BLASTP 2.2.21 [Jun-14-2009]


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.

Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= cds
         (90 letters)

Database: base 
           13 sequences; 610 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

D89965_5 [19 - 432] Rattus norvegicus mRNA for RSS, complete cds.     188   4e-53
D89965_13 [375 - 1] (REVERSE SENSE) Rattus norvegicus mRNA for R...    12   5.5  

>D89965_5 [19 - 432] Rattus norvegicus mRNA for RSS, complete cds.
          Length = 138

 Score =  188 bits (478), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 90/90 (100%), Positives = 90/90 (100%)

Query: 1   MALMHFQFTFKQFEQRKSIRSTARKARDDFVVVQTADLFHVAFHYGIAQRGLTITSDDHM 60
           MALMHFQFTFKQFEQRKSIRSTARKARDDFVVVQTADLFHVAFHYGIAQRGLTITSDDHM
Sbjct: 49  MALMHFQFTFKQFEQRKSIRSTARKARDDFVVVQTADLFHVAFHYGIAQRGLTITSDDHM 108

Query: 61  AVTAYAYYSCHELTPWLRIQSTNPVQKYGA 90
           AVTAYAYYSCHELTPWLRIQSTNPVQKYGA
Sbjct: 109 AVTAYAYYSCHELTPWLRIQSTNPVQKYGA 138



 Score = 14.6 bits (26), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 4/7 (57%), Positives = 6/7 (85%)

Query: 52 LTITSDD 58
          +T+T DD
Sbjct: 8  VTVTGDD 14


>D89965_13 [375 - 1] (REVERSE SENSE) Rattus norvegicus mRNA for
          RSS, complete cds.
          Length = 125

 Score = 12.3 bits (20), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 4/10 (40%), Positives = 6/10 (60%)

Query: 8  FTFKQFEQRK 17
          FT  +  +RK
Sbjct: 55 FTLFELFERK 64


  Database: base
    Posted date:  Oct 31, 2009 12:04 PM
  Number of letters in database: 610
  Number of sequences in database:  13
  
Lambda     K      H
   0.327    0.134    0.409 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13
Number of Hits to DB: 201
Number of extensions: 4
Number of successful extensions: 3
Number of sequences better than 10.0: 2
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 90
Length of database: 610
Length adjustment: 19
Effective length of query: 71
Effective length of database: 363
Effective search space:    25773
Effective search space used:    25773
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 18 (11.4 bits)
S2: 18 (11.5 bits)