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苯丙氨酸-PAL

银虫 (小有名气)

应助: 0 (幼儿园)
金币: 432.3
散金: 60
红花: 1
帖子: 110
在线: 42.8小时
虫号: 3877156
注册: 2015-05-18
专业: 植物病理学

[求助] 新手关于CODEHOP结果筛选有几个问题请教大家已有1人参与

费了好大劲终于出了引物结果，最后筛选把我给难住了，有几个问题想要请教虫友：
1.举个例子，在BLOCKA里，有上游引物和下游引物之分（分2段，第二段是Complement，不知道我理解的对不对），在这么短的一个氨基酸序列里，有什么意义吗？
2.acccantacctTAGATACTTATTCCCTTGACT -5'  Core: degen=4 len=11  Clamp: score=76, len=21 temp= 60.4 这算是一条完整的引物吗，为什么还分大小写，大写和小写有什么区别？后面提到长度11，我需要的是前面小写的片段吗，但是长度是不是太短。
下面放部分CODEHOP的引物结果
Complement of Block PALxxxx__A
Oligos

W  V  M  E  S  M  N  K  G  T  D  S  Y  G  V  T  T  G  F  G  A  T  S
acccantacctTAGATACTTATTCCCTTGACT -5'  Core: degen=4 len=11  Clamp: score=76, len=21 temp= 60.4
cccantacctnwGATACTTATTCCCTTGACTAAGAATACC -5'  Core: degen=32 len=12  Clamp: score=80, len=28 temp= 60.7
  ccantacctnwsATACTTATTCCCTTGACTAAGAATACC -5'  Core: degen=64 len=12  Clamp: score=81, len=27 temp= 60.0
cantacctnwsATACTTATTCCCTTGACTAAGAATACC -5'  Core: degen=64 len=11  Clamp: score=81, len=27 temp= 60.0
   tacctnwsntaCTTATTCCCTTGACTAAGAATACC -5'  Core: degen=64 len=11  Clamp: score=80, len=24 temp= 60.0
                                 atrccncantgATGACCTAAACCTCGATGAAGA -5'  Core: degen=32 len=11  Clamp: score=77, len=22 temp= 57.0 *** CLAMP NEEDS EXTENSION
                                             tgnccnaarccTCGATGAAGA -5'  Core: degen=32 len=11  Clamp: score=73, len=10 temp= 25.7 *** CLAMP NEEDS EXTENSION
                                                ccnaarccncgATGAAGA -5'  Core: degen=32 len=11  Clamp: score=69, len=7 temp= 2.2 *** CLAMP NEEDS EXTENSION
                                                   aarccncgntgAAGA -5'  Core: degen=32 len=11  Clamp: score=54, len=4 temp=-38.0 *** CLAMP NEEDS EXTENSION

Block PALxxxx__B
Oligos

H  R  R  T  K  Q  G  G  A  L  Q  K  E  L  I  R  F  L  N  A  G  I  F  G  N  G  T  E  S  C  H  T  L  P  H  S  A  T  R  A  A  M  L  V  R  I
                                                                                                CCTCATACTGCTACTAGAGCTGCTatgytngtnmg -3'  Core: degen=64 len=11  Clamp: score=74, len=24 temp= 61.2
                                                                                                GCCTCATACTGCTACTAGAGCTgcnatgytngt -3'  Core: degen=32 len=11  Clamp: score=72, len=22 temp= 61.0
                                                                                          CTCTGCCTCATACTGCTACTAGAgcngcnatgyt -3'  Core: degen=32 len=11  Clamp: score=70, len=23 temp= 60.2
                                                                  GGAAATGGAACAGAATCTTGTCATacnytnccnca -3'  Core: degen=128 len=11  Clamp: score=75, len=24 temp= 61.2
                                                                  GGAAATGGAACAGAATCTTGTcayacnytncc -3'  Core: degen=64 len=11  Clamp: score=72, len=21 temp= 60.3
                                       GATTAGATTTCTGAATGCTGGAATTttyggnaaygg -3'  Core: degen=16 len=11  Clamp: score=76, len=25 temp= 61.2
                                    TGATTAGATTTCTGAATGCTGGAathttyggnaa -3'  Core: degen=24 len=11  Clamp: score=76, len=23 temp= 60.3
                                 AACTGATTAGATTTCTGAATGCTggnathttygg -3'  Core: degen=24 len=11  Clamp: score=75, len=23 temp= 60.0
            CAAGGAGGTGCTCTGCAAaargarytnat -3'  Core: degen=32 len=11  Clamp: score=75, len=18 temp= 61.5
            GCAAGGAGGTGCTCTGcaraargaryt -3'  Core: degen=16 len=11  Clamp: score=72, len=16 temp= 61.3
GAAGAACTAAGCAAGGAGGTGCTytncaraarga -3'  Core: degen=32 len=11  Clamp: score=76, len=23 temp= 60.4

