TBLASTN 2.2.10 [Oct-19-2004]


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= HAHU | 1114 |  Hemoglobin alpha chain - Human, chimpanzee, and
pygmy chimpanzee
         (141 letters)

Database: testnt.fa 
           2 sequences; 13,260 total letters

Searching..done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|10040111|emb|AL390796.6|AL390796 Homo sapiens chromosome 1 cl...    18   2.3  
test6                                                                  16   6.7  

>gi|10040111|emb|AL390796.6|AL390796 Homo sapiens chromosome 1 clone
            RP11-562F3, *** SEQUENCING IN PROGRESS ***, 16 unordered
            pieces /len=164198
          Length = 8160

 Score = 17.7 bits (34), Expect = 2.3
 Identities = 8/23 (34%), Positives = 11/23 (47%)
 Frame = +1

Query: 56   KGHGKKVADALTNAVAHVDDMPN 78
            KGH KK+     N  ++  D  N
Sbjct: 7603 KGHLKKITSFFFNHTSNYRDEYN 7671



 Score = 17.3 bits (33), Expect = 3.0
 Identities = 9/28 (32%), Positives = 13/28 (46%)
 Frame = +1

Query: 31   RMFLSFPTTKTYFPHFDLSHGSAQVKGH 58
            RM+  F    TY+ +F L      V G+
Sbjct: 7069 RMYFCFLKVLTYYFNFFLFFNIFYVLGY 7152


>test6
          Length = 5100

 Score = 16.2 bits (30), Expect = 6.7
 Identities = 6/9 (66%), Positives = 7/9 (77%)
 Frame = +3

Query: 72   HVDDMPNAL 80
            H+D M NAL
Sbjct: 3822 HMDYMSNAL 3848



 Score = 15.8 bits (29), Expect = 8.8
 Identities = 5/7 (71%), Positives = 6/7 (85%)
 Frame = -2

Query: 93   VDPVNFK 99
            +DP NFK
Sbjct: 1814 IDP*NFK 1794


  Database: testnt.fa
    Posted date:  Feb 5, 2005  6:26 PM
  Number of letters in database: 13,260
  Number of sequences in database:  2
  
Lambda     K      H
   0.319    0.130    0.385 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1998
Number of Sequences: 2
Number of extensions: 23
Number of successful extensions: 4
Number of sequences better than 10.0: 2
Number of HSP's better than 10.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 4
length of query: 141
length of database: 4420
effective HSP length: 39
effective length of query: 102
effective length of database: 4342
effective search space:   442884
effective search space used:   442884
frameshift window, decay const: 40,  0.1
T: 13
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 29 (16.3 bits)
S2: 29 (15.8 bits)