKYETRVGDKGTQLSGGQKQRIAIARALIRQPQI
MDR3_MOUSE  SRVVSYEEIVRAAKEANIHQFIDSLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHI
MDR3_CRIGR  SRVVSQDEIVRAAKAANIHPFIETLPQKYKTRVGDKGTQLSGGQKQRLAIRRALIRQPRV
MDR3_CAEEL  N--ITQDQVEKAATLANIHTFVMGLPDGYDTSVGASGGRLSGGQKQRVAIARAIVRDPKI
                .  ..                   . *  *  *  ********.** * ..* *..
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
                            
Pls check the notes and the above results carefully if I made any 
mistake.