CODEHOP Version 10/14/04.1
COPYRIGHT 1997-2004, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

Parameters:
 Amino acids PSSM calculated with odds ratios normalized to 100
 and back-translated with Standard genetic code
 and codon usage table "../../docs/arab.codon.use"
 Maximum core degeneracy 128    Core strictness 0.00
 Clamp strictness 1.00   Target clamp temperature 60.00 C
 DNA Concentration 50.00 nM   Salt Concentration 50.00 mM
 Codon boundary 0   Most common codon 0
 Verbose 0   Output 3
 Begin 1   PolyX 5
Suggested CODEHOPS: The degenerate region (core) is printed in lower case,
the non-degenerate region (clamp) is printed in upper case.

Processing Block MethylaA
L  D  V  F  S  G  C  G  G  M  S  H  G  F  H  M  A  G  I  S  E  T  V  W  A  I  E  M  W  
CTGGATGTCTTTTCnggntgyggng -3'  Core: degen=128 len=11  Clamp: score=69, len=14 temp= 35.8 *** CLAMP NEEDS EXTENSION

Processing Complement of Block MethylaA
L  D  V  F  S  G  C  G  G  M  S  H  G  F  H  M  A  G  I  S  E  T  V  W  A  I  E  M  W  
               ccnacrccncsATACAGAGTACCTAAAGTATTCCGA -5'  Core: degen=64 len=11  Clamp: score=66, len=25 temp= 60.2

Processing Block MethylaB
E  P  A  C  Q  A  F  R  H  N  H  P  E  T  T  V  F  N  E  D  C  N  D  F  L  K  L  V  M  
   CCTGCTTGTCAAGCTTTTAGACAnaaymayccng -3'  Core: degen=128 len=11  Clamp: score=69, len=23 temp= 60.9
GAACCTGCTTGTCAAGCTTTTAGAywnaaymaycc -3'  Core: degen=128 len=11  Clamp: score=67, len=24 temp= 61.2

Processing Complement of Block MethylaB
E  P  A  C  Q  A  F  R  H  N  H  P  E  T  T  V  F  N  E  D  C  N  D  F  L  K  L  V  M  
                           ttrktrggncyTTGATGTCAAAAATTACTTCTAACATTACAAAA -5'  Core: degen=64 len=11  Clamp: score=67, len=33 temp= 60.5

Processing Block MethylaC
L  P  Q  P  G  D  V  Y  M  L  C  G  G  P  P  C  Q  G  F  S  G  M  N  R  F  N  
                          GGTTTGTGGAGGACCTCCTtgycarggnwt -3'  Core: degen=32 len=11  Clamp: score=77, len=19 temp= 63.1
                         TGGTTTGTGGAGGACCTccntgycargg -3'  Core: degen=16 len=11  Clamp: score=76, len=17 temp= 60.9
                   TTGATATGGTTTGTGGAGGAccnccntgyca -3'  Core: degen=32 len=11  Clamp: score=74, len=20 temp= 61.0

Processing Complement of Block MethylaC
L  P  Q  P  G  D  V  Y  M  L  C  G  G  P  P  C  Q  G  F  S  G  M  N  R  F  N  
                                       ggnggnacrgtTCCTAAAAGACCTTACTTATCTAA -5'  Core: degen=32 len=11  Clamp: score=74, len=24 temp= 60.1
                                          ggnacrgtyccTAAAAGACCTTACTTATCTAAATTA -5'  Core: degen=16 len=11  Clamp: score=71, len=25 temp= 58.5 *** CLAMP NEEDS EXTENSION
                                             acrgtyccnwaAAGACCTTACTTATCTAAATTA -5'  Core: degen=32 len=11  Clamp: score=72, len=22 temp= 52.0 *** CLAMP NEEDS EXTENSION

Processing Block MethylaD
C  F  V  R  M  G  Y  Q  C  R  F  G  M  M  Q  A  G  Q  Y  G  V  P  Q  T  R  R  R  A  F  I  W  A  A  A  P  G  E  K  L  P  M  Y  P  E  P  M  H  V  
TGTTTTGTTGGAatgrrntayca -3'  Core: degen=32 len=11  Clamp: score=60, len=12 temp= 42.3 *** CLAMP NEEDS EXTENSION
TGTTTTGTTGGnatgrrntayc -3'  Core: degen=128 len=11  Clamp: score=63, len=11 temp= 25.6 *** CLAMP NEEDS EXTENSION

Processing Complement of Block MethylaD
C  F  V  R  M  G  Y  Q  C  R  F  G  M  M  Q  A  G  Q  Y  G  V  P  Q  T  R  R  R  A  F  I  W  A  A  A  P  G  E  K  L  P  M  Y  P  E  P  M  H  V  
            tacyynatrgtTACATCTAAACCTTACTACGTT -5'  Core: degen=32 len=11  Clamp: score=71, len=22 temp= 61.1

Processing Block MethylaE
F  R  T  I  T  V  R  D  T  M  S  D  L  P  P  V  T  N  G  A  S  N  D  E  I  S  Y  N  
No suggested primers found.

