Animal-Genome cDNA 20110601C-001845

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-001845
         (1241 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001074392.1| MHC cell surface glycoprotein [Bos taurus].       396   e-110
Alignment   gi|NP_001029840.2| boLa class II histocompatibility antigen, DQ...   387   e-107
Alignment   gi|NP_001012694.2| major histocompatibility complex, class II, ...   368   e-102
Alignment   gi|NP_001012697.1| major histocompatibility complex, class II, ...   297   1e-80
Alignment   gi|NP_001012698.2| major histocompatibility complex, class II, ...   294   1e-79
Alignment   gi|XP_001253929.2| PREDICTED: major histocompatibility complex,...   282   5e-76
Alignment   gi|XP_002697362.1| PREDICTED: histocompatibility complex, class...   268   7e-72
Alignment   gi|XP_582099.3| PREDICTED: histocompatibility complex, class II...   268   7e-72
Alignment   gi|NP_001013618.1| major histocompatibility complex, class II, ...   255   6e-68
Alignment   gi|NP_001077254.1| MHC class II antigen DS beta [Bos taurus].        251   9e-67

>ref|NP_001074392.1| MHC cell surface glycoprotein [Bos taurus].
          Length = 261

 Score =  396 bits (1017), Expect = e-110
 Identities = 191/261 (73%), Positives = 217/261 (83%)
 Frame = +1

Query: 76  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVA 255
           MSGMVAL +PRGLW AAV V+LVVL  P AEGRDSPQDF+ QF G+CYF NGT+RVR V 
Sbjct: 1   MSGMVALWIPRGLWIAAVMVILVVLSTPGAEGRDSPQDFLVQFLGQCYFTNGTERVRSVT 60

Query: 256 RWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEG 435
           R++YN+EEYVRFDSDV E+RAVTPLG P+A+YWN Q+D+LE++RAEVD VC+HNYQ+E  
Sbjct: 61  RYIYNREEYVRFDSDVNEYRAVTPLGRPSAEYWNSQEDILERVRAEVDTVCRHNYQLELI 120

Query: 436 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 615
           T+LQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYP Q+KV+WFRN QEETAGVVSTPLI
Sbjct: 121 TSLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETAGVVSTPLI 180

Query: 616 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 795
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGVGGFVL 240

Query: 796 XXXXXXXXXXXRHRSQKGLVR 858
                       HRSQKGL+R
Sbjct: 241 GLIFLGLGLIVHHRSQKGLMR 261


>ref|NP_001029840.2| boLa class II histocompatibility antigen, DQB*0101 beta chain
           precursor [Bos taurus].
          Length = 261

 Score =  387 bits (993), Expect = e-107
 Identities = 190/261 (72%), Positives = 211/261 (80%)
 Frame = +1

Query: 76  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVA 255
           MSGMVAL +PRGLWTA V V LV+L  P AEGRDSP+DFV QFKG CYF NGT+RVR V 
Sbjct: 1   MSGMVALWIPRGLWTAVVMVTLVMLSTPGAEGRDSPKDFVVQFKGLCYFTNGTERVRYVT 60

Query: 256 RWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEG 435
           R++YNQEEYVRFDSD   +RA+TPLG P A+YWN QKD LEQ RAE D VC+HNYQ E  
Sbjct: 61  RYIYNQEEYVRFDSDWDLYRALTPLGRPDAEYWNSQKDFLEQTRAEADTVCRHNYQAELI 120

Query: 436 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 615
           T+LQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYPSQ+KV+WFRN +EETAGVVSTPLI
Sbjct: 121 TSLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPSQIKVRWFRNDREETAGVVSTPLI 180

Query: 616 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 795
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH SLQSPI+VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPIMVEWRAQSESAQSKMLSGVGGFVL 240

Query: 796 XXXXXXXXXXXRHRSQKGLVR 858
                       HRSQKGL+R
Sbjct: 241 GLIFLGLGLIIHHRSQKGLMR 261


>ref|NP_001012694.2| major histocompatibility complex, class II, DQ beta [Bos taurus].
          Length = 261

 Score =  368 bits (945), Expect = e-102
 Identities = 181/260 (69%), Positives = 207/260 (79%)
 Frame = +1

