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【求助】引物做BLAST结果如何分析?(大家多多指导)
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这个帖子发布于10年零191天前，其中的信息可能已发生改变或有所发展。
用PRIME PRIMER 5.0设计引物，在NCBI上BLAST想看看引物特异性如何，有几个问题想向大家请教：1.我用mRNA序列设计引物,BLAST时输入下游引物序列是按照5'到3'方向输入还是按照PRIME
PRIMER 5.0软件设计后的3'到5'方向输入?我发现按照5'到3'方向输入没有我的目的基因,而按照软件设计的默认3'到5'方向输入就能有我的目的基因.2.BLAST 后有很多结果,它们的SCORE 和 E Value值是不一样的,是不是与我的目的基因的结果SCORE值越高,E值越低越好呢?3.设计了几次引物,BLAST后的结果不是只有几条,而是有几十条,如果我的目的基因的E值与其他序列E值差距大,是不是对RT-PCR的结果不会有大的影响呢?下面是我用PRIMER 5.0设计的上下游引物,请大家帮我看看BLAST后的结果能否合适做引物?初次设计引物,感觉有很多关键的问题不懂,离课题结题时间不多了,希望大家帮助,万分感谢!上游:5' CCAAAATACACAGCACCACCATGAG 3'下游:3' CCTGCCAAGTTTGACTCTCTCGC
5'(E值最低的序列是我的目的基因)
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xiguawang 用PRIME PRIMER 5.0设计引物，在NCBI上BLAST想看看引物特异性如何，有几个问题想向大家请教：1.我用mRNA序列设计引物,BLAST时输入下游引物序列是按照5'到3'方向输入还是按照PRIME
PRIMER 5.0软件设计后的3'到5'方向输入?我发现按照5'到3'方向输入没有我的目的基因,而按照软件设计的默认3'到5'方向输入就能有我的目的基因.2.BLAST 后有很多结果,它们的SCORE 和 E Value值是不一样的,是不是与我的目的基因的结果SCORE值越高,E值越低越好呢?3.设计了几次引物,BLAST后的结果不是只有几条,而是有几十条,如果我的目的基因的E值与其他序列E值差距大,是不是对RT-PCR的结果不会有大的影响呢?后面的结果只要你的模板中不含有他们就没什么问题！你的因物我认为还不错！下面是我用PRIMER 5.0设计的上下游引物,请大家帮我看看BLAST后的结果能否合适做引物?初次设计引物,感觉有很多关键的问题不懂,离课题结题时间不多了,希望大家帮助,万分感谢!上游:5' CCAAAATACACAGCACCACCATGAG 3'下游:3' CCTGCCAAGTTTGACTCTCTCGC
5'(E值最低的序列是我的目的基因)1.其实，都可以！注意中间加入15个以上的n，所用的程序是“Search for short, nearly exact matches ’‘！2.我认为你说的对！你的因物我认为还不错！请注意，引物设计的好坏，试验后才知道，理论上好不一定好，反之亦然！
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xiaoguangli79 edited on
楼主，问题解决了吗？我现在也是这样的问题，能否解答一下呢？谢谢
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广告宣传推广
政治敏感、违法虚假信息
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关于丁香园blast结果分析(引物,基因) - PCR实验 - 生物秀
标题: blast结果分析(引物,基因)
摘要: [blast结果分析(引物,基因)] 我参考外文文献的做Cx43基因PCR 引物,用pubmed的blast结果,因为是新手,也看了园子里一些帖子,还是不怎么会分析,请大家帮我看看这个引物可以用不,十分感谢!gi||ref|NM_|
Rattus norvegicus gap junction m
gi||emb|AL|
Hum 关键词:[引物 基因]……
我参考外文文献的做Cx43基因PCR 引物,用pubmed的blast结果,因为是新手,也看了里一些帖子,还是不怎么会分析,请大家帮我看看这个引物可以用不,十分感谢!gi||ref|NM_|
Rattus norvegicus gap junction m...
gi||emb|AL|
sequence from clone RP...
