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Masked Sequence

GGGGAAATGGGTCGAATCAAGCTTAAATGATCAGTATTATATGTTAACCATAGAGT
AAAAAAATTCAACATACGAACACAAACATATACATTGAATACAGGCTATAATCTAC
AGTATCATTTTATCAAAATAACAGTATTGATAAGATAGNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAATATAACATGGATTGCACAGTTG
TATTCCAGTACTTCAATCATTCATCAATTCATTCATGTAATTCATTGGTCCCTCCT
AGCTTTCAACAAATTWWAAAACAAAGGGGRAAAAAATTTTGKCVASATGA
Dataset = ArabidopsisN
Size of dataset = 220172187 (DNA)
Length of query = 330 (DNA)

BLAST query on Arabidopsis sequences

Query performed by the The Arabidopsis Information Resource (TAIR) for full BLAST options and parameters, refer to the NCBI BLAST Documentation

Your comments and suggestions are requested: Send a Message to TAIR

Summary of BLAST to Arabidopsis GenBank DNA sequences using a minimum match cutoff of 75%. When many high scoring pairs (HSP) are found only a subset of the best HSPs are presented in the graphic.

The full results of this search are below.






BLASTN 2.0.8 [Jan-05-1999]
BLASTN 5.1.0.14 (beta) [Oct-04-1999]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
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.

Query= user-submitted sequence
         (330 letters)

Database: ArabidopsisN
           119,079 sequences; 220,172,187 total letters



[SCORES]
                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

GSDB:S:3263998|AB020742|AB020742|Arabidopsis thaliana genomic D...    41  0.038
GSDB:S:6351233|AL163812|ATF14F18|Arabidopsis thaliana DNA chrom...    39  0.15
GSDB:S:6182121|AL161550|ATCHRIV50|Arabidopsis thaliana DNA chro...    39  0.15
GSDB:S:2220705|AL021687|ATT18B16|Arabidopsis thaliana DNA chrom...    39  0.15
GSDB:S:2098574|AB007727|AB007727|Arabidopsis thaliana genomic D...    39  0.15
GSDB:S:6182118|AL161548|ATCHRIV48|Arabidopsis thaliana DNA chro...    37  0.62
GSDB:S:2220685|AL021710|ATF28J12|Arabidopsis thaliana DNA chrom...    37  0.62
GSDB:S:2466944|AL023094|ATT4L20|Arabidopsis thaliana DNA chromo...    37  0.62
GSDB:S:3274706|AC006218|AC006218|Arabidopsis thaliana chromosom...    35  2.5
GSDB:S:1755108|B22142|B22142|T3I24-T7 TAMU Arabidopsis thaliana...    35  2.5
GSDB:S:3858872|AB025617|AB025617|Arabidopsis thaliana genomic D...    35  2.5
GSDB:S:2782287|AB016884|AB016884|Arabidopsis thaliana genomic D...    35  2.5
GSDB:S:5777249|AQ967875|AQ967875|LERIV40TF LERG Arabidopsis tha...    35  2.5
GSDB:S:4606271|AB019944|AB019944|Arabidopsis thaliana gene for ...    35  2.5
GSDB:S:5776161|AQ966688|AQ966688|LERIL57TR LERG Arabidopsis tha...    35  2.5
GSDB:S:4049091|AL049915|T16I18|Arabidopsis thaliana DNA *** SEQ...    35  2.5
GSDB:S:3725216|AL049500|ATT5C23|Arabidopsis thaliana DNA chromo...    35  2.5
GSDB:S:5776160|AQ966687|AQ966687|LERIL57TFB LERG Arabidopsis th...    35  2.5
GSDB:S:6182151|AL161582|ATCHRIV78|Arabidopsis thaliana DNA chro...    35  2.5
GSDB:S:5470283|AL132960|ATF5K20|Arabidopsis thaliana DNA chromo...    35  2.5
GSDB:S:1397967|B10401|B10401|F12F22-T7 IGF Arabidopsis thaliana...    35  2.5

[ALIGNMENTS]
________________________________________________________________________________

RANK  1  ITERATION 0

GSDB:S:3263998|AB020742|AB020742|Arabidopsis thaliana genomic DNA,
              chromosome 5, TAC clone: K21H1.
              Length = 74342
              
 Score = 40.7 bits (20), Expect = 0.038
 Identities = 23/24 (95%)
 Strand = Plus / Plus

                                      
Query: 127    aaaataacagtattgataagatag 150
              ||||||| ||||||||||||||||
Sbjct: 28224  aaaataagagtattgataagatag 28247


