BLASTN 2.2.13 [Nov-27-2005]


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= Bos_taurus_chr4.trna418-SeCTCA (12402013-12402084)  SeC (TCA)
72 bp  Sc: 50.54
         (72 letters)

Database: genome.fa 
           1185 sequences; 56,660,578 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_14                                                            32   0.64 
scaffold_261                                                           30   2.5  
scaffold_68                                                            28   10.0 
scaffold_23                                                            28   10.0 
scaffold_13                                                            28   10.0 
scaffold_8                                                             28   10.0 
scaffold_7                                                             28   10.0 
scaffold_6                                                             28   10.0 
scaffold_4                                                             28   10.0 
scaffold_2                                                             28   10.0 
scaffold_1                                                             28   10.0 

>scaffold_14
          Length = 1107847

 Score = 32.2 bits (16), Expect = 0.64
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                              
Query: 37     ctacgaggagcacagg 52
              ||||||||||||||||
Sbjct: 836540 ctacgaggagcacagg 836555



 Score = 30.2 bits (15), Expect = 2.5
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                             
Query: 2      ccctggtggtccagt 16
              |||||||||||||||
Sbjct: 462636 ccctggtggtccagt 462650



 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                            
Query: 53     ttcgatccctggtc 66
              ||||||||||||||
Sbjct: 630755 ttcgatccctggtc 630742


>scaffold_261
          Length = 9938

 Score = 30.2 bits (15), Expect = 2.5
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                           
Query: 42   aggagcacaggttcg 56
            |||||||||||||||
Sbjct: 5376 aggagcacaggttcg 5362


>scaffold_68
          Length = 86324

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                           
Query: 36    actacgaggagcac 49
             ||||||||||||||
Sbjct: 17587 actacgaggagcac 17600


>scaffold_23
          Length = 674037

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                            
Query: 35     cactacgaggagca 48
              ||||||||||||||
Sbjct: 172788 cactacgaggagca 172775


>scaffold_13
          Length = 1338096

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 17/18 (94%)
 Strand = Plus / Minus

                                
Query: 40     cgaggagcacaggttcga 57
              ||||||||||| ||||||
Sbjct: 391173 cgaggagcacatgttcga 391156


>scaffold_8
          Length = 1961717

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                            
Query: 2      ccctggtggtccag 15
              ||||||||||||||
Sbjct: 680168 ccctggtggtccag 680181


>scaffold_7
          Length = 2177197

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                            
Query: 37     ctacgaggagcaca 50
              ||||||||||||||
Sbjct: 971293 ctacgaggagcaca 971280



 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                             
Query: 37      ctacgaggagcaca 50
               ||||||||||||||
Sbjct: 1614550 ctacgaggagcaca 1614563


>scaffold_6
          Length = 2755913

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 17/18 (94%)
 Strand = Plus / Minus

                                 
Query: 40      cgaggagcacaggttcga 57
               |||||||||||| |||||
Sbjct: 1287995 cgaggagcacagcttcga 1287978


>scaffold_4
          Length = 3024044

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                             
Query: 36      actacgaggagcac 49
               ||||||||||||||
Sbjct: 1482133 actacgaggagcac 1482146


>scaffold_2
          Length = 3465789

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                            
Query: 36     actacgaggagcac 49
              ||||||||||||||
Sbjct: 511174 actacgaggagcac 511161



 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                             
Query: 37      ctacgaggagcaca 50
               ||||||||||||||
Sbjct: 2480894 ctacgaggagcaca 2480907



 Score = 28.2 bits (14), Expect = 10.0
 Identities = 17/18 (94%)
 Strand = Plus / Minus

                                 
Query: 40      cgaggagcacaggttcga 57
               ||||||||||||| ||||
Sbjct: 2844550 cgaggagcacaggatcga 2844533


>scaffold_1
          Length = 3520325

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 17/18 (94%)
 Strand = Plus / Plus

                                 
Query: 27      ccacgcttcactacgagg 44
               ||||||||||||| ||||
Sbjct: 3506164 ccacgcttcactatgagg 3506181