0.075gi||gb|BC|
Homo sapiens gap junction protein,...
gi||gb|BC|
Rattus norvegicus gap junction mem...
gi|55978|emb|X06656.1|RNCONN43
Rat heart mRNA for gap junction p
gi|4755136|ref|NM_|
Homo sapiens gap junction protein...
gi||ref|XM_|
PREDICTED: Macaca mulatta co...
gi||ref|XM_|
PREDICTED: Macaca mulatta co...
gi||gb|AY|
Cercopithecus aethiops connexin 43 ge
0.075gi||dbj|AB|
Macaca fascicularis brain c, c...
gi||emb|CR|
Homo sapiens full open reading fr...
gi||gb|AY|
Rattus norvegicus gap junction mem...
gi|6563407|gb|AF|AF151980
Homo sapiens connexin 43 (CX43
gi||dbj|AK|
Homo sapiens mRNA for connexin 43 va
gi||gb|AY|
Synthetic construct Homo sapiens c...
0.075gi||gb|AY|
Synthetic construct Homo sapiens c...
0.075gi||gb|AY|
Synthetic construct Homo sapiens c...
0.075gi|29916|emb|X52947.1|HSCGJP
Human mRNA for cardiac gap junction
gi|181208|gb|M65188.1|HUMCX43
Human connexin 43 (GJA1, Cx43) mRN
gi||gb|AY|
Oryctolagus cuniculus connexin 43 gen
0.29 gi||gb|AY|
Canis familiaris connexin 43 (Gja1) m
gi||gb|AC|
Homo sapiens chromosome 5 clone CTC-2
0.29 gi||ref|NG_|
Homo sapiens gap junction protei...
gi|6102634|gb|AC|AC011421
Homo sapiens chromosome 5 clon
gi||ref|NM_|
Canis familiaris gap junction...
gi|181210|gb|M65189.1|HUMCX43PS
Human connexin 43 processed pseu
gi||gb|AY|
Cricetulus griseus gap junction pr...
gi||gb|AY|
Mesocricetus auratus gap junction ...
gi||gb|AY|
Sus scrofa connexin 43 gene, partial
gi||gb|AY|
Spermophilus citellus connexin 43 gen
gi||gb|AY|
Phodopus sungorus connexin 43 gene, p
gi||gb|AC|
Mus musculus BAC clone RP23-280N9 ...
gi||gb|AC|
Mus musculus BAC clone RP23-149E9 ...
gi||emb|BX|
Zebrafish DNA sequence from clone...
gi||gb|AC|
Homo sapiens chromosome 8, clone RP11
gi||gb|AC|
Mus musculus BAC clone RP24-303N21...
gi||gb|AF|
Mesocricetus auratus connexin 47 mRNA
gi||dbj|AK|
Mus musculus 0 day neonate thymus...
gi||gb|AC|
Homo sapiens, clone RP11-16G11, comp
gi||ref|XM_|
PREDICTED: Danio rerio similar t...
gi||gb|AC|
Mus musculus BAC clone RP24-432B3 ...
gi||dbj|AP|
Homo sapiens genomic DNA, chromos...
gi|8072467|gb|AC|AC009567
Homo sapiens chromosome 4, clo
gi||gb|AC|
Homo sapiens chromosome 8, clone CTD-
gi||gb|BC|
Danio rerio cDNA clone IMAGE:7149102
gi||emb|AL|
Mouse DNA sequence from clone RP2...
gi||emb|AL|
Mouse DNA sequence from clone RP2...
gi||emb|CR|
Pig DNA sequence from clone PigE-...
18gi||ref|NM_|
Mus musculus gap junction membra...
gi||emb|CR|
Human DNA sequence from clone DAM...
18gi||emb|BX|
Rhesus DNA sequence from clone bRH-1
18gi||emb|CT|
Mus musculus full open reading fr...
gi||emb|CR|CNS0FDDJ
Tetraodon nigroviridis full-
18gi||ref|XM_|
PREDICTED: Apis mellifera simil...
gi||emb|AL|HS873P14
Human DNA sequence from c...
18gi||gb|BC|
Mus musculus gap junction membrane...
gi||emb|BX|
Mycobacterium tuberculosis H37Rv com
18gi||emb|BX|
Mycobacterium bovis subsp. bovis ...
18gi||emb|AL|
Mouse DNA sequence from clone RP...
18gi||ref|XR_|
PREDICTED: Rattus norvegicus si...
gi||ref|XM_|
PREDICTED: Rattus norvegicus si...
gi||gb|AE|
Mycobacterium tuberculosis CDC1551, c
18gi||gb|AC|
Mus musculus chromosome 7, clone RP2
18gi||dbj|AP|
Oryza sativa (japonica cultivar-g...
