NCBI BLAST Search Results

BLASTN Search Results with RepeatMasker filtering, Entrez and SRS links

BLAST search performed using the National Center for Biotechnology Information's BLAST WWW Server. Repeat reporting and filtering performed by RepeatMasker from U. Washington.
Links to Entrez and to the Sequence Retrieval System (SRS) provided by the Human Genome Sequencing Center, Baylor College of Medicine:
= Retrieve Entrez links (e.g., Medline abstracts, FASTA-formatted sequence reports).
= Retrieve Entrez links to Related sequences (neighbors).
= Retrieve SRS links (if present).


Repeat sequence:
   SW  perc perc perc  query     position in query    matching     repeat       position in  repeat
score  div. del. ins.  sequence  begin  end (left)    repeat       class/family begin  end (left)

  229  26.8  0.0  0.0  ECOPGSA     789  844  (112) +  tRNA-Lys-AAG tRNA             8   63   (13)  

Alignments:
 229 26.79 0.00 0.00  ECOPGSA      789   844 (112)    tRNA-Lys-AAG#tRNA        8    63 (13)  

  ECOPGSA            789 TAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCG 838
                                  i         i  vvi vii  vv  i      i i     
  tRNA-Lys-AAG#tR      8 TAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGTCGTGGGTTCG 57

  ECOPGSA            839 AGTCTC 844
                           i i 
  tRNA-Lys-AAG#tR     58 AGCCCC 63

Transitions / transversions = 2.00 (10 / 5)
Gap_init rate = 0.00 (0 / 56), avg. gap size = 0.00 (0 / 0)  

Masked Sequence:
>ECOPGSA
GATCTTCTGGTCGTTGAAACATTGATGTCTCTGTAGCAACATAGGGGTAA
TCTTACTGACAACAGATAGTTACCCGTCATTATGCAATTTAATATCCCTA
CGTTGCTTACACTGTTCCGTGTCATCCTTATCCCATTCTTTGTATTGGTC
TTTTATCTGCCTGTCACCTGGTCGCCGTTTGCCGCCGCGCTCATTTTCTG
CGTCGCGGCGGTGACTGACTGGTTCGATGGTTTTCTGGCACGCCGCTGGA
ACCAGAGTACCCGGTTTGGTGCTTTCCTTGACCCTGTGGCAGATAAAGTT
CTCGTGGCTATCGCCATGGTGCTGGTAACCGAGCATTATCACAGCTGGTG
GGTGACATTACCGGCGGCAACGATGATCGCCCGTGAAATTATTATTTCTG
CGCTACGCGAATGGATGGCGGAGTTGGGTAAACGCAGTAGCGTGGCCGTC
TCCTGGATTGGGAAAGTGAAAACCACTGCCCAGATGGTGGCGTTGGCATG
GCTGCTGTGGCGTCCGAACATTTGGGTTGAGTACGCCGGTATTGCACTTT
TCTTTGTGGCTGCGGTACTGACTCTGTGGTCAATGTTGCAATATTTGAGC
GCTGCGCGTGCAGATTTGCTTGATCAGTGATCGTTTCGGCGTAATTTTCA
GCAAACGATCAAAAGTGGTGAAAAATATCGTTGACTCATCGCGCCAGGTA
AGTAGAATGCAACGCATCGAACGGCGGCACTGATTGCCAGACGATAATAA
AATCAAGTGATTAACTGATTGCTTGATGAATGCGGGAANNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTTCC
CGCTCCAGTTTAAAAGACATCGGCGTCAAGCGGATGTCTGGCTGAAAGGC
CTGAAGAATTTGGCGCGTTAACAAAGCGGTTATGTAGCGGATTGCAAATC
CGTCTA

Summary:
==================================================
file name: /repeatmasker/tmp/RM2seq
sequences:          1
total length:     956 bp
GC level:       49.90 %
bases masked       56 bp (  5.86 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
SINEs:               0           0 bp     0.00 %
      ALUs           0           0 bp     0.00 %
      MIRs           0           0 bp     0.00 %

LINEs:               0           0 bp     0.00 %
      LINE1          0           0 bp     0.00 %
      LINE2          0           0 bp     0.00 %

LTR elements:        0           0 bp     0.00 %
      MaLRs          0           0 bp     0.00 %
      Retrov.        0           0 bp     0.00 %
      MER4_group     0           0 bp     0.00 %

DNA elements:        0           0 bp     0.00 %
      MER1_type      0           0 bp     0.00 %
      MER2_type      0           0 bp     0.00 %
      Mariners       0           0 bp     0.00 %

Unclassified:        0           0 bp     0.00 %

Total interspersed repeats:      0 bp     0.00 %


Small RNA:           1          56 bp     5.86 %

Satellites:          0           0 bp     0.00 %
Simple repeats:      0           0 bp     0.00 %
Low complexity:      0           0 bp     0.00 %
==================================================

* most repeats fragmented by insertions or deletions
  have been counted as one element

The sequence(s) were assumed to be of primate origin.
RepeatMasker version  05/05/99               default
ProcessRepeats version  05/05/99
Repbase version 3.04




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.