  Database: genome.fa
    Posted date:  Feb 16, 2009  1:41 PM
  Number of letters in database: 56,660,578
  Number of sequences in database:  1185
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 1439
Number of Sequences: 1185
Number of extensions: 1439
Number of successful extensions: 20
Number of sequences better than 10.0: 14
Number of HSP's better than 10.0 without gapping: 14
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): 20
length of query: 72
length of database: 56,660,578
effective HSP length: 16
effective length of query: 56
effective length of database: 56,641,618
effective search space: 3171930608
effective search space used: 3171930608
T: 0
A: 0
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 14 (28.2 bits)
BLASTN 2.2.13 [Nov-27-2005]


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= Caenorhabditis_briggsae_chrUn.trna29-SeCTCA (5435433-5435500)
SeC (TCA) 68 bp  Sc: 28.83
         (68 letters)

Database: genome.fa 
           1185 sequences; 56,660,578 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_10                                                            30   2.3  
scaffold_9                                                             30   2.3  
scaffold_1085                                                          28   9.3  
scaffold_62                                                            28   9.3  
scaffold_53                                                            28   9.3  
scaffold_52                                                            28   9.3  
scaffold_51                                                            28   9.3  
scaffold_3                                                             28   9.3  
scaffold_2                                                             28   9.3  
scaffold_1                                                             28   9.3  

>scaffold_10
          Length = 1654512

 Score = 30.2 bits (15), Expect = 2.3
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                             
Query: 19     agcgcgttcgacttc 33
              |||||||||||||||
Sbjct: 369812 agcgcgttcgacttc 369798


>scaffold_9
          Length = 1602328

 Score = 30.2 bits (15), Expect = 2.3
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                            
Query: 19    agcgcgttcgacttc 33
             |||||||||||||||
Sbjct: 79654 agcgcgttcgacttc 79640



 Score = 30.2 bits (15), Expect = 2.3
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                             
Query: 3      tgcttggcgcaatgg 17
              |||||||||||||||
Sbjct: 871371 tgcttggcgcaatgg 871385


>scaffold_1085
          Length = 3426

 Score = 28.2 bits (14), Expect = 9.3
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                          
Query: 20   gcgcgttcgacttc 33
            ||||||||||||||
Sbjct: 1119 gcgcgttcgacttc 1106


>scaffold_62
          Length = 159868

 Score = 28.2 bits (14), Expect = 9.3
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                           
Query: 20    gcgcgttcgacttc 33
             ||||||||||||||
Sbjct: 78661 gcgcgttcgacttc 78674


>scaffold_53
          Length = 203801

 Score = 28.2 bits (14), Expect = 9.3
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                           
Query: 20    gcgcgttcgacttc 33
             ||||||||||||||
Sbjct: 68689 gcgcgttcgacttc 68676


>scaffold_52
          Length = 183308

 Score = 28.2 bits (14), Expect = 9.3
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                           
Query: 20    gcgcgttcgacttc 33
             ||||||||||||||
Sbjct: 60049 gcgcgttcgacttc 60036


>scaffold_51
          Length = 214248

 Score = 28.2 bits (14), Expect = 9.3
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                            
Query: 20     gcgcgttcgacttc 33
              ||||||||||||||
Sbjct: 154446 gcgcgttcgacttc 154433


>scaffold_3
          Length = 3001400

 Score = 28.2 bits (14), Expect = 9.3
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                             
Query: 20      gcgcgttcgacttc 33
               ||||||||||||||
Sbjct: 1037555 gcgcgttcgacttc 1037568



 Score = 28.2 bits (14), Expect = 9.3
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                             
Query: 14      atggtagcgcgttc 27
               ||||||||||||||
Sbjct: 1966077 atggtagcgcgttc 1966090


>scaffold_2
          Length = 3465789

 Score = 28.2 bits (14), Expect = 9.3
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                            
Query: 19     agcgcgttcgactt 32
              ||||||||||||||
Sbjct: 215675 agcgcgttcgactt 215688


>scaffold_1
          Length = 3520325

 Score = 28.2 bits (14), Expect = 9.3
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                           
Query: 4     gcttggcgcaatgg 17
             ||||||||||||||
Sbjct: 28880 gcttggcgcaatgg 28867