Query: 76  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVA 255
           MSGMVAL +PRGLWTAAV V L VL  P AEGRDSPQD V  F  +CYF NGT+RVR V 
Sbjct: 1   MSGMVALWIPRGLWTAAVMVTLAVLSTPGAEGRDSPQDTVVHFMCQCYFTNGTERVRYVT 60

Query: 256 RWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEG 435
           R++YNQEE   +DSDVGE+RAVT LG   A+YWN QKD+LEQ RAE+D VC+HNYQ+E  
Sbjct: 61  RYIYNQEETAYYDSDVGEYRAVTQLGRTLAEYWNSQKDILEQTRAELDTVCRHNYQLEVI 120

Query: 436 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 615
           T+LQR+V+PTVTIS S+ EALNHHNLLVC+VTDFYP Q+KV+WF+NG+EETAG+VSTPLI
Sbjct: 121 TSLQRQVEPTVTISLSRTEALNHHNLLVCSVTDFYPGQIKVRWFQNGKEETAGIVSTPLI 180

Query: 616 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 795
           RNGDWT+Q+LVMLEM  +RGDVYTCRVEH SLQSPI VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPKRGDVYTCRVEHPSLQSPISVEWRAQSESAQSKMLSGVGGFVL 240

Query: 796 XXXXXXXXXXXRHRSQKGLV 855
                      R RSQKGL+
Sbjct: 241 GLIFLGLGLIVRRRSQKGLM 260


>ref|NP_001012697.1| major histocompatibility complex, class II, DY beta [Bos taurus].
          Length = 259

 Score =  297 bits (760), Expect = 1e-80
 Identities = 149/227 (65%), Positives = 174/227 (76%), Gaps = 2/227 (0%)
 Frame = +1

Query: 100 LPRGLWTAAVTVMLV--VLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQ 273
           +PR   T A  VM V  VL  P A  RD+P++FVYQFKG CYF NGT+ VR VAR +YN+
Sbjct: 5   IPRNPGTVAGMVMAVFLVLRIPEAHCRDAPKNFVYQFKGMCYFTNGTEHVRLVARQIYNK 64

Query: 274 EEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRR 453
           EE + FDSD+GEF AVT LG   A+ WN QKD+L + RA VD +C+HNY+   G T+QRR
Sbjct: 65  EEILHFDSDLGEFVAVTELGRVCAEIWNTQKDLLAEFRAYVDTLCRHNYKETAGFTVQRR 124

Query: 454 VQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWT 633
           V+PTVT+SP+  EALNHHNLLVC+VTDFYP QVKV+WFRN QE+TAGV  TPL +NGDWT
Sbjct: 125 VEPTVTVSPASTEALNHHNLLVCSVTDFYPRQVKVKWFRNQQEQTAGVGFTPLTQNGDWT 184

Query: 634 YQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 774
           YQ+ VMLE   Q GDVY C V+H SLQSPI VEWRAQSESAQSKM S
Sbjct: 185 YQIHVMLETVPQLGDVYVCHVDHPSLQSPITVEWRAQSESAQSKMQS 231


>ref|NP_001012698.2| major histocompatibility complex, class II, DRB3 [Bos taurus].
          Length = 266

 Score =  294 bits (753), Expect = 1e-79
 Identities = 145/255 (56%), Positives = 179/255 (70%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           MV L    G W AA+ VML+VL  P+A  R+    F+  +KGEC+F+NGT+RVR + R  
Sbjct: 1   MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKGECHFFNGTERVRFLDRHF 60

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           YN EE+VRFDSD GEFRAVT LG P A++WN QKD LEQ RAEVDRVC+HNY   E  T+
Sbjct: 61  YNGEEFVRFDSDWGEFRAVTELGRPAAEHWNSQKDFLEQKRAEVDRVCRHNYGGVESFTV 120

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
           QRRV+PTVT+ P+K + L HHNLLVC+V  FYP  ++V+WFRNG EE AGV+ST LI+NG
Sbjct: 121 QRRVEPTVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 804
           DWT+Q +VMLE   Q G+VYTC+V+H    SPI VEWRA+S+SAQSKM+S          
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVDHPKRTSPITVEWRARSDSAQSKMMSGVGGFVLGLL 240

