TBLASTN 2.2.20 [Feb-08-2009]


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= HBB1_XENLA
         (145 letters)

Database: data/hbb1_mouse.fa 
           1 sequences; 444 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

dbj|AB364477.1| Mus musculus HBB1 mRNA for hemoglobin beta chain...   145   3e-40

>dbj|AB364477.1| Mus musculus HBB1 mRNA for hemoglobin beta chain subunit, complete
           cds
          Length = 444

 Score =  145 bits (366), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 65/144 (45%), Positives = 93/144 (64%)
 Frame = +1

Query: 2   LTAHDRQLINSTWGKLCAKTIGQEALGRLLWTYPWTQRYFSSFGNLNSADAVFHNEAVAA 61
           LT  ++  ++  WGK+ +  +G EALGRLL  YPWTQRYF SFG+L+SA A+  N  V A
Sbjct: 10  LTDAEKAAVSGLWGKVNSDEVGGEALGRLLVVYPWTQRYFDSFGDLSSASAIMGNAKVKA 189

Query: 62  HGEKVVTSIGEAIKHMDDIKGYYAQLSKYHSETLHVDPLNFKRFGGCLSIALARHFHEEY 121
           HG+KV+T+  E + H+D +KG +A LS+ H + LHVDP NF+  G  + I L  H  +++
Sbjct: 190 HGKKVITAFNEGLNHLDSLKGTFASLSELHCDKLHVDPENFRLLGNMIVIVLGHHLGKDF 369

Query: 122 TPELHAAYEHLFDAIADALGKGYH 145
           TP   AA++ +   +A AL   YH
Sbjct: 370 TPAAQAAFQKVMAGVATALAHKYH 441


  Database: data/hbb1_mouse.fa
    Posted date:  Mar 4, 2009 12:10 PM
  Number of letters in database: 444
  Number of sequences in database:  1
  
Lambda     K      H
   0.321    0.135    0.427 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 148
Number of extensions: 3
Number of successful extensions: 1
Number of sequences better than 1.0e-03: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 145
Length of database: 148
Length adjustment: 16
Effective length of query: 129
Effective length of database: 132
Effective search space:    17028
Effective search space used:    17028
Neighboring words threshold: 13
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 30 (16.2 bits)
