Animal-Genome cDNA 20110601C-003578


Search to RefSeqBP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


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= 20110601C-003578
         (1218 letters)

Database: RefSeq49_BP.fasta 
           33,088 sequences; 17,681,374 total letters

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

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


  Database: RefSeq49_BP.fasta
    Posted date:  Oct 17, 2011  1:42 PM
  Number of letters in database: 17,681,374
  Number of sequences in database:  33,088
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33088
Number of Hits to DB: 49,711,514
Number of extensions: 1431890
Number of successful extensions: 4355
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 4350
Number of HSP's successfully gapped: 0
Length of query: 406
Length of database: 17,681,374
Length adjustment: 105
Effective length of query: 301
Effective length of database: 14,207,134
Effective search space: 4276347334
Effective search space used: 4276347334
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)

Search to RefSeqCP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


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= 20110601C-003578
         (1218 letters)

Database: RefSeq49_CP.fasta 
           33,336 sequences; 18,874,504 total letters

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

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


  Database: RefSeq49_CP.fasta
    Posted date:  Oct 17, 2011  1:42 PM
  Number of letters in database: 18,874,504
  Number of sequences in database:  33,336
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33336
Number of Hits to DB: 51,742,836
Number of extensions: 1466578
Number of successful extensions: 4507
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 4505
Number of HSP's successfully gapped: 0
Length of query: 406
Length of database: 18,874,504
Length adjustment: 105
Effective length of query: 301
Effective length of database: 15,374,224
Effective search space: 4627641424
Effective search space used: 4627641424
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)

Search to RefSeqHP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


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= 20110601C-003578
         (1218 letters)

Database: RefSeq49_HP.fasta 
           32,964 sequences; 18,297,164 total letters

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

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


  Database: RefSeq49_HP.fasta
    Posted date:  Oct 17, 2011  1:42 PM
  Number of letters in database: 18,297,164
  Number of sequences in database:  32,964
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 32964
Number of Hits to DB: 50,803,737
Number of extensions: 1442274
Number of successful extensions: 4205
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 4201
Number of HSP's successfully gapped: 0
Length of query: 406
Length of database: 18,297,164
Length adjustment: 105
Effective length of query: 301
Effective length of database: 14,835,944
Effective search space: 4465619144
Effective search space used: 4465619144
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)

Search to RefSeqMP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


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= 20110601C-003578
         (1218 letters)

Database: RefSeq49_MP.fasta 
           30,036 sequences; 15,617,559 total letters

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

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


  Database: RefSeq49_MP.fasta
    Posted date:  Oct 17, 2011  1:42 PM
  Number of letters in database: 15,617,559
  Number of sequences in database:  30,036
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 30036
Number of Hits to DB: 43,050,203
Number of extensions: 1207869
Number of successful extensions: 3672
Number of sequences better than 1.0e-05: 0
Number of HSP's gapped: 3666
Number of HSP's successfully gapped: 0
Length of query: 406
Length of database: 15,617,559
Length adjustment: 104
Effective length of query: 302
Effective length of database: 12,493,815
Effective search space: 3773132130
Effective search space used: 3773132130
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)

Search to RefSeqSP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


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= 20110601C-003578
         (1218 letters)

Database: RefSeq49_SP.fasta 
           24,897 sequences; 11,343,932 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|XP_003121773.2| PREDICTED: hypothetical protein LOC100511731...   204   8e-53

>ref|XP_003121773.2| PREDICTED: hypothetical protein LOC100511731 [Sus scrofa].
          Length = 106

 Score =  204 bits (519), Expect = 8e-53
 Identities = 94/97 (96%), Positives = 96/97 (98%)
 Frame = +3

Query: 399 KGEGQGLKPSQARGLAHTACRTRERGRHHLTGTEGALGPEKTFAHCKSNESLKHPGPPWS 578
           +GEGQGLKPSQARGLAHTACRTRERGRHHLT TEGALGPEKTFA+CKSNESLKHPGPPWS
Sbjct: 10  QGEGQGLKPSQARGLAHTACRTRERGRHHLTDTEGALGPEKTFAYCKSNESLKHPGPPWS 69