Query: 805 XXXXXXXXRHRSQKG 849
                     R+QKG
Sbjct: 241 FLAVGLFIYFRNQKG 255


>ref|XP_001253929.2| PREDICTED: major histocompatibility complex, class II, DR beta
           3-like [Bos taurus].
          Length = 266

 Score =  282 bits (721), Expect = 5e-76
 Identities = 140/255 (54%), Positives = 175/255 (68%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           MV L    G W AA+ VML+VL  P+A  R+    F+  +K EC+F+NGT+RVR + R+ 
Sbjct: 1   MVCLYFSGGSWMAALIVMLMVLCPPLAWAREIQPHFLEYYKRECHFFNGTERVRFLDRYF 60

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           +N EEYVRFDSD GE+RAVT LG   A+Y N QKD LE+ RA VD  C+HNY + E  T+
Sbjct: 61  HNGEEYVRFDSDWGEYRAVTELGQRVAEYCNSQKDFLERARAAVDTYCRHNYGVGESFTV 120

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
           QRRV+P VT+ P+K + L HHNLLVC+V  FYP  ++V+WFRNG EE AGV+ST LI+NG
Sbjct: 121 QRRVEPIVTVYPAKTQPLQHHNLLVCSVNGFYPGHIEVRWFRNGHEEEAGVISTGLIQNG 180

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 804
           DWT+Q +VMLE   Q G+VYTC+VEH S  SPI VEWRAQS+SAQSKM+S          
Sbjct: 181 DWTFQTMVMLETVPQSGEVYTCQVEHPSRTSPITVEWRAQSDSAQSKMMSGVRVFALGLL 240

Query: 805 XXXXXXXXRHRSQKG 849
                     R+QKG
Sbjct: 241 FLVVGLFTHFRNQKG 255


>ref|XP_002697362.1| PREDICTED: histocompatibility complex, class II, DR beta 2 [Bos
           taurus].
          Length = 365

 Score =  268 bits (685), Expect = 7e-72
 Identities = 131/243 (53%), Positives = 168/243 (69%)
 Frame = +1

Query: 121 AAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEEYVRFDSD 300
           AA+ V+L+VL  P +  R++   F++QFKGEC F NG +R+R  AR++YN +E V FDSD
Sbjct: 2   AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDSD 61

Query: 301 VGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPTVTISP 480
           VGEF A+T LG   A+YWN QKD +EQMRA+VD +C+ NYQ       QRRV+PTVT+ P
Sbjct: 62  VGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVYP 121

Query: 481 SKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEM 660
           +K + L HHNLLVC+V  FYP  ++V+WF N  EE AGV+ST LI+NGDWT+Q +VMLE 
Sbjct: 122 AKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLET 181

Query: 661 NLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXRHRS 840
             Q G+VYTC+VEH S  SP+ VEWRAQS+SAQSKM+S                    R+
Sbjct: 182 VPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQSKMMSGTGGFALGLLFLVVGLFTHFRN 241

Query: 841 QKG 849
           QKG
Sbjct: 242 QKG 244


>ref|XP_582099.3| PREDICTED: histocompatibility complex, class II, DR beta 2 [Bos
           taurus].
          Length = 365

 Score =  268 bits (685), Expect = 7e-72
 Identities = 131/243 (53%), Positives = 168/243 (69%)
 Frame = +1

Query: 121 AAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEEYVRFDSD 300
           AA+ V+L+VL  P +  R++   F++QFKGEC F NG +R+R  AR++YN +E V FDSD
Sbjct: 2   AALAVLLMVLSLPFSWARETQPHFIHQFKGECRFSNGLERMRFFARYIYNTQEDVHFDSD 61

Query: 301 VGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPTVTISP 480
           VGEF A+T LG   A+YWN QKD +EQMRA+VD +C+ NYQ       QRRV+PTVT+ P
Sbjct: 62  VGEFTALTELGRLDAEYWNQQKDFMEQMRAKVDTLCRSNYQGIGSFLRQRRVEPTVTVYP 121

Query: 481 SKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEM 660
           +K + L HHNLLVC+V  FYP  ++V+WF N  EE AGV+ST LI+NGDWT+Q +VMLE 
Sbjct: 122 AKTQPLQHHNLