Sample Output from University of Minnesota's Sequence Analysis Project

(A collaboration between the University of Minnesota and Michigan State University, funded by NSF)
This page shows only a small portion of the output available from the University of Minnesota's database. For further information regarding this work, go to the University of Minnesota's Computational Biology Centers' Home Page OR Back to the Sample TC Report
Sequence Analysis for 40F11T7

Sequence Analysis for 40F11T7

Sequence Origin: Michigan State University Arabidopsis cDNA Sequencing Project

Analysis Origin: University of Minnesota Plant Molecular Informatics Center

dbEST ID for this sequence: 21241

GenBank Accession Number for this sequence: T04426

Table of Contents

Processed Sequence after Filtering and/or Trimming for Quality

Visualization of BLAST Hits

Percentage of Unknown (N) bases in Sequence

Low Complexity Regions

Blastx Results Summary

Blastx Hits Ordered by P-value

Plus Strand Processed

DNA Sequence after Vector Filtering and End Trimming for Quality

(Each Full Line is 40 bp Long) 

CTCCATTTCTCTATCTTTCTCTCTCGCTGCTTCTCGAATC
TNCTGTATCATCTTCTTCTTCTTCAAGTGAAAAATGGCCG
ATGGTGAGGATATTCAGCCACTTGTCTGTGACAATGGAAC
TGGAATGGTGAAGGCTGGTTTTGCTGGTGATGATGCCCCG
AGAGCAGTGTTCCCAAGTATTGTTGGTCGTCCTAGGCACA
CTGGTGTCATGGTTGGTATGGGTCAGAAAGATGCTTACGT
TGGTGATGAAGCTCAGTCCAAGAGAGGTATCCTCACTCTG
AAGTATCCAATCGAACATGGTATTGTAAGTAACNTGGGAT
GACATGGAAAAGATATGGCATCACACTTTCTACAACGAGC
TTCGTGTTGCCCCTGAGGGAGCACCCAAGTTCTACTCACA

Sequence Length: 400

Percentage of Unknown (N) bases in Sequence

 400 original bp (0.5% unknown bases), reduced to 400 bp (0.5% unknown bases).

Visualization of Blastx Hits from AlignmentViewer Tool

Visualization of Blastp Hits (where Low Complexity Regions have been removed) from AlignmentViewer Tool

Hits in a frame will be displayed if and only if there were low complexity regions within the BLASTX hits for any given frame. Otherwise nothing will be displayed. Lack of hits may be because the low complexity regions were only found in the incorrect frames. In the future the visualization will be improved to eliminate this and improve clarity.

Low Complexity Regions from XNU program

Low complexity regions found for translated frame +1 :

None

Low complexity regions found for translated frame +2 :

Translated Protein: start = 16, end = 22

Corresponding DNA : start = 47, end = 67

Low complexity regions found for translated frame +3 :

Translated Protein: start = 45, end = 75

Corresponding DNA : start = 135, end = 227

Translated Protein: start = 2, end = 23

Corresponding DNA : start = 6, end = 71

The function of this Sequence can possibly be determined by the following BLASTX, BLASTN, AND/OR BLASTP hits.

Summary of Blastx Hits on Plus Strand with P-value <= 1.000e-01

BLAST DB SEARCHED: Non-redundant PIR (RELEASE 44.00) plus GenPept, from GenBank (RELEASE 89.0)

DATE SEARCHED: Mon Jul 10 09:11:08 CDT 1995

Click on the "goto" in the first column to see more details: e.g. alignment and longer description of hit sequence from databank.

                          High  
More DB  Acc    Fr Shift? Score P-value  Description
---- --  ---    -- ------ ----- -------  -----------
goto pir S31933    2     Y      380   1.2e-35   actin - common tobaccoPEP:pir|S35257|S35257 acti... 
goto pir JA0066    2     Y      379   1.5e-35   actin - Arabidopsis thaliana PEP:gi|166582|gp|M2 ... 
goto pir S20098    2     Y      378   2.0e-35   actin - potato PEP:gi|21544|gp|X55751|STPOAC97_1 ... 
goto pir S20094    2     Y      377   2.7e-35   actin - potato PEP:gi|21536|gp|X55749|STPOAC58_1 ... 
goto pir S10020    2     Y      376   3.5e-35   actin 1 - rice                                    
goto pir S47090    2     Y      376   3.5e-35   actin - sorghum PEP:gi|499012|gp|X79378|SVSOAC1_1... 
goto  gi  20322    2     Y      376   3.5e-35   Oryza sativa RAc1 mRNA for actin. [Oryza sativa]  
goto  gi 295885    2     Y      376   3.5e-35   actin [Oryza sativa]                              
goto pir S07002    2     Y      376   3.8e-35   actin 1 - carrot                                  
goto pir S20093    2     Y      374   6.1e-35   actin - potato PEP:gi|21534|gp|X55752|STPOAC101_1...

BLASTX Hits by P-value

Hit Accession Number S31933 of PIR database
Hit Sequence Description :
actin - common tobaccoPEP_:pir|S35257|S35257 actin - common tobaccoPEP_:gi|22609|gp|X63603|NTACTI_1 actin [Nicotiana tabacum]

Length of Hit Sequence = 377

P-value = 1.200000e-35

HSP Alignments:

  Score: 380  Frame = 2   Identities = 100%   Positives = 100%

     74 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 253

        MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA

      1 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 60


    254 QSKRGILTLKYPIEHGIVSN 313

        QSKRGILTLKYPIEHGIVSN

      1 QSKRGILTLKYPIEHGIVSN 80


  Score: 135  Frame = 3   Identities = 91%   Positives = 91%

    315 WDDMEKIWHHTFYNELRVAPEGAP 386

        WDDMEKIWHHTFYNELRVAPE  P

      1 WDDMEKIWHHTFYNELRVAPEEHP 104
Note: A potential frame shift has occurred amongst these alignments. 

____________________________
Hit Accession Number JA0066 of PIR database
Hit Sequence Description :
actin - Arabidopsis thalianaPEP_:gi|166582|gp|M20016|ATHACT1A_1 A.thaliana AAc1 gene encoding actin-1, complete cds. [Arabidopsis thaliana]

Length of Hit Sequence = 377

P-value = 1.500000e-35

HSP Alignments:

  Score: 379  Frame = 2   Identities = 98%   Positives = 100%

     74 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 253

        MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA

      1 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 60


    254 QSKRGILTLKYPIEHGIVSN 313

        QSKRGILTLKYPIEHGIV+N

      1 QSKRGILTLKYPIEHGIVNN 80


  Score: 135  Frame = 3   Identities = 91%   Positives = 91%

    315 WDDMEKIWHHTFYNELRVAPEGAP 386

        WDDMEKIWHHTFYNELRVAPE  P

      1 WDDMEKIWHHTFYNELRVAPEEHP 104
Note: A potential frame shift has occurred amongst these alignments. 

____________________________
Hit Accession Number S20098 of PIR database
Hit Sequence Description :
actin - potatoPEP_:gi|21544|gp|X55751|STPOAC97_1 actin [Solanum tuberosum]

Length of Hit Sequence = 377

P-value = 2.000000e-35

HSP Alignments:

  Score: 378  Frame = 2   Identities = 98%   Positives = 100%

     74 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 253

        MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRH+GVMVGMGQKDAYVGDEA

      1 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHSGVMVGMGQKDAYVGDEA 60


    254 QSKRGILTLKYPIEHGIVSN 313

        QSKRGILTLKYPIEHGIVSN

      1 QSKRGILTLKYPIEHGIVSN 80


  Score: 135  Frame = 3   Identities = 91%   Positives = 91%

    315 WDDMEKIWHHTFYNELRVAPEGAP 386

        WDDMEKIWHHTFYNELRVAPE  P

      1 WDDMEKIWHHTFYNELRVAPEEHP 104
Note: A potential frame shift has occurred amongst these alignments. 

____________________________
Hit Accession Number S20094 of PIR database
Hit Sequence Description :
actin - potatoPEP_:gi|21536|gp|X55749|STPOAC58_1 actin [Solanum tuberosum]

Length of Hit Sequence = 377

P-value = 2.700000e-35

HSP Alignments:

  Score: 377  Frame = 2   Identities = 97%   Positives = 98%

     74 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 253

        MA+GEDIQPLVCDNGTGMVKAGFAGDDAPRAVFP IVGRPRHTGVMVGMGQKDAYVGDEA

      1 MAEGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPRIVGRPRHTGVMVGMGQKDAYVGDEA 60


    254 QSKRGILTLKYPIEHGIVSN 313

        QSKRGILTLKYPIEHGIVSN

      1 QSKRGILTLKYPIEHGIVSN 80


  Score: 135  Frame = 3   Identities = 91%   Positives = 91%

    315 WDDMEKIWHHTFYNELRVAPEGAP 386

        WDDMEKIWHHTFYNELRVAPE  P

      1 WDDMEKIWHHTFYNELRVAPEEHP 104
Note: A potential frame shift has occurred amongst these alignments. 

____________________________
Hit Accession Number S10020 of PIR database
Hit Sequence Description :
actin 1 - rice

Length of Hit Sequence = 377

P-value = 3.500000e-35

HSP Alignments:

  Score: 376  Frame = 2   Identities = 98%   Positives = 100%

     74 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 253

        MAD+EDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA

      1 MADAEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 60


    254 QSKRGILTLKYPIEHGIVSN 313

        QSKRGILTLKYPIEHGIVSN

      1 QSKRGILTLKYPIEHGIVSN 80


  Score: 135  Frame = 3   Identities = 91%   Positives = 91%

    315 WDDMEKIWHHTFYNELRVAPEGAP 386

        WDDMEKIWHHTFYNELRVAPE  P

      1 WDDMEKIWHHTFYNELRVAPEEHP 104
Note: A potential frame shift has occurred amongst these alignments. 

____________________________
Hit Accession Number S47090 of PIR database
Hit Sequence Description :
actin - sorghumPEP_:gi|499012|gp|X79378|SVSOAC1_1 actin [Sorghum bicolor]