________________________________________________________________________________

RANK  2  ITERATION 0

GSDB:S:6351233|AL163812|ATF14F18|Arabidopsis thaliana DNA chromosome 5,
              BAC clone F14F18 (ESSA project)
              Length = 103638
              
 Score = 38.7 bits (19), Expect = 0.15
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                                 
Query: 115    tatcattttatcaaaataa 133
              |||||||||||||||||||
Sbjct: 87908  tatcattttatcaaaataa 87926


________________________________________________________________________________

RANK  3  ITERATION 0

GSDB:S:6182121|AL161550|ATCHRIV50|Arabidopsis thaliana DNA chromosome 4,
              contig fragment No. 50
              Length = 199382
              
 Score = 38.7 bits (19), Expect = 0.15
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                                 
Query: 114    gtatcattttatcaaaata 132
              |||||||||||||||||||
Sbjct: 75752  gtatcattttatcaaaata 75770


________________________________________________________________________________

RANK  4  ITERATION 0

GSDB:S:2220705|AL021687|ATT18B16|Arabidopsis thaliana DNA chromosome 4,
              BAC clone T18B16 (ESSA project)
              Length = 96574
              
 Score = 38.7 bits (19), Expect = 0.15
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                                 
Query: 114    gtatcattttatcaaaata 132
              |||||||||||||||||||
Sbjct: 59313  gtatcattttatcaaaata 59331


________________________________________________________________________________

RANK  5  ITERATION 0

GSDB:S:2098574|AB007727|AB007727|Arabidopsis thaliana genomic DNA,
             chromosome 5, P1 clone: MXC9.
             Length = 79590
             
 Score = 38.7 bits (19), Expect = 0.15
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                                
Query: 115   tatcattttatcaaaataa 133
             |||||||||||||||||||
Sbjct: 1871  tatcattttatcaaaataa 1889


________________________________________________________________________________

RANK  6  ITERATION 0

GSDB:S:6182118|AL161548|ATCHRIV48|Arabidopsis thaliana DNA chromosome 4,
               contig fragment No. 48
               Length = 194143
               
 Score = 36.7 bits (18), Expect = 0.62
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                                 
Query: 74      gaacacaaacatatacat 91
               ||||||||||||||||||
Sbjct: 122896  gaacacaaacatatacat 122879


________________________________________________________________________________

RANK  7  ITERATION 0

GSDB:S:2220685|AL021710|ATF28J12|Arabidopsis thaliana DNA chromosome 4,
              BAC clone F28J12 (ESSAII project)
              Length = 110102
              
 Score = 36.7 bits (18), Expect = 0.62
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                                
Query: 74     gaacacaaacatatacat 91
              ||||||||||||||||||
Sbjct: 14931  gaacacaaacatatacat 14914


________________________________________________________________________________

RANK  8  ITERATION 0

GSDB:S:2466944|AL023094|ATT4L20|Arabidopsis thaliana DNA chromosome 4,
              BAC clone T4L20 (ESSA project)
              Length = 125502
              
 Score = 36.7 bits (18), Expect = 0.62
 Identities = 21/22 (95%)
 Strand = Plus / Plus

                                    
Query: 80     aaacatatacattgaatacagg 101
              ||||||||||||| ||||||||
Sbjct: 99809  aaacatatacattaaatacagg 99830


________________________________________________________________________________

RANK  9  ITERATION 0

GSDB:S:3274706|AC006218|AC006218|Arabidopsis thaliana chromosome II
             section 78 of 255 of the complete sequence. Sequence from
             clones F17L24.
             Length = 73045
             
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                              
Query: 79    caaacatatacattgaa 95
             |||||||||||||||||
Sbjct: 8659  caaacatatacattgaa 8643


________________________________________________________________________________

RANK  10  ITERATION 0

GSDB:S:1755108|B22142|B22142|T3I24-T7 TAMU Arabidopsis thaliana
            genomic clone T3I24, genomic survey sequence.
            Length = 476
            
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 20/21 (95%)
 Strand = Plus / Minus

                                 
Query: 234  acttcaatcattcatcaattc 254
            |||| ||||||||||||||||
Sbjct: 248  acttgaatcattcatcaattc 228


________________________________________________________________________________

RANK  11  ITERATION 0

GSDB:S:3858872|AB025617|AB025617|Arabidopsis thaliana genomic DNA,
             chromosome 5, TAC clone: K7B16.
             Length = 26721
             
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                              
Query: 79    caaacatatacattgaa 95
             |||||||||||||||||
Sbjct: 8638  caaacatatacattgaa 8622


________________________________________________________________________________

RANK  12  ITERATION 0

GSDB:S:2782287|AB016884|AB016884|Arabidopsis thaliana genomic DNA,
              chromosome 5, TAC clone: K16H17.
              Length = 45529
              
