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[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
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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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