Query: 579 SRGELRRRDEILGSEMGSRSRPLESSPRMPYQDLCHW 689
           SRGELRRRDEILGSEMGSRSRPLESSPRMPYQDLCHW
Sbjct: 70  SRGELRRRDEILGSEMGSRSRPLESSPRMPYQDLCHW 106


  Database: RefSeq49_SP.fasta
    Posted date:  Oct 17, 2011  1:42 PM
  Number of letters in database: 11,343,932
  Number of sequences in database:  24,897
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24897
Number of Hits to DB: 32,021,343
Number of extensions: 923804
Number of successful extensions: 2948
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 2943
Number of HSP's successfully gapped: 1
Length of query: 406
Length of database: 11,343,932
Length adjustment: 101
Effective length of query: 305
Effective length of database: 8,829,335
Effective search space: 2692947175
Effective search space used: 2692947175
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)

Search to Sscrofa10_2

BLASTN 2.2.24 [Aug-08-2010]


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= 20110601C-003578
         (1218 letters)

Database: Sscrofa_10.2.fasta 
           4582 sequences; 2,808,509,378 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Sscrofa_Chr01                                                        1312   0.0  

>Sscrofa_Chr01 
||          Length = 315321322

 Score = 1312 bits (662), Expect = 0.0
 Identities = 665/666 (99%)
 Strand = Plus / Minus

                                                                             
Query: 540       agtaatgaaagcctgaagcatccagggcccccctggagcagcagaggggagctcagacgc 599
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179918219 agtaatgaaagcctgaagcatccagggcccccctggagcagcagaggggagctcagacgc 179918160

                                                                             
Query: 600       cgcgatgagattctgggaagtgaaatgggctcaagatctcgaccactagagagctctcca 659
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179918159 cgcgatgagattctgggaagtgaaatgggctcaagatctcgaccactagagagctctcca 179918100

                                                                             
Query: 660       aggatgccctaccaggacctttgtcactggtgaactgtttcctccccaagattctttcca 719
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179918099 aggatgccctaccaggacctttgtcactggtgaactgtttcctccccaagattctttcca 179918040

                                                                             
Query: 720       gctgagctaagagatttctggagcctctcgccatggtcagaacatctcttgaatgaccag 779
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179918039 gctgagctaagagatttctggagcctctcgccatggtcagaacatctcttgaatgaccag 179917980

                                                                             
Query: 780       gaaatggggcttcctgtttaaatctctcgggcagagacaaggcagatgagcctgcctaag 839
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179917979 gaaatggggcttcctgtttaaatctctcgggcagagacaaggcagatgagcctgcctaag 179917920

                                                                             
Query: 840       tctttagaaagagctgtagggaaggccagagatggctcatcatgccaagatgtccactgt 899
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179917919 tctttagaaagagctgtagggaaggccagagatggctcatcatgccaagatgtccactgt 179917860

                                                                             
Query: 900       ggccgcacccagtgtgccagaggtctatggcagcgataggggttacctgggaatctaggg 959
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179917859 ggccgcacccagtgtgccagaggtctatggcagcgataggggttacctgggaatctaggg 179917800

                                                                             
Query: 960       ttggtattcggtgtgagtcttggtgaaagtgcccaggggaaaagttcccatgaagacagt 1019
                 ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
Sbjct: 179917799 ttggtattcggtgtgagtcttggtgaaagtgcccaggggaaaagttcccctgaagacagt 179917740

                                                                             
Query: 1020      gagtctaacagtggccaagtggcaccttcctgctgcctggcacacctgtaaaggtgagcc 1079
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179917739 gagtctaacagtggccaagtggcaccttcctgctgcctggcacacctgtaaaggtgagcc 179917680