18gi||dbj|AP|
Oryza sativa (japonica cultivar-g...
18gi||gb|AC|
Mus musculus BAC clone RP23-401P15...
18gi||gb|BC|
Mus musculus gap junction membrane...
gi||gb|AC|
Mus musculus BAC clone RP23-466I14...
18gi||gb|AC|
Mus musculus BAC clone RP23-387F14...
18gi||gb|AC|
Mus musculus BAC clone RP23-110K10 fr
18gi||gb|AC|
Homo sapiens BAC clone RP11-560I19 fr
18gi||gb|BC|
Mus musculus gap junction membrane...
gi||ref|XM_|
PREDICTED: Mus musculus RIKEN...
gi||ref|XM_|
PREDICTED: Mus musculus RIKEN cD...
gi||ref|XM_|
PREDICTED: Mus musculus RIKEN cD...
gi||gb|AC|
Mus musculus chromosome 5, clone RP2
18gi||emb|BX|
Human DNA sequence from clone DAM...
18gi||gb|AC|
Mus musculus chromosome 7, clone RP2
18gi||gb|AC|
Homo sapiens chromosome 18, clone ...
18gi||gb|AC|
Mus musculus chromosome 18, clone RP2
18gi||dbj|AK|
Mus musculus adult female vagina ...
gi||gb|AC|
Homo sapiens chromosome 8, clone RP11
18gi||dbj|AK|
Mus musculus adult male testis cD...
gi||dbj|AK|
Mus musculus 0 day neonate head c...
gi||gb|AC|
Homo sapiens BAC clone RP11-362J18 fr
18gi||gb|AC|
Homo sapiens chromosome 18, clone RP1
18gi||dbj|AK|
Mus musculus blastocyst blastocys...
gi||gb|AC|
Pan troglodytes clone rp43-26k12, co
18gi||dbj|AK|
Mus musculus 16 days embryo head ...
gi||gb|AC|
Homo sapiens chromosome 8, clone RP1
18gi||gb|AC|
Mus musculus BAC clone RP23-42I13 ...
18gi||gb|AC|
Pan troglodytes BAC clone CH251-52...
18gi||dbj|AK|
Mus musculus activated spleen cDN...
gi||dbj|AK|
Mus musculus lung RCB-0558 LLC cD...
gi||gb|AC|
Macaca mulatta Major Histocompatib...
18gi||emb|CT|
Pig DNA sequence from clone CH24...
18gi||gb|AC|
Pan troglodytes BAC clone CH251-14...
18gi||gb|AC|
Pan troglodytes BAC clone CH251-35...
18gi||dbj|BA|
Homo sapiens genomic DNA, chromosome
gi|6997384|dbj|AP|
Homo sapiens genomic DNA, chromoso...
18Alignments
>gi||ref|NM_|
Rattus norvegicus gap junction membrane channel protein alpha 1 (Gja1), mRNALength=3148 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1050>gi||emb|AL|
Human DNA sequence from clone RP1-276J11 on chromosome 6 Contains the 5" end of the gene for a novel protein, a ribosomal protein S15 (RPS15) pseudogene, a putative novel gene and the GJA1 gene for gap junction protein, alpha 1, 43 kD (connexin 43) (CX43). Contains a CpG island, complete sequenceLength=131501 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
113859 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
114070>gi||gb|BC|
Homo sapiens gap junction protein, alpha 1, 43kDa (connexin 43), mRNA (cDNA clone MGC:26323 IMAGE:4794131), complete cdsLength=3000 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
942 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1153>gi||gb|BC|
Rattus norvegicus gap junction membrane channel protein alpha 1, mRNA (cDNA clone MGC:93610 IMAGE:7105924), complete cdsLength=3156 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1046>gi|55978|emb|X06656.1|RNCONN43
Rat heart mRNA for gap junction protein connexin43Length=2768 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1055>gi|4755136|ref|NM_|
Homo sapiens gap junction protein, alpha 1, 43kDa (connexin 43) (GJA1), mRNALength=3088 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1061 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1272>gi||ref|XM_|
PREDICTED: Macaca mulatta connexin 43, transcript variant 2 (GJA1), mRNALength=3171 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1125 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1336>gi||ref|XM_|
PREDICTED: Macaca mulatta connexin 43, transcript variant 1 (GJA1), mRNALength=3121 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1075 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1286>gi||gb|AY|
Cercopithecus aethiops connexin 43 gene, partial cdsLength=1146 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
854 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1065>gi||dbj|AB|
Macaca fascicularis brain cDNA, clone: QflA-10385, similar to human gap junction protein, alpha 1, 43kDa (connexin 43)(GJA1), mRNA, RefSeq: NM_Length=3071 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1028 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1239>gi||emb|CR|
Homo sapiens full open reading frame cDNA clone RZPDo834A1127D for gene GJA1, gap junction protein, alpha 1, 43kDa (connexin 43); complete cds, without stopcodonLength=1146 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
854 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1065>gi||gb|AY|
Rattus norvegicus gap junction membrane channel protein alpha1 (Gja1) mRNA, complete cdsLength=3148 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1050>gi|6563407|gb|AF|AF151980
Homo sapiens connexin 43 (CX43) gene, complete cdsLength=1149 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
854 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1065>gi||dbj|AK|
Homo sapiens mRNA for connexin 43 variant, clone: SYN08454Length=1828 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1057 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1268>gi||gb|AY|
Synthetic construct Homo sapiens clone FLHL gap junction protein alpha 1 (GJA1) mRNA, partial cdsLength=1149 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
854 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1065>gi||gb|AY|
Synthetic construct Homo sapiens clone FLHX gap junction protein alpha 1 (GJA1) mRNA, complete cdsLength=1149 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
854 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1065>gi||gb|AY|
Synthetic construct Homo sapiens clone FLHL gap junction protein alpha 1 (GJA1) mRNA, partial cdsLength=1149 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
854 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1065>gi|29916|emb|X52947.1|HSCGJP
Human mRNA for cardiac gap junction proteinLength=3038 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1011 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1222>gi|181208|gb|M65188.1|HUMCX43
Human connexin 43 (GJA1, Cx43) mRNA, complete cdsLength=1314 Score = 42.1 bits (21),
Expect = 0.075 Identities = 21/21 (100%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCCTGG
1019 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1230>gi||gb|AY|
Oryctolagus cuniculus connexin 43 gene, partial cdsLength=1146 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1065>gi||gb|AY|
Canis familiaris connexin 43 (Gja1) mRNA, complete cdsLength=1251 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1065>gi||gb|AC|
Homo sapiens chromosome 5 clone CTC-298B17, complete sequenceLength=78680 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
18565 Score = 34.2 bits (17),
18 Identities = 20/21 (95%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||| ||||||Sbjct
CTCGCCTATGTCTCTTCCTGG
18354>gi||ref|NG_|
Homo sapiens gap junction protein, alpha 1, 43kDa (connexin 43) pseudogene 1 (GJA1P1) on chromosome 5Length=3272 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1361 Score = 34.2 bits (17),
18 Identities = 20/21 (95%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||| ||||||Sbjct
CTCGCCTATGTCTCTTCCTGG
1150>gi|6102634|gb|AC|AC011421
Homo sapiens chromosome 5 clone CTD-2303O5, complete sequenceLength=148142 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
105752 Score = 34.2 bits (17),
18 Identities = 20/21 (95%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||| ||||||Sbjct
CTCGCCTATGTCTCTTCCTGG
105541>gi||ref|NM_|
Canis familiaris gap junction protein, alpha 1, 43kDa (connexin 43) (GJA1), mRNALength=1251 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1065>gi|181210|gb|M65189.1|HUMCX43PS
Human connexin 43 processed pseudogeneLength=1397 Score = 40.1 bits (20),
Expect = 0.29 Identities = 20/20 (100%), Gaps = 0/20 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAGT
||||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAGT
1313 Score = 34.2 bits (17),
18 Identities = 20/21 (95%), Gaps = 0/21 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGG
|||||||||||||| ||||||Sbjct
CTCGCCTATGTCTCTTCCTGG
1102>gi||gb|AY|
Cricetulus griseus gap junction protein connexin 43 mRNA, complete cdsLength=1477 Score = 38.2 bits (19),
Expect = 1.2 Identities = 19/19 (100%), Gaps = 0/19 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAG
|||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAG
1256 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCC
||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCC
1041>gi||gb|AY|
Mesocricetus auratus gap junction protein connexin 43 mRNA, complete cdsLength=1488 Score = 38.2 bits (19),
Expect = 1.2 Identities = 19/19 (100%), Gaps = 0/19 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAG
|||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAG
1259 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCC
||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCC
1044>gi||gb|AY|
Sus scrofa connexin 43 gene, partial cdsLength=1146 Score = 38.2 bits (19),
Expect = 1.2 Identities = 19/19 (100%), Gaps = 0/19 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAG
|||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAG
1066>gi||gb|AY|
Spermophilus citellus connexin 43 gene, partial cdsLength=1146 Score = 38.2 bits (19),
Expect = 1.2 Identities = 19/19 (100%), Gaps = 0/19 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAG
|||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAG
1066 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCC
||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCC
851>gi||gb|AY|
Phodopus sungorus connexin 43 gene, partial cdsLength=1146 Score = 38.2 bits (19),
Expect = 1.2 Identities = 19/19 (100%), Gaps = 0/19 (0%) Strand=Plus/MinusQuery
GCTGGTCCACAATGGCTAG
|||||||||||||||||||Sbjct
GCTGGTCCACAATGGCTAG
1066 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCC
||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCC
851>gi||gb|AC|
Mus musculus BAC clone RP23-280N9 from chromosome 19, complete sequenceLength=225527 Score = 38.2 bits (19),
Expect = 1.2 Identities = 25/27 (92%), Gaps = 0/27 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCCTGGCTGGTC
||||||| |||||||||||||| ||||Sbjct
CTCGCCTTTGTCTCCTCCTGGCAGGTC
47663>gi||gb|AC|
Mus musculus BAC clone RP23-149E9 from chromosome 19, complete sequenceLength=246177 Score = 38.2 bits (19),
Expect = 1.2 Identities = 25/27 (92%), Gaps = 0/27 (0%) Strand=Plus/MinusQuery
CTCGCCTATGTCTCCTCCTGGCTGGTC
||||||| |||||||||||||| ||||Sbjct
CTCGCCTTTGTCTCCTCCTGGCAGGTC
7943>gi||emb|BX|
Zebrafish DNA sequence from clone DKEYP-118B1, complete sequenceLength=47625 Score = 36.2 bits (18),
Expect = 4.6 Identities = 24/26 (92%), Gaps = 0/26 (0%) Strand=Plus/MinusQuery
ATGTCTCCTCCTGGCTGGTCCACAAT
|||||| |||| ||||||||||||||Sbjct
ATGTCTACTCCAGGCTGGTCCACAAT
38027>gi||gb|AC|
Homo sapiens chromosome 8, clone RP11-665N23, complete sequenceLength=183763 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/MinusQuery
TATGTCTCCTCCTGGCTG
||||||||||||||||||Sbjct
TATGTCTCCTCCTGGCTG
48263>gi||gb|AC|
Mus musculus BAC clone RP24-303N21 from chromosome 8, complete sequenceLength=167996 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/MinusQuery
CTATGTCTCCTCCTGGCT
||||||||||||||||||Sbjct
CTATGTCTCCTCCTGGCT
111336>gi||gb|AF|
Mesocricetus auratus connexin 47 mRNA, partial cdsLength=482 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/PlusQuery
CTCGCCTATGTCTCCTCC
||||||||||||||||||Sbjct
CTCGCCTATGTCTCCTCC
385>gi||dbj|AK|
Mus musculus 0 day neonate thymus cDNA, RIKEN full-length enriched library, clone:A product:unclassifiable, full insert sequenceLength=2783 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/PlusQuery
GTCTCCTCCTGGCTGGTC