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                               
Query: 57     aaaaaaattcaacatac 73
              |||||||||||||||||
Sbjct: 16155  aaaaaaattcaacatac 16139


________________________________________________________________________________

RANK  13  ITERATION 0

GSDB:S:5777249|AQ967875|AQ967875|LERIV40TF LERG Arabidopsis
           thaliana genomic clone LERIV40, genomic survey sequence.
           Length = 614
           
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                            
Query: 31  tcagtattatatgttaa 47
           |||||||||||||||||
Sbjct: 47  tcagtattatatgttaa 31


________________________________________________________________________________

RANK  14  ITERATION 0

GSDB:S:4606271|AB019944|AB019944|Arabidopsis thaliana gene for sigma
            factor SigC, complete cds.
            Length = 3640
            
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                             
Query: 80   aaacatatacattgaat 96
            |||||||||||||||||
Sbjct: 404  aaacatatacattgaat 420


________________________________________________________________________________

RANK  15  ITERATION 0

GSDB:S:5776161|AQ966688|AQ966688|LERIL57TR LERG Arabidopsis thaliana
            genomic clone LERIL57, genomic survey sequence.
            Length = 571
            
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                             
Query: 80   aaacatatacattgaat 96
            |||||||||||||||||
Sbjct: 424  aaacatatacattgaat 408


________________________________________________________________________________

RANK  16  ITERATION 0

GSDB:S:4049091|AL049915|T16I18|Arabidopsis thaliana DNA *** SEQUENCING
             IN PROGRESS *** BAC clone T16I18 (ESSAII project)
             Length = 52094
             
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                              
Query: 42    tgttaaccatagagtaa 58
             |||||||||||||||||
Sbjct: 7619  tgttaaccatagagtaa 7635


________________________________________________________________________________

RANK  17  ITERATION 0

GSDB:S:3725216|AL049500|ATT5C23|Arabidopsis thaliana DNA chromosome 4,
              BAC clone T5C23 (ESSA project)
              Length = 87104
              
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                               
Query: 31     tcagtattatatgttaa 47
              |||||||||||||||||
Sbjct: 35441  tcagtattatatgttaa 35457


________________________________________________________________________________

RANK  18  ITERATION 0

GSDB:S:5776160|AQ966687|AQ966687|LERIL57TFB LERG Arabidopsis thaliana
            genomic clone LERIL57, genomic survey sequence.
            Length = 605
            
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                             
Query: 80   aaacatatacattgaat 96
            |||||||||||||||||
Sbjct: 177  aaacatatacattgaat 193


________________________________________________________________________________

RANK  19  ITERATION 0

GSDB:S:6182151|AL161582|ATCHRIV78|Arabidopsis thaliana DNA chromosome 4,
              contig fragment No. 78
              Length = 198669
              
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                               
Query: 42     tgttaaccatagagtaa 58
              |||||||||||||||||
Sbjct: 46328  tgttaaccatagagtaa 46344


________________________________________________________________________________

RANK  20  ITERATION 0

GSDB:S:5470283|AL132960|ATF5K20|Arabidopsis thaliana DNA chromosome 3,
              BAC clone F5K20
              Length = 119407
              
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                               
Query: 80     aaacatatacattgaat 96
              |||||||||||||||||
Sbjct: 66589  aaacatatacattgaat 66573


________________________________________________________________________________

RANK  21  ITERATION 0

GSDB:S:1397967|B10401|B10401|F12F22-T7 IGF Arabidopsis thaliana
            genomic clone F12F22, genomic survey sequence.
            Length = 980
            
 Score = 34.7 bits (17), Expect = 2.5
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                             
Query: 29   gatcagtattatatgtt 45
            |||||||||||||||||
Sbjct: 506  gatcagtattatatgtt 490


[END ALIGNMENTS]

  Database: ArabidopsisN
    Posted date:  Apr 29, 2000  4:45 AM
  Number of letters in database: 220,172,187
  Number of sequences in database:  119,079
  
Lambda     K      H
    1.39    0.713     1.32 

Gapped
Lambda     K      H
    1.39    0.713     1.32 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 50289
Number of Sequences: 119079
Number of extensions: 50289
Number of successful extensions: 14133
Number of sequences better than 10.0: 38
length of query: 330
length of database: 220172187
effective HSP length: 18
effective length of query: 312
effective length of database: 218028765
effective search space: 68024974680
effective search space used: 68024974680
T: 0
A: 40
X1: 5 (10.1 bits)
X2: 24 (48.3 bits)
S1: 12 (24.6 bits)
S2: 17 (34.7 bits)
 
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