                                                                             
Query: 1080      agggtcacagacaggagctggaggatgtcagtcacaaacaaatcaaaatagtgaaacaga 1139
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179917679 agggtcacagacaggagctggaggatgtcagtcacaaacaaatcaaaatagtgaaacaga 179917620

                                                                             
Query: 1140      aaacaaggggctgatgctgcacagttaaaacatatatatgttatagatcttgatagaact 1199
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179917619 aaacaaggggctgatgctgcacagttaaaacatatatatgttatagatcttgatagaact 179917560

                       
Query: 1200      ggaaag 1205
                 ||||||
Sbjct: 179917559 ggaaag 179917554



 Score =  999 bits (504), Expect = 0.0
 Identities = 529/538 (98%), Gaps = 1/538 (0%)
 Strand = Plus / Minus

                                                                             
Query: 1         gcttccaaatattggtcaagagctctaagtaggatgagccaaggatacagttaatgtaat 60
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179921824 gcttccaaatattggtcaagagctctaagtaggatgagccaaggatacagttaatgtaat 179921765

                                                                             
Query: 61        aggttcacacgatcaggtgacnnnnnnngggtctagaaatctgaggaggtgacgatgtac 120
                 |||||||||||||||||||||       ||||||||||||||||||||||||||||||||
Sbjct: 179921764 aggttcacacgatcaggtgactttttt-gggtctagaaatctgaggaggtgacgatgtac 179921706

                                                                             
Query: 121       tgaacggcagtcttcctgcgaggaaagagttaaaaacacatccagatcagggtttctgag 180
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179921705 tgaacggcagtcttcctgcgaggaaagagttaaaaacacatccagatcagggtttctgag 179921646

                                                                             
Query: 181       ggacaaggtgttcagcagggctgagggcctccctttctgccggctgctcccccacgcagc 240
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179921645 ggacaaggtgttcagcagggctgagggcctccctttctgccggctgctcccccacgcagc 179921586

                                                                             
Query: 241       aggggtgatgcggaccttccggtcctgctgagtgtgcttgaccaaaggtgacgatgacta 300
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179921585 aggggtgatgcggaccttccggtcctgctgagtgtgcttgaccaaaggtgacgatgacta 179921526

                                                                             
Query: 301       agggctaaggccgtgccctccctccctccaaatcgatcctttaatgtgacttatcagaaa 360
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179921525 agggctaaggccgtgccctccctccctccaaatcgatcctttaatgtgacttatcagaaa 179921466

                                                                             
Query: 361       gagaaagaactgtttactttcaaaccctggatcccataaagggagaggggcaaggcctaa 420
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179921465 gagaaagaactgtttactttcaaaccctggatcccataaagggagaggggcaaggcctaa 179921406

                                                                             
Query: 421       aaccctcacaagctcgaggcttggcccacacagcctgcagaactagggagcgcggaagac 480
                 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 179921405 aaccctcacaagctcgaggcttggcccacacagcctgcagaactagggagcgcggaagac 179921346

                                                                           
Query: 481       accatctcacgggcacagaaggggccctgggcccagagaagaccttcgcacactgcaa 538
                 |||||||||||| ||||||||||||||||||||||||||||||||||||| |||||||
Sbjct: 179921345 accatctcacggacacagaaggggccctgggcccagagaagaccttcgcatactgcaa 179921288


  Database: Sscrofa_10.2.fasta
    Posted date:  Nov 16, 2011 10:34 AM
  Number of letters in database: 2,808,509,378
  Number of sequences in database:  4582
  
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 Sequences: 4582
Number of Hits to DB: 36,762,710
Number of extensions: 321
Number of successful extensions: 321
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 321
Number of HSP's successfully gapped: 3
Length of query: 1218
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1197
Effective length of database: 2,808,413,156
Effective search space: 3361670547732
Effective search space used: 3361670547732
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 30 (60.0 bits)