Length of Hit Sequence = 377

P-value = 3.500000e-35

HSP Alignments:

  Score: 376  Frame = 2   Identities = 98%   Positives = 100%

     74 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 253

        MAD+EDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA

      1 MADAEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 60


    254 QSKRGILTLKYPIEHGIVSN 313

        QSKRGILTLKYPIEHGIVSN

      1 QSKRGILTLKYPIEHGIVSN 80


  Score: 135  Frame = 3   Identities = 91%   Positives = 91%

    315 WDDMEKIWHHTFYNELRVAPEGAP 386

        WDDMEKIWHHTFYNELRVAPE  P

      1 WDDMEKIWHHTFYNELRVAPEEHP 104
Note: A potential frame shift has occurred amongst these alignments. 

____________________________
Hit Accession Number 20322 of GenInfo database
Hit Sequence Description :
Oryza sativa RAc1 mRNA for actin. [Oryza sativa]

Length of Hit Sequence = 377

P-value = 3.500000e-35

HSP Alignments:

  Score: 376  Frame = 2   Identities = 98%   Positives = 100%

     74 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 253

        MAD+EDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA

      1 MADAEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 60


    254 QSKRGILTLKYPIEHGIVSN 313

        QSKRGILTLKYPIEHGIVSN

      1 QSKRGILTLKYPIEHGIVSN 80


  Score: 135  Frame = 3   Identities = 91%   Positives = 91%

    315 WDDMEKIWHHTFYNELRVAPEGAP 386

        WDDMEKIWHHTFYNELRVAPE  P

      1 WDDMEKIWHHTFYNELRVAPEEHP 104
Note: A potential frame shift has occurred amongst these alignments. 

____________________________
Hit Accession Number 295885 of GenInfo database
Hit Sequence Description :
actin [Oryza sativa]

Length of Hit Sequence = 377

P-value = 3.500000e-35

HSP Alignments:

  Score: 376  Frame = 2   Identities = 98%   Positives = 100%

     74 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 253

        MAD+EDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA

      1 MADAEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 60


    254 QSKRGILTLKYPIEHGIVSN 313

        QSKRGILTLKYPIEHGIVSN

      1 QSKRGILTLKYPIEHGIVSN 80


  Score: 135  Frame = 3   Identities = 91%   Positives = 91%

    315 WDDMEKIWHHTFYNELRVAPEGAP 386

        WDDMEKIWHHTFYNELRVAPE  P

      1 WDDMEKIWHHTFYNELRVAPEEHP 104
Note: A potential frame shift has occurred amongst these alignments. 

____________________________
Hit Accession Number S07002 of PIR database
Hit Sequence Description :
actin 1 - carrot

Length of Hit Sequence = 380

P-value = 3.800000e-35

HSP Alignments:

  Score: 376  Frame = 2   Identities = 98%   Positives = 100%

     74 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 253

        MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA

      1 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 60


    254 QSKRGILTLKYPIEHGIVSN 313

        QSKRGI+TLKYPIEHGIVSN

      1 QSKRGIITLKYPIEHGIVSN 80


  Score: 93  Frame = 3   Identities = 73%   Positives = 84%

    330 KIWHHTFYNELRVAPEGAP 386

        +IWHHTFYNELR +PE  P

      1 RIWHHTFYNELRASPEEHP 103
Note: A potential frame shift has occurred amongst these alignments. 

____________________________
Hit Accession Number S20093 of PIR database
Hit Sequence Description :
actin - potatoPEP_:gi|21534|gp|X55752|STPOAC101_1 actin [Solanum tuberosum]

Length of Hit Sequence = 377

P-value = 6.100000e-35

HSP Alignments:

  Score: 374  Frame = 2   Identities = 97%   Positives = 100%

     74 MADGEDIQPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 253

        MAD+EDI+PLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA

      1 MADAEDIEPLVCDNGTGMVKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDAYVGDEA 60


    254 QSKRGILTLKYPIEHGIVSN 313

        QSKRGILTLKYPIEHGIVSN

      1 QSKRGILTLKYPIEHGIVSN 80


  Score: 133  Frame = 3   Identities = 83%   Positives = 91%

    315 WDDMEKIWHHTFYNELRVAPEGAP 386

        WDDMEKIWHHTFYNELRV+P+  P

      1 WDDMEKIWHHTFYNELRVSPDEHP 104
Note: A potential frame shift has occurred amongst these alignments.

Citations and Credits

 The script for creating this results file is the work of Libby Shoop.

The BLAST programs whose results are listed here are documented in:

Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol. 215:403-410.

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