Processing Complement of Block MethylaE
F  R  T  I  T  V  R  D  T  M  S  D  L  P  P  V  T  N  G  A  S  N  D  E  I  S  Y  N  
No suggested primers found.

Processing Block MethylaF
D  H  H  C  K  D  M  S  D  D  D  L  C  R  M  S  H  I  P  K  F  P  G  S  D  W  R  D  M  P  N  I  Q  V  H  N  N  D  G  T  I  N  R  K  L  R  Y  C  H  H  D  K  K  N  
No suggested primers found.

Processing Complement of Block MethylaF
D  H  H  C  K  D  M  S  D  D  D  L  C  R  M  S  H  I  P  K  F  P  G  S  D  W  R  D  M  P  N  I  Q  V  H  N  N  D  G  T  I  N  R  K  L  R  Y  C  H  H  D  K  K  N  
No suggested primers found.

Processing Block MethylaG
M  G  H  Q  G  C  V  I  H  P  M  Q  H  R  V  V  S  V  R  E  C  A  R  S  Q  G  F  P  D  C  Y  R  F  C  G  N  I  L  D  K  H  R  Q  V  G  N  A  V  P  P  P  L  A  K  A  I  G  
                                                                                                               AAGGATAAGCATAGACAAGTTGGAaaygcngtnsc -3'  Core: degen=64 len=11  Clamp: score=73, len=24 temp= 60.7
                                                                                                        AAATATTAAGGATAAGCATAGACAAGTTggnaaygcngt -3'  Core: degen=32 len=11  Clamp: score=71, len=28 temp= 60.6
                                                                                                    GTGGAAATATTAAGGATAAGCATAGACAArtnggnaaygc -3'  Core: degen=64 len=11  Clamp: score=72, len=29 temp= 60.3
                                                                                                   TGTGGAAATATTAAGGATAAGCATAGAcarrtnggnaa -3'  Core: degen=64 len=11  Clamp: score=69, len=27 temp= 61.4
                                                  TGTTAGAGAATGTGCTAGATCTCAAggnttyccnga -3'  Core: degen=32 len=11  Clamp: score=72, len=25 temp= 61.4
                                              TTTCTGTTAGAGAATGTGCTAGATCTCArggnttyccng -3'  Core: degen=64 len=11  Clamp: score=73, len=28 temp= 61.1
                                              TTTCTGTTAGAGAATGTGCTAGATCTcarggnttycc -3'  Core: degen=16 len=11  Clamp: score=69, len=26 temp= 61.1
                                           TTGTTTCTGTTAGAGAATGTGCTAGATCncarggnttyc -3'  Core: degen=64 len=11  Clamp: score=71, len=28 temp= 60.5
                               TGCAACATAGAGTTGTTTCTGTTAGAgarwrygcnmg -3'  Core: degen=128 len=11  Clamp: score=70, len=26 temp= 61.8
                           CCTATGCAACATAGAGTTGTTTCTGTTmgngarwrygc -3'  Core: degen=128 len=11  Clamp: score=71, len=27 temp= 61.1
   GGTCATCAAGGATGTGTTTTTcayccnrwrca -3'  Core: degen=64 len=11  Clamp: score=56, len=21 temp= 61.1

Processing Complement of Block MethylaG
M  G  H  Q  G  C  V  I  H  P  M  Q  H  R  V  V  S  V  R  E  C  A  R  S  Q  G  F  P  D  C  Y  R  F  C  G  N  I  L  D  K  H  R  Q  V  G  N  A  V  P  P  P  L  A  K  A  I  G  
                        gtrggnywygtTGTATCTCAACAAAGACAATCTCTTAC -5'  Core: degen=64 len=11  Clamp: score=71, len=27 temp= 60.1
                                                         ctywyrcgnkcTAGAGTTCCTAAAGGACTAACAATA -5'  Core: degen=128 len=11  Clamp: score=74, len=25 temp= 60.1
                                                                        gtyccnaarggACTAACAATATCTAAAACACCTTTATA -5'  Core: degen=16 len=11  Clamp: score=72, len=27 temp= 60.1
                                                                         tyccnaarggncTAACAATATCTAAAACACCTTTATAATTCC -5'  Core: degen=64 len=12  Clamp: score=72, len=30 temp= 60.1
                                                                           ccnaarggnctAACAATATCTAAAACACCTTTATAATTCC -5'  Core: degen=32 len=11  Clamp: score=70, len=29 temp= 60.1
                                                                              aarggnctrwsAATATCTAAAACACCTTTATAATTCCTATTCG -5'  Core: degen=64 len=11  Clamp: score=70, len=32 temp= 60.7
                                                                                                                              gtyyanccnttACGACAAGGAGGAGGACAC -5'  Core: degen=64 len=11  Clamp: score=74, len=19 temp= 61.6
                                                                                                                                    ccnttrcgncaAGGAGGAGGACACCGATAAC -5'  Core: degen=32 len=11  Clamp: score=66, len=20 temp= 62.2
                                                                                                                                       ttrcgncansgAGGAGGACACCGATAACGATAA -5'  Core: degen=64 len=11  Clamp: score=64, len=22 temp= 61.0