||||||||||||||||||Sbjct
GTCTCCTCCTGGCTGGTC
513>gi||gb|AC|
Homo sapiens, clone RP11-16G11, complete sequenceLength=154768 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/PlusQuery
TATGTCTCCTCCTGGCTG
||||||||||||||||||Sbjct
TATGTCTCCTCCTGGCTG
28108>gi||ref|XM_|
PREDICTED: Danio rerio similar to ataxin 7-like 3 (LOC559983), mRNALength=797 Score = 36.2 bits (18),
Expect = 4.6 Identities = 24/26 (92%), Gaps = 0/26 (0%) Strand=Plus/MinusQuery
ATGTCTCCTCCTGGCTGGTCCACAAT
|||||| |||| ||||||||||||||Sbjct
ATGTCTACTCCAGGCTGGTCCACAAT
474>gi||gb|AC|
Mus musculus BAC clone RP24-432B3 from chromosome 9, complete sequenceLength=174264 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/PlusQuery
GTCTCCTCCTGGCTGGTC
||||||||||||||||||Sbjct
GTCTCCTCCTGGCTGGTC
22829>gi||dbj|AP|
Homo sapiens genomic DNA, chromosome 8q23, clone: KB1356F10, complete sequenceLength=159115 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/MinusQuery
TATGTCTCCTCCTGGCTG
||||||||||||||||||Sbjct
TATGTCTCCTCCTGGCTG
15783>gi|8072467|gb|AC|AC009567
Homo sapiens chromosome 4, clone RP11-21G20, complete sequenceLength=164823 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/MinusQuery
CCTATGTCTCCTCCTGGC
||||||||||||||||||Sbjct
CCTATGTCTCCTCCTGGC
30004>gi||gb|AC|
Homo sapiens chromosome 8, clone CTD-2517M22, complete sequenceLength=197294 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/MinusQuery
CCTCCTGGCTGGTCCACA
||||||||||||||||||Sbjct
CCTCCTGGCTGGTCCACA
37186>gi||gb|BC|
Danio rerio cDNA clone IMAGE:7149102Length=1934 Score = 36.2 bits (18),
Expect = 4.6 Identities = 24/26 (92%), Gaps = 0/26 (0%) Strand=Plus/MinusQuery
ATGTCTCCTCCTGGCTGGTCCACAAT
|||||| |||| ||||||||||||||Sbjct
ATGTCTACTCCAGGCTGGTCCACAAT
458>gi||emb|AL|
Mouse DNA sequence from clone RP23-468E16 on chromosome 9, complete sequenceLength=182503 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/MinusQuery
GTCTCCTCCTGGCTGGTC
||||||||||||||||||Sbjct
GTCTCCTCCTGGCTGGTC
89636>gi||emb|AL|
Mouse DNA sequence from clone RP23-76M15 on chromosome 4, complete sequenceLength=188568 Score = 36.2 bits (18),
Expect = 4.6 Identities = 18/18 (100%), Gaps = 0/18 (0%) Strand=Plus/MinusQuery
CCTGGCTGGTCCACAATG
||||||||||||||||||Sbjct
CCTGGCTGGTCCACAATG
42981>gi||emb|CR|
Pig DNA sequence from clone PigE-150I6 on chromosome 7, complete sequenceLength=122162 Score = 34.2 bits (17),
18 Identities = 17/17 (100%), Gaps = 0/17 (0%) Strand=Plus/MinusQuery
TCTCCTCCTGGCTGGTC
|||||||||||||||||Sbjct
TCTCCTCCTGGCTGGTC
79122>gi||ref|NM_|
Mus musculus gap junction membrane channel protein alpha 1 (Gja1), mRNALength=3071 Score = 34.2 bits (17),
18 Identities = 17/17 (100%), Gaps = 0/17 (0%) Strand=Plus/PlusQuery
CCTATGTCTCCTCCTGG
|||||||||||||||||Sbjct
CCTATGTCTCCTCCTGG
1039>gi||emb|CR|
Human DNA sequence from clone DAMC-81L12 on chromosome 6, complete sequenceLength=55481 Score = 34.2 bits (17),
18 Identities = 17/17 (100%), Gaps = 0/17 (0%) Strand=Plus/MinusQuery
TGTCTCCTCCTGGCTGG
|||||||||||||||||Sbjct
TGTCTCCTCCTGGCTGG
Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
Posted date:
Number of letters in database: 756,130,373
Number of sequences in database:
4,309,818Lambda
1.31 GappedLambda
1.31 Matrix: blastn matrix:1 -3Gap Penalties: Existence: 5, Extension: 2Number of Sequences: 4309818Number of Hits to DB: Number of extensions: 7664803Number of successful extensions: 10095Number of sequences better than Number of HSP"s better than 1000 without gapping: 0Number of HSP"s gapped: 10095Number of HSP"s successfully gapped: 233Length of query: 40Length of database: Length adjustment: 20Effective length of query: 20Effective length of database: Effective search space: Effective search space used: A: 0X1: 11 (21.8 bits)X2: 15 (29.7 bits)X3: 25 (49.6 bits)S1: 12 (24.3 bits)S2: 15 (30.2 bits)
为防非特异扩增,只要正,反引物没有到一个基因(非目的)上可以,或者到同一基因但可根据大小分清目的片段也可以.
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