Query= ECOPGSA
         (956 letters)

 
If you have any problems or questions with the results of this search 
please refer to the BLAST FAQs


 Distribution of 6 Blast Hits on the Query Sequence













                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

gi|6015230|gb|AC011522.1|AC011522  Homo sapiens chromosome 1...   264  2e-68
gi|5686083|gb|AC008992.1|AC008992  Homo sapiens chromosome 1...   196  4e-48
gi|5809728|gb|AC009758.1|AC009758  Homo sapiens chromosome 1...    38  2.1
gi|5923636|gb|AC010184.4|AC010184  Homo sapiens clone RPCI11...    38  2.1
gi|5815559|gb|AC009791.1|AC009791  Homo sapiens chromosome 4...    38  2.1

 gi|6015230|gb|AC011522.1|AC011522 Homo sapiens chromosome 19 clone LLNL-F_208A9, WORKING DRAFT SEQUENCE,
             111 unordered pieces
             Length = 121479
             
 Score =  264 bits (133), Expect = 2e-68
 Identities = 133/133 (100%)
 Strand = Plus / Minus

                                                                         
Query: 1     gatcttctggtcgttgaaacattgatgtctctgtagcaacataggggtaatcttactgac 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 36942 gatcttctggtcgttgaaacattgatgtctctgtagcaacataggggtaatcttactgac 36883

                                                                         
Query: 61    aacagatagttacccgtcattatgcaatttaatatccctacgttgcttacactgttccgt 120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 36882 aacagatagttacccgtcattatgcaatttaatatccctacgttgcttacactgttccgt 36823

                          
Query: 121   gtcatccttatcc 133
             |||||||||||||
Sbjct: 36822 gtcatccttatcc 36810


 gi|5686083|gb|AC008992.1|AC008992 Homo sapiens chromosome 19 clone LLNL-F_95F7, WORKING DRAFT SEQUENCE,
            134 unordered pieces
            Length = 89525
            
 Score =  196 bits (99), Expect = 4e-48
 Identities = 108/110 (98%), Gaps = 2/110 (1%)
 Strand = Plus / Minus

                                                                        
Query: 556  gtggctgcggtactgactctgtggtcaatgttgcaatatttgagcgctgcgcgtgcagat 615
            |||||||||||||||||||||||||||||||||||||||||||||  |||||||||||||
Sbjct: 3534 gtggctgcggtactgactctgtggtcaatgttgcaatatttgagc--tgcgcgtgcagat 3477

                                                              
Query: 616  ttgcttgatcagtgatcgtttcggcgtaattttcagcaaacgatcaaaag 665
            ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 3476 ttgcttgatcagtgatcgtttcggcgtaattttcagcaaacgatcaaaag 3427


 gi|5809728|gb|AC009758.1|AC009758 Homo sapiens chromosome 11 clone 101_E_04 map 11, WORKING DRAFT
            SEQUENCE, 8 unordered pieces
            Length = 145072
            
 Score = 38.2 bits (19), Expect = 2.1
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                               
Query: 493  ttggcatggctgctgtggc 511
            |||||||||||||||||||
Sbjct: 8069 ttggcatggctgctgtggc 8051


 Score = 38.2 bits (19), Expect = 2.1
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                                
Query: 493   ttggcatggctgctgtggc 511
             |||||||||||||||||||
Sbjct: 56371 ttggcatggctgctgtggc 56389


 gi|5923636|gb|AC010184.4|AC010184 Homo sapiens clone RPCI11-438D8, WORKING DRAFT SEQUENCE, 40 unordered
              pieces
              Length = 193453
              
 Score = 38.2 bits (19), Expect = 2.1
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                                 
Query: 446    ccgtctcctggattgggaa 464
              |||||||||||||||||||
Sbjct: 115099 ccgtctcctggattgggaa 115081


 gi|5815559|gb|AC009791.1|AC009791 Homo sapiens chromosome 4 clone 165_D_10 map 4, LOW-PASS SEQUENCE
            SAMPLING
            Length = 29343
            
 Score = 38.2 bits (19), Expect = 2.1
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                               
Query: 493  ttggcatggctgctgtggc 511
            |||||||||||||||||||
Sbjct: 5911 ttggcatggctgctgtggc 5929


CPU time:     0.10 user secs.	    0.08 sys. secs	    0.18 total secs.

  Database: High-Throughput Genome Sequences
    Posted date:  Oct 8, 1999  6:37 PM
  Number of letters in database: 676,966,081
  Number of sequences in database:  5929
  
Lambda     K      H
    1.37    0.711     0.00 

Gapped
Lambda     K      H
    1.37    0.711 4.94e-324 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 255813
Number of Sequences: 5929
Number of extensions: 255813
Number of successful extensions: 16901
Number of sequences better than 10.0: 5
length of query: 956
length of database: 676,966,081
effective HSP length: 20
effective length of query: 936
effective length of database: 676,847,501
effective search space: 633529260936
effective search space used: 633529260936
T: 0
A: 0
X1: 6 (11.9 bits)
X2: 25 (49.6 bits)
S1: 12 (24.3 bits)
S2: 18 (36.2 bits)


  

   
    
  
   
     
     
        
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              This document last modified 19 Aug 2003

               This document's location: http://searchlauncher.bcm.tmc.edu/seq-search/Examples/blastn_htgs.html

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