VecScreen

BLAST

PubMed

Entrez

Nucleotide

Genome

If you need help evaluating the significance of the results, please see Interpretation of VecScreen Results.

BLASTN 2.2.12 [Aug-07-2005]

Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman 
(1997), "Gapped BLAST and PSI-BLAST: a new generation of 
protein database search programs", Nucleic Acids Res. 25:3389-3402.

RID: 1130968697-15533-63348408207.BLASTQ3

Database: UniVec 
           2113 sequences; 539,198 total letters

Query=  gnl|VecScreen|Example Database sequence with vector contamination
          (1057 letters)

Distribution of Vector Matches on the Query Sequence

1
264
528
792
1057


Match to Vector:  Strong   Moderate   Weak  
Segment of suspect origin: 

Segments matching vector:  
Strong match: 1009-1057
Moderate match: 12-33
Weak match: 34
Suspect origin: 1-11

Alignments
>gnl|uv|X52328.1:714-808 pBluescript II SK(+) vector DNA, phagemid 
            excised from lambda ZAPII
          Length=95

 Score = 84.4 bits (42),  Expect = 7e-14
 Identities = 48/49 (97%), Gaps = 1/49 (2%)
 Strand=Plus/Plus

Query  1009  GCCGCCACCGCGGTGGAGCTCCCAGCTTTTGTTCCCTTTAGTGAGGGTT  1057
             |||||||||||||||||||||| ||||||||||||||||||||||||||
Sbjct  27    GCCGCCACCGCGGTGGAGCTCC-AGCTTTTGTTCCCTTTAGTGAGGGTT  74


>gnl|uv|U02448.1:3446-3536 Cloning vector pMAMneo-LUC
          Length=91

 Score = 44.4 bits (22),  Expect = 0.075
 Identities = 22/22 (100%), Gaps = 0/22 (0%)
 Strand=Plus/Plus

Query  12  GGGcccccccTCGAGGTCGACC  33
           ||||||||||||||||||||||
Sbjct  29  GGGCCCCCCCTCGAGGTCGACC  50


>gnl|uv|U13860.1:6124-7626-49 pMSG cloning vector
          Length=1552

 Score = 32.4 bits (16),  Expect =   308
 Identities = 16/16 (100%), Gaps = 0/16 (0%)
 Strand=Plus/Minus

Query  19    cccTCGAGGTCGACCC  34
             ||||||||||||||||
Sbjct  1528  CCCTCGAGGTCGACCC  1513


  Database: 
    Posted date:  Dec 12, 2002  2:17 PM
  Number of letters in database: 539,198
  Number of sequences in database:  2,113
Lambda     K      H
    1.39    0.747     1.38 
Gapped
Lambda     K      H
    1.39    0.747     1.38 
Matrix: blastn matrix:1 -5
Gap Penalties: Existence: 3, Extension: 3
Number of Sequences: 2113
Number of Hits to DB: 4605
Number of extensions: 360
Number of successful extensions: 360
Number of sequences better than 700: 82
Number of HSP's better than 700 without gapping: 82
Number of HSP's gapped: 352
Number of HSP's successfully gapped: 88
Number of extra gapped extensions for HSPs above 700: 230
Length of query: 1057
Length of database: 539198
Length adjustment: 14
Effective length of query: 1043
Effective length of database: 509616
Effective search space: 531529488
Effective search space used: 1750000000000
A: 0
X1: 10 (20.0 bits)
X2: 15 (30.0 bits)
X3: 25 (50.0 bits)
S1: 10 (20.4 bits)
S2: 16 (32.4 bits)

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Revised: December 13, 2010.