Complement of Block PALxxxx__B
Oligos

H  R  R  T  K  Q  G  G  A  L  Q  K  E  L  I  R  F  L  N  A  G  I  F  G  N  G  T  E  S  C  H  T  L  P  H  S  A  T  R  A  A  M  L  V  R  I
      tgnttnstyccTCCACGAGACGTTTTCC -5'  Core: degen=64 len=11  Clamp: score=73, len=17 temp= 60.9
         ttnstyccncsACGAGACGTTTTCCTTGACTA -5'  Core: degen=128 len=11  Clamp: score=76, len=21 temp= 60.0
                     cgnrangtyttCCTTGACTAATCTAAAGACTTACG -5'  Core: degen=64 len=11  Clamp: score=75, len=24 temp= 60.4
                        angtyttyctyrACTAATCTAAAGACTTACGACCTT -5'  Core: degen=64 len=12  Clamp: score=76, len=24 temp= 60.1
                           gtyttyctyraCTAATCTAAAGACTTACGACCTT -5'  Core: degen=16 len=11  Clamp: score=74, len=23 temp= 60.1
                           tyttyctyrantAATCTAAAGACTTACGACCTTAAAAA -5'  Core: degen=64 len=12  Clamp: score=76, len=26 temp= 60.8
                              ttyctyrantaATCTAAAGACTTACGACCTTAAAAA -5'  Core: degen=32 len=11  Clamp: score=74, len=25 temp= 60.8
                                                         ccntadaarccTTTACCTTGTCTTAGAACAGT -5'  Core: degen=24 len=11  Clamp: score=75, len=21 temp= 60.3
                                                            tadaarccnttACCTTGTCTTAGAACAGTATGAGAC -5'  Core: degen=24 len=11  Clamp: score=74, len=25 temp= 61.1
                                                               aarccnttrccTTGTCTTAGAACAGTATGAGACG -5'  Core: degen=16 len=11  Clamp: score=72, len=23 temp= 60.5
                                                                                       gtrtgnranggAGTATGACGATGATCTCGACGATAC -5'  Core: degen=64 len=11  Clamp: score=72, len=25 temp= 61.2
                                                                                          tgnranggngtATGACGATGATCTCGACGATACGAC -5'  Core: degen=128 len=11  Clamp: score=72, len=25 temp= 62.1
                                                                                                                  cgncgntacraCCAATCTTAA -5'  Core: degen=32 len=11  Clamp: score=70, len=10 temp= 18.6 *** CLAMP NEEDS EXTENSION
                                                                                                                     cgntacrancaATCTTAA -5'  Core: degen=32 len=11  Clamp: score=66, len=7 temp=-2.4 *** CLAMP NEEDS EXTENSION
                                                                                                                        tacrancankcTTAA -5'  Core: degen=64 len=11  Clamp: score=73, len=4 temp=-50.0 *** CLAMP NEEDS EXTENSION

Block PALxxxx__C
Oligos

N  T  L  L  Q  G  Y  S  G  I  R  F  E  I  L  E  A  I  T  K  L  L  N  H  N  I  T
                                    AATTCTGGAAGCTATTACTAAGTTTATTAATcayaayrtnac -3'  Core: degen=32 len=11  Clamp: score=72, len=31 temp= 60.0
                                 TGAAATTCTGGAAGCTATTACTAAGTTTATTaaycayaayrt -3'  Core: degen=16 len=11  Clamp: score=70, len=31 temp= 60.7
                              TTTGAAATTCTGGAAGCTATTACTAAGTTThtnaaycayaa -3'  Core: degen=48 len=11  Clamp: score=73, len=30 temp= 60.6
         GCAAGGATATTCTGGAATTAGATTTgarathytnga -3'  Core: degen=48 len=11  Clamp: score=75, len=25 temp= 61.9
      CTGCAAGGATATTCTGGAATTAGAttygarathyt -3'  Core: degen=24 len=11  Clamp: score=74, len=24 temp= 60.2
   TGCTGCAAGGATATTCTGGAATTmgnttygarat -3'  Core: degen=32 len=11  Clamp: score=76, len=23 temp= 62.1
   TGCTGCAAGGATATTCTGGAathmgnttyga -3'  Core: degen=48 len=11  Clamp: score=74, len=20 temp= 60.9

Complement of Block PALxxxx__C
Oligos

N  T  L  L  Q  G  Y  S  G  I  R  F  E  I  L  E  A  I  T  K  L  L  N  H  N  I  T
                        tadkcnaarctTTAAGACCTTCGATAATGATTCAAATAATTAG -5'  Core: degen=48 len=11  Clamp: score=73, len=32 temp= 60.3
                              aarctytadraCCTTCGATAATGATTCAAATAATTAGTATTATAATGA -5'  Core: degen=24 len=11  Clamp: score=73, len=37 temp= 59.8 *** CLAMP NEEDS EXTENSION
                                 ctytadranctTCGATAATGATTCAAATAATTAGTATTATAATGA -5'  Core: degen=48 len=11  Clamp: score=73, len=34 temp= 56.1 *** CLAMP NEEDS EXTENSION
                                                            anttrgtrttryAATGA -5'  Core: degen=64 len=12  Clamp: score=80, len=5 temp=-61.3 *** CLAMP NEEDS EXTENSION
                                                               ttrgtrttryaATGA -5'  Core: degen=16 len=11  Clamp: score=70, len=4 temp=-61.3 *** CLAMP NEEDS EXTENSION
                                                               trgtrttryantGA -5'  Core: degen=64 len=12  Clamp: score=78, len=2 temp=-126.6 *** CLAMP NEEDS EXTENSION
                                                                  gtrttryantgA -5'  Core: degen=32 len=11  Clamp: score=34, len=1 temp=-126.6 *** CLAMP NEEDS EXTENSION

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