TBLASTN 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= TR1
         (499 letters)

Database: genome.fa 
           218 sequences; 41,633,360 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_5                                                            268   9e-72
scaffold_35                                                            62   2e-14
scaffold_36                                                            57   6e-08
scaffold_23                                                            41   0.003
scaffold_2                                                             31   3.2  
scaffold_31                                                            30   5.5  
scaffold_7                                                             30   5.5  
scaffold_3                                                             30   7.2  
scaffold_28                                                            29   9.4  
scaffold_13                                                            29   9.4  

>scaffold_5 
          Length = 1613056

 Score =  268 bits (685), Expect = 9e-72
 Identities = 141/285 (49%), Positives = 181/285 (63%), Gaps = 33/285 (11%)
 Frame = +3

Query: 227     GFDQDMANKIGEHMEEHG-IKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYN 285
               GFD ++A KIG+HME H  +KF+RQ  P ++E+ E G     R+V   T + E +  E++
Sbjct: 1514796 GFDSEIAQKIGDHMERHAHVKFVRQATPDRIEKREDG-----RLVVHYTQNGEAVSDEFD 1514960

Query: 286     TVMLAIGRDACTRKIGLETVGVKINEKT-------------------------------- 313
               TV+ AIGRDACT  +GL+  GV++NE++                                
Sbjct: 1514961 TVLFAIGRDACTSTMGLDKAGVQLNERSVFFLIFRLHKTLHGDSTHGDVCTDGNTDTNSN 1515140

Query: 314     GKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTT 373
               GK+   + +QTNVP IYAIGD+LE K ELTPVAIQAG+LLA+RLY  S    DY+NV TT
Sbjct: 1515141 GKVVANEADQTNVPNIYAIGDVLEGKPELTPVAIQAGKLLARRLYGQSAALMDYQNVCTT 1515320

Query: 374     VFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNE 433
               VFTPLEYG CG SE+ A+++FGE+ IEV+H  F PLEWT+P R  N C+ K++   K  +
Sbjct: 1515321 VFTPLEYGCCGFSEDDALDQFGED-IEVFHQSFTPLEWTVPHRPENVCFCKLVVQ-KSTD 1515494

Query: 434     RVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEV 478
               RV+G H LGPNAGEVTQGF  ALK   TK Q D  +GIHP  AEV
Sbjct: 1515495 RVLGLHFLGPNAGEVTQGFGMALKLKATKAQFDDLVGIHPTVAEV 1515629



 Score =  147 bits (371), Expect(2) = 4e-55
 Identities = 69/114 (60%), Positives = 86/114 (75%)
 Frame = +2

Query: 100     RMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLI 159
               R+++ VQNHI SLNWGYRVALR+K V Y NAYG  +  H I   N +GKE++ +A++ ++
Sbjct: 1514084 RVMQLVQNHIRSLNWGYRVALRDKNVTYLNAYGSLLDAHTINTVNKRGKEQVITADKIIL 1514263

Query: 160     ATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIG 213
                 G RPRY  IPG KE+ I+SDD+FSL   PGKTLV+GASYVALECAGFLA  G
Sbjct: 1514264 CPGGRPRYPDIPGAKEFGITSDDIFSLDREPGKTLVIGASYVALECAGFLAAFG 1514425



 Score = 87.4 bits (215), Expect(2) = 4e-55
 Identities = 44/131 (33%), Positives = 61/131 (46%), Gaps = 35/131 (26%)
 Frame = +3

Query: 11      YDYDLIIIXXXXXXXXXXXXXXXXXXXVMVLDFVTPTPLGTRWGLGGTCVNV-------- 62
               +DYDL+++                     VLDFV P+P GT WGLGGTCVNV        
Sbjct: 1513590 FDYDLVVVGGGSGGLAASKEAASLGAKTAVLDFVQPSPQGTTWGLGGTCVNVRPESFFFI 1513769

Query: 63      ---------------------------GCIPKKLMHQAALLGQALQDSRNYGWKVEETVK 95
                                          GCIPKKLMHQAA++G  ++D+ ++GW ++   K
Sbjct: 1513770 LFIFLSHVKPAVVAYAGHQCAVGHD*VGCIPKKLMHQAAIIGHTIEDATSFGWDLQRPEK 1513949

Query: 96      HDWDRMIEAVQ 106
                +W  ++E VQ
Sbjct: 1513950 PNWSTLVEGVQ 1513982



