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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
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