  Database: genome.fa
    Posted date:  Feb 16, 2009  1:41 PM
  Number of letters in database: 56,660,578
  Number of sequences in database:  1185
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 1516
Number of Sequences: 1185
Number of extensions: 1516
Number of successful extensions: 12
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 10
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): 12
length of query: 68
length of database: 56,660,578
effective HSP length: 16
effective length of query: 52
effective length of database: 56,641,618
effective search space: 2945364136
effective search space used: 2945364136
T: 0
A: 0
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 14 (28.2 bits)
BLASTN 2.2.13 [Nov-27-2005]


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= Danio_rerio_chr1.trna309-SeCTCA (20132204-20132132)  SeC (TCA)
73 bp  Sc: 51.80
         (73 letters)

Database: genome.fa 
           1185 sequences; 56,660,578 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_38                                                            38   0.011
scaffold_24                                                            38   0.011
scaffold_26                                                            34   0.16 
scaffold_25                                                            34   0.16 
scaffold_15                                                            34   0.16 
scaffold_39                                                            30   2.6  
scaffold_30                                                            30   2.6  

>scaffold_38
          Length = 387118

 Score = 38.2 bits (19), Expect = 0.011
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                                 
Query: 47     ttgtgggttcaagtcccac 65
              |||||||||||||||||||
Sbjct: 143767 ttgtgggttcaagtcccac 143749


>scaffold_24
          Length = 564861

 Score = 38.2 bits (19), Expect = 0.011
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                                 
Query: 47     ttgtgggttcaagtcccac 65
              |||||||||||||||||||
Sbjct: 244901 ttgtgggttcaagtcccac 244883


>scaffold_26
          Length = 549629

 Score = 34.2 bits (17), Expect = 0.16
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                               
Query: 7      gtggcctaatggataag 23
              |||||||||||||||||
Sbjct: 507461 gtggcctaatggataag 507477


>scaffold_25
          Length = 552203

 Score = 34.2 bits (17), Expect = 0.16
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                               
Query: 7      gtggcctaatggataag 23
              |||||||||||||||||
Sbjct: 245067 gtggcctaatggataag 245051



 Score = 30.2 bits (15), Expect = 2.6
 Identities = 18/19 (94%)
 Strand = Plus / Minus

                                 
Query: 46     attgtgggttcaagtccca 64
              ||||||||||| |||||||
Sbjct: 245028 attgtgggttcgagtccca 245010


>scaffold_15
          Length = 987846

 Score = 34.2 bits (17), Expect = 0.16
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                               
Query: 7      gtggcctaatggataag 23
              |||||||||||||||||
Sbjct: 965311 gtggcctaatggataag 965295


>scaffold_39
          Length = 370504

 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                             
Query: 35     caaagctgggtattg 49
              |||||||||||||||
Sbjct: 198041 caaagctgggtattg 198055


>scaffold_30
          Length = 484759

 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                            
Query: 35    caaagctgggtattg 49
             |||||||||||||||
Sbjct: 36508 caaagctgggtattg 36522


  Database: genome.fa
    Posted date:  Feb 16, 2009  1:41 PM
  Number of letters in database: 56,660,578
  Number of sequences in database:  1185
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 656
Number of Sequences: 1185
Number of extensions: 656
Number of successful extensions: 15
Number of sequences better than 10.0: 7
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 7
Number of HSP's gapped (non-prelim): 8
length of query: 73
length of database: 56,660,578
effective HSP length: 16
effective length of query: 57
effective length of database: 56,641,618
effective search space: 3228572226
effective search space used: 3228572226
T: 0
A: 0
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
BLASTN 2.2.13 [Nov-27-2005]


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= Equus_caballus_chr4.trna76-SeCTCA (90817839-90817768)  SeC
(TCA) 72 bp  Sc: 52.50
         (72 letters)

Database: genome.fa 
           1185 sequences; 56,660,578 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_14                                                            42   7e-04
scaffold_1                                                             34   0.16 
scaffold_22                                                            30   2.5  
scaffold_204                                                           28   10.0 
scaffold_54                                                            28   10.0 

>scaffold_14
          Length = 1107847

 Score = 42.1 bits (21), Expect = 7e-04
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                                   
Query: 3      gggtatagctcaggggtagag 23
              |||||||||||||||||||||
Sbjct: 790875 gggtatagctcaggggtagag 790855


>scaffold_1
          Length = 3520325

 Score = 34.2 bits (17), Expect = 0.16
 Identities = 20/21 (95%)
 Strand = Plus / Minus

                                    
Query: 3       gggtatagctcaggggtagag 23
               |||||||||||||||| ||||
Sbjct: 1678311 gggtatagctcaggggcagag 1678291


>scaffold_22
          Length = 725242

 Score = 30.2 bits (15), Expect = 2.5
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                             
Query: 15     ggggtagagaatttg 29
              |||||||||||||||
Sbjct: 637695 ggggtagagaatttg 637709


>scaffold_204
          Length = 10935

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                          
Query: 54   tcaaatgcgggtgc 67
            ||||||||||||||
Sbjct: 7324 tcaaatgcgggtgc 7311


>scaffold_54
          Length = 191110

 Score = 28.2 bits (14), Expect = 10.0
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                           
Query: 54    tcaaatgcgggtgc 67
             ||||||||||||||
Sbjct: 44708 tcaaatgcgggtgc 44721


  Database: genome.fa
    Posted date:  Feb 16, 2009  1:41 PM
  Number of letters in database: 56,660,578
  Number of sequences in database:  1185
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 512
Number of Sequences: 1185
Number of extensions: 512
Number of successful extensions: 7
Number of sequences better than 10.0: 6
Number of HSP's better than 10.0 without gapping: 6
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): 7
length of query: 72
length of database: 56,660,578
effective HSP length: 16
effective length of query: 56
effective length of database: 56,641,618
effective search space: 3171930608
effective search space used: 3171930608
T: 0
A: 0
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 14 (28.2 bits)
BLASTN 2.2.13 [Nov-27-2005]


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= Felis_catus_scaffold_189999.trna6-SeCTCA (127772-127688)  SeC
(TCA) 85 bp  Sc: 50.01
         (85 letters)

Database: genome.fa 
           1185 sequences; 56,660,578 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_106                                                           38   0.013
scaffold_14                                                            38   0.013
scaffold_698                                                           32   0.79 
scaffold_246                                                           32   0.79 
scaffold_9                                                             32   0.79 
scaffold_3                                                             32   0.79 
scaffold_51                                                            30   3.1  

>scaffold_106
          Length = 21576

 Score = 38.2 bits (19), Expect = 0.013
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                              
Query: 59  tcgtgggttcgagccccac 77
           |||||||||||||||||||
Sbjct: 833 tcgtgggttcgagccccac 851



 Score = 38.2 bits (19), Expect = 0.013
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                               
Query: 59   tcgtgggttcgagccccac 77
            |||||||||||||||||||
Sbjct: 6283 tcgtgggttcgagccccac 6265


>scaffold_14
          Length = 1107847

 Score = 38.2 bits (19), Expect = 0.013
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                                 
Query: 59     tcgtgggttcgagccccac 77
              |||||||||||||||||||
Sbjct: 522558 tcgtgggttcgagccccac 522576


>scaffold_698
          Length = 6408

 Score = 32.2 bits (16), Expect = 0.79
 Identities = 16/16 (100%)
 Strand = Plus / Minus

                           
Query: 60  cgtgggttcgagcccc 75
           ||||||||||||||||
Sbjct: 483 cgtgggttcgagcccc 468


>scaffold_246
          Length = 35382

 Score = 32.2 bits (16), Expect = 0.79
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                            
Query: 60   cgtgggttcgagcccc 75
            ||||||||||||||||
Sbjct: 3782 cgtgggttcgagcccc 3797


>scaffold_9
          Length = 1602328

 Score = 32.2 bits (16), Expect = 0.79
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                               
Query: 60      cgtgggttcgagcccc 75
               ||||||||||||||||
Sbjct: 1581439 cgtgggttcgagcccc 1581454


>scaffold_3
          Length = 3001400

 Score = 32.2 bits (16), Expect = 0.79
 Identities = 16/16 (100%)
 Strand = Plus / Minus

                               
Query: 9       ggctcagtcggttgag 24
               ||||||||||||||||
Sbjct: 1701800 ggctcagtcggttgag 1701785


>scaffold_51
          Length = 214248

 Score = 30.2 bits (15), Expect = 3.1
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                            
Query: 61    gtgggttcgagcccc 75
             |||||||||||||||
Sbjct: 82413 gtgggttcgagcccc 82427


  Database: genome.fa
    Posted date:  Feb 16, 2009  1:41 PM
  Number of letters in database: 56,660,578
  Number of sequences in database:  1185
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 1264
Number of Sequences: 1185
Number of extensions: 1264
Number of successful extensions: 8
Number of sequences better than 10.0: 7
Number of HSP's better than 10.0 without gapping: 7
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): 8
length of query: 85
length of database: 56,660,578
effective HSP length: 16
effective length of query: 69
effective length of database: 56,641,618
effective search space: 3908271642
effective search space used: 3908271642
T: 0
A: 0
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
BLASTN 2.2.13 [Nov-27-2005]


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= Mus_musculus_chr5.trna13-SeCTCA (5627681-5627751)  SeC (TCA) 71
bp  Sc: 53.42
         (71 letters)

Database: genome.fa 
           1185 sequences; 56,660,578 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_106                                                           34   0.16 
scaffold_14                                                            34   0.16 
scaffold_698                                                           30   2.5  
scaffold_246                                                           30   2.5  
scaffold_51                                                            30   2.5  
scaffold_9                                                             30   2.5  
scaffold_38                                                            28   9.8  
scaffold_25                                                            28   9.8  
scaffold_24                                                            28   9.8  
scaffold_19                                                            28   9.8  
scaffold_17                                                            28   9.8  
scaffold_5                                                             28   9.8  
scaffold_2                                                             28   9.8  

>scaffold_106
          Length = 21576

 Score = 34.2 bits (17), Expect = 0.16
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                            
Query: 47  gtgggttcgagccccac 63
           |||||||||||||||||
Sbjct: 835 gtgggttcgagccccac 851



 Score = 34.2 bits (17), Expect = 0.16
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                             
Query: 47   gtgggttcgagccccac 63
            |||||||||||||||||
Sbjct: 6281 gtgggttcgagccccac 6265



 Score = 32.2 bits (16), Expect = 0.63
 Identities = 19/20 (95%)
 Strand = Plus / Plus

                               
Query: 6   gctagctcagtgggtagagc 25
           ||||||||||| ||||||||
Sbjct: 792 gctagctcagtcggtagagc 811



 Score = 32.2 bits (16), Expect = 0.63
 Identities = 19/20 (95%)
 Strand = Plus / Minus

                                
Query: 6    gctagctcagtgggtagagc 25
            ||||||||||| ||||||||
Sbjct: 6324 gctagctcagtcggtagagc 6305


>scaffold_14
          Length = 1107847

 Score = 34.2 bits (17), Expect = 0.16
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                               
Query: 47     gtgggttcgagccccac 63
              |||||||||||||||||
Sbjct: 522560 gtgggttcgagccccac 522576



 Score = 32.2 bits (16), Expect = 0.63
 Identities = 19/20 (95%)
 Strand = Plus / Plus

                                  
Query: 6      gctagctcagtgggtagagc 25
              ||||||||||| ||||||||
Sbjct: 522517 gctagctcagtcggtagagc 522536


>scaffold_698
          Length = 6408

 Score = 30.2 bits (15), Expect = 2.5
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                          
Query: 47  gtgggttcgagcccc 61
           |||||||||||||||
Sbjct: 482 gtgggttcgagcccc 468


>scaffold_246
          Length = 35382

 Score = 30.2 bits (15), Expect = 2.5
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                           
Query: 47   gtgggttcgagcccc 61
            |||||||||||||||
Sbjct: 3783 gtgggttcgagcccc 3797


>scaffold_51
          Length = 214248

 Score = 30.2 bits (15), Expect = 2.5
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                            
Query: 47    gtgggttcgagcccc 61
             |||||||||||||||
Sbjct: 82413 gtgggttcgagcccc 82427


>scaffold_9
          Length = 1602328

 Score = 30.2 bits (15), Expect = 2.5
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                              
Query: 47      gtgggttcgagcccc 61
               |||||||||||||||
Sbjct: 1581440 gtgggttcgagcccc 1581454


>scaffold_38
          Length = 387118

 Score = 28.2 bits (14), Expect = 9.8
 Identities = 20/22 (90%)
 Strand = Plus / Minus

                                    
Query: 42     gggttgtgggttcgagccccac 63
              ||||||||||||| || |||||
Sbjct: 143770 gggttgtgggttcaagtcccac 143749


>scaffold_25
          Length = 552203

 Score = 28.2 bits (14), Expect = 9.8
 Identities = 17/18 (94%)
 Strand = Plus / Minus

                                
Query: 45     ttgtgggttcgagcccca 62
              ||||||||||||| ||||
Sbjct: 245027 ttgtgggttcgagtccca 245010


>scaffold_24
          Length = 564861

 Score = 28.2 bits (14), Expect = 9.8
 Identities = 20/22 (90%)
 Strand = Plus / Minus

                                    
Query: 42     gggttgtgggttcgagccccac 63
              ||||||||||||| || |||||
Sbjct: 244904 gggttgtgggttcaagtcccac 244883


>scaffold_19
          Length = 762245

 Score = 28.2 bits (14), Expect = 9.8
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                            
Query: 17     gggtagagcatgag 30
              ||||||||||||||
Sbjct: 156831 gggtagagcatgag 156818


>scaffold_17
          Length = 902323

 Score = 28.2 bits (14), Expect = 9.8
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                            
Query: 50     ggttcgagccccac 63
              ||||||||||||||
Sbjct: 758103 ggttcgagccccac 758116


>scaffold_5
          Length = 3000003

 Score = 28.2 bits (14), Expect = 9.8
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                            
Query: 17     gggtagagcatgag 30
              ||||||||||||||
Sbjct: 671799 gggtagagcatgag 671812



 Score = 28.2 bits (14), Expect = 9.8
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                             
Query: 17      gggtagagcatgag 30
               ||||||||||||||
Sbjct: 2031603 gggtagagcatgag 2031616


>scaffold_2
          Length = 3465789

 Score = 28.2 bits (14), Expect = 9.8
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                             
Query: 50      ggttcgagccccac 63
               ||||||||||||||
Sbjct: 2260706 ggttcgagccccac 2260693



 Score = 28.2 bits (14), Expect = 9.8
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                             
Query: 49      gggttcgagcccca 62
               ||||||||||||||
Sbjct: 2488252 gggttcgagcccca 2488239


  Database: genome.fa
    Posted date:  Feb 16, 2009  1:41 PM
  Number of letters in database: 56,660,578
  Number of sequences in database:  1185
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 829
Number of Sequences: 1185
Number of extensions: 829
Number of successful extensions: 21
Number of sequences better than 10.0: 14
Number of HSP's better than 10.0 without gapping: 14
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): 21
length of query: 71
length of database: 56,660,578
effective HSP length: 16
effective length of query: 55
effective length of database: 56,641,618
effective search space: 3115288990
effective search space used: 3115288990
T: 0
A: 0
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 14 (28.2 bits)
BLASTN 2.2.13 [Nov-27-2005]


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= Homo_sapiens_chr17.trna25-SeCTCA (35527152-35527079)  SeC (TCA)
74 bp  Sc: 47.88
         (74 letters)

Database: genome.fa 
           1185 sequences; 56,660,578 total letters

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

 ***** No hits found ******

  Database: genome.fa
    Posted date:  Feb 16, 2009  1:41 PM
  Number of letters in database: 56,660,578
  Number of sequences in database:  1185
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 445
Number of Sequences: 1185
Number of extensions: 445
Number of successful extensions: 5
Number of sequences better than 10.0: 1
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 4
Number of HSP's gapped (non-prelim): 1
length of query: 74
length of database: 56,660,578
effective HSP length: 16
effective length of query: 58
effective length of database: 56,641,618
effective search space: 3285213844
effective search space used: 3285213844
T: 0
A: 0
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