 Score = 42.4 bits (98), Expect = 0.001
 Identities = 59/263 (22%), Positives = 97/263 (36%), Gaps = 73/263 (27%)
 Frame = +2

Query: 55      LGGTCVNVGCIPKKLMHQAA----LLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIG 110
               +GG C+NVGC+P K + +AA     L +A+ D    G  +E +VK D+++ +   +    
Sbjct: 1240493 VGGDCLNVGCVPSKALLKAAKTAHTLRKAIDDEAELGVSLEGSVKVDFEK-VRLSRADPA 1240669

Query: 111     SLNWGYRVA------------------------LREKKVVYENA---------------- 130
               S  W  RV                         LR +++  E A                
Sbjct: 1240670 SPGWSARVCTVMVPSPACSCGLINDFDLETQVMLRVRRLRAEIADADSVSRFADKLGVDV 1240849

Query: 131     ---YGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPG----------DKEYC 177
                   GQF+  + +      G+E  +   + +IATG  P    IPG           +   
Sbjct: 1240850 FLGAGQFVDRNTVVV---NGQELRFI--KCVIATGGSPALPDIPGLQAAYANQTQSQPVI 1241014

Query: 178     ISSDDLFSLPYCPGKTLVVGASYVALECAGFL-------AGIGLDVTVMVRSILLR---- 226
               +++++LF+    P +  V+GA  + +E A             GL V  +    L+R    
Sbjct: 1241015 LTNENLFNRTVLPPRLAVIGAGAIGMEMAQAFER*VRQPCSFGLHV*ALSLRTLMRVRFN 1241194

Query: 227     -----GFDQDMANKIGEHMEEHG 244
                    GF       IG H  + G
Sbjct: 1241195 TLR*LGFQSHGLGSIGAHSPQGG 1241263



 Score = 38.9 bits (89), Expect = 0.012
 Identities = 40/185 (21%), Positives = 77/185 (41%)
 Frame = +1

Query: 298     RKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRL 357
               R +  E   VK +   G I V D  Q++   I+A+GD+   + + T  +    R++ +  
Sbjct: 1241584 RSLNCEAADVKYDAVNG-IQVNDRLQSSNDAIFAVGDVCS-RYQFTHASDFMARMVVRNT 1241757

Query: 358     YAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRD 417
                     K     +P + +T  E    G   E    +  E   +VY       +  I   +
Sbjct: 1241758 LFFGGDKFSNLLIPWSTYTSPEVAHVGAYAEDLDAQ--EVAYDVYEKRLDSNDRCILEGE 1241931

Query: 418     NNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAE 477
                     +I+C  + +++++G  ++GPNAG++      A++  +    L S I  +P  A+
Sbjct: 1241932 TEGLI-RIVCK-RGSDKIIGATIVGPNAGDMISEITLAMQAEVGLGTLASVIHPYPTRAD 1242105

Query: 478     VFTTL 482
                   L
Sbjct: 1242106 AIRAL 1242120


>scaffold_35 
          Length = 432256

 Score = 61.6 bits (148), Expect(2) = 2e-14
 Identities = 46/180 (25%), Positives = 73/180 (40%), Gaps = 42/180 (23%)
 Frame = +3

Query: 55     LGGTCVNVGCIPKKLMH------------------------------------------Q 72
              +GGTCVNVGC+PKK+M+                                           
Sbjct: 293667 IGGTCVNVGCVPKKVMYVHLYFCIAGGRPAWLPFAQSGSKPDGSILYCSVLNLCCACRYY 293846

Query: 73     AALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYG 132
              AA + +AL D+++YG+ + +    DW  + +    +I  LN  Y   L +  +     + 
Sbjct: 293847 AATMSEALHDAKDYGFDITQHAPFDWPTLKKKRDAYIERLNGIYDRNLEKGNIEKIVGHA 294026

Query: 133    QFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGK 192
              +F+  + +     +     Y+A+  +IATG  P    IPG  E  I+SD  F L   P K
Sbjct: 294027 KFVDKNTVDVDGTQ-----YTADHIVIATGGYPTLPNIPG-AELGITSDGFFDLETLPKK 294188



 Score = 43.5 bits (101), Expect = 5e-04
 Identities = 28/62 (45%), Positives = 39/62 (62%)
 Frame = +2

Query: 283    EYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVEL 342
              E + V+ AIGR   + KI LE  GV+ + K G I V +++ T+ P IYA+GD+   K EL
Sbjct: 294869 ELDCVLFAIGRTPHS-KINLEAAGVQADAK-GYIQVDEDQNTSQPGIYALGDVC-GKYEL 295039

Query: 343    TP 344
              TP
Sbjct: 295040 TP 295045



 Score = 36.2 bits (82), Expect(2) = 2e-14
 Identities = 16/28 (57%), Positives = 21/28 (75%)
 Frame = +1

Query: 194    LVVGASYVALECAGFLAGIGLDVTVMVR 221
              LVVGA Y+A+E AG L  +G DVT+ +R
Sbjct: 294295 LVVGAGYIAVEMAGILNALGSDVTLSIR 294378



 Score = 35.8 bits (81), Expect = 0.10
 Identities = 14/26 (53%), Positives = 20/26 (76%)
 Frame = +2

Query: 381    GACGLSEEKAVEKFGEENIEVYHSYF 406
              G CG +E++A EKFG +NI+VY + F
Sbjct: 295358 GTCGFTEDEAREKFGSDNIKVYKATF 295435



 Score = 33.1 bits (74), Expect = 0.65
 Identities = 14/28 (50%), Positives = 18/28 (64%)
 Frame = +2

Query: 435    VVGFHVLGPNAGEVTQGFAAALKCGLTK 462
              VVG H++G    E+ QGF  A+K G TK
Sbjct: 295697 VVGLHMIGLGCDEMLQGFGVAMKMGATK 295780


>scaffold_36 
          Length = 406081

 Score = 56.6 bits (135), Expect = 6e-08
 Identities = 55/244 (22%), Positives = 101/244 (41%), Gaps = 36/244 (14%)
 Frame = +1

Query: 285   NTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTP 344
             + V++ +GR      +GL+ VG+K++ + G+I V D  +TNV  IYAIGD ++  + L  
Sbjct: 32824 DVVLVCVGRRPNVDALGLDKVGIKLDSR-GRIEVDDHFRTNVSNIYAIGDCIKGPM-LAH 32997

Query: 345   VAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHS 404
              A   G +  + +  G     DY  VP+ ++T  E    G +E++  E   E N+  +  
Sbjct: 32998 KAEDEGIICVEGMLGGHP-HIDYNCVPSVIYTHPEVAWVGQNEQQLKEAGIEYNVGTF-- 33168

Query: 405   YFWPLEWTIPSRDNNKCYAKI-ICNTKDNERVVGFHVLGP-------------------- 443
                P+     ++ N+     + + + K  +R++G  ++                      
Sbjct: 33169 ---PMSANSRAKCNDDTDGLMKVLSDKKTDRILGVFMINKVRQP*RSPLYLDRCPMLLLV 33339

Query: 444   ---------------NAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRS 488
                             AGE+    A A++ G + + +      HP  AE F   ++    
Sbjct: 33340 LVHAHIHLPPPFPF*TAGEMINEAALAMEYGASAEDVARVCHAHPTEAEAFREAALAAYC 33519

Query: 489   GASI 492
             G SI
Sbjct: 33520 GKSI 33531



 Score = 36.2 bits (82), Expect = 0.077
 Identities = 19/37 (51%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
 Frame = +1

Query: 52    RWGLGGTCVNVGCIP-KKLMHQAALLGQALQDSRNYG 87
             R  LGGTC+NVGCIP K L++ + L  QA  D    G
Sbjct: 31762 RGKLGGTCLNVGCIPSKSLLNNSHLYHQAQHDFAQRG 31872


>scaffold_23 
          Length = 690264

 Score = 40.8 bits (94), Expect = 0.003
 Identities = 49/219 (22%), Positives = 91/219 (41%), Gaps = 10/219 (4%)
 Frame = +2

Query: 146    KGKEKIYSAERFLIATGERPRYLGIPGDKEY-------CISSDDLFSLPYCPGKTLVVGA 198
              K  ++  +A+  ++ATG   R L  PG   +       C   D    + Y     +V+G 
Sbjct: 220694 KSGDRTVTADTVIVATGAVARRLHFPGADTFWQRGISACAVCDGAAPI-YRNKPLIVIGG 220870

Query: 199    SYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEH--MEEHGIKFIRQFVPIKV 256
                 A+E A FL      V ++ R       D+  A+KI ++  M    ++F+     +  
Sbjct: 220871 GDSAMEEATFLTKYASKVYIVHRR------DELRASKIMQNRAMNNPKVEFV-----LSA 221017

Query: 257    EQIEA-GTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGK 315
              E +EA G       + +   + E  E E N +  AIG +  +  +  +   ++++E    
Sbjct: 221018 EVVEARGDKLMTSAIIEDKKTGEKREVEANGIFFAIGHEPASAFLNGQ---LELDEDRYI 221188

Query: 316    IPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLA 354
              +   D   T++P ++A GD+ + K      A   G + A
Sbjct: 221189 VTKPDSTATSIPGVFACGDVQDKKYRQAITAAGTGCMSA 221305


>scaffold_2 
          Length = 3607471

 Score = 30.8 bits (68), Expect = 3.2
 Identities = 16/57 (28%), Positives = 30/57 (52%)
 Frame = +3

Query: 53     WGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHI 109
              WG G   VN+GC  K   H   L+  A+ + +    KV  +++H ++  +E +Q+ +
Sbjct: 525924 WGKGSPYVNLGCRGKHATHGQQLVQLAI-NLKGRNIKVHMSLRHKFECRLEKLQSRL 526091


>scaffold_31 
          Length = 566198

 Score = 30.0 bits (66), Expect = 5.5
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
 Frame = -1

Query: 264    PGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQ 323
              PG+   V  ST     +EG   T+ L +G   C     L     K+ ++  K   TD   
Sbjct: 211247 PGQPARVCSSTMHTSSLEGFATTMTLRVGHKCCLP--SLPASSAKMLDEHMKRQRTDLIL 211074

Query: 324    TNVPYIYA---IGDILEDKVEL 342
              + +PY+YA   +G  + D++ L
Sbjct: 211073 SCLPYLYAGVGVGTAVLDRINL 211008


>scaffold_7 
          Length = 1435906

 Score = 30.0 bits (66), Expect = 5.5
 Identities = 12/25 (48%), Positives = 15/25 (60%)
 Frame = +3

Query: 64     CIPKKLMHQAALLGQALQDSRNYGW 88
              C PK   HQA   GQAL++   +GW
Sbjct: 228723 CTPKPRQHQARGKGQALENGGEHGW 228797


>scaffold_3 
          Length = 2609234

 Score = 29.6 bits (65), Expect = 7.2
 Identities = 11/39 (28%), Positives = 20/39 (51%)
 Frame = +1

Query: 158    LIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVV 196
              L+++  +  +L +P    YC S D +  L +CP   L +
Sbjct: 667297 LVSSASKKTFLVLPHQSRYCFSIDSIKILSFCPRSQLTL 667413


>scaffold_28 
          Length = 614053

 Score = 29.3 bits (64), Expect = 9.4
 Identities = 14/44 (31%), Positives = 20/44 (45%)
 Frame = +1

Query: 408   PLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQG 451
             P+ WT   R  NK ++  + N  D E    FH  G  A  ++ G
Sbjct: 84031 PMRWTPTLRQTNKIWSHRLANNSDMEMPSSFHSDGAGAHLLSAG 84162


>scaffold_13 
          Length = 1102880

 Score = 29.3 bits (64), Expect = 9.4
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
 Frame = -2

Query: 177    CISSDDLFSLPYCPGKTLVVGASYVA----LECAGFLAGIGLDVTVMVRSILLRGFDQD 231
              C    D+++L  CPGKT  +  ++      L+ +G+L G+ +D  +   S      D D
Sbjct: 866779 CQRDVDMYTLSLCPGKTASLAMTFDTLAGDLDVSGYLNGVLVDADLGTGSYNFLAIDAD 866603


  Database: genome.fa
    Posted date:  Jan 19, 2010  5:06 PM
  Number of letters in database: 41,633,360
  Number of sequences in database:  218
  
Lambda     K      H
   0.319    0.138    0.417 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,609,519
Number of Sequences: 218
Number of extensions: 395970
Number of successful extensions: 1674
Number of sequences better than 10.0: 11
Number of HSP's better than 10.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1429
Number of HSP's gapped (non-prelim): 544
length of query: 499
length of database: 13,877,786
effective HSP length: 106
effective length of query: 393
effective length of database: 13,854,678
effective search space: 5444888454
effective search space used: 5444888454
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: 41 (21.7 bits)
S2: 64 (29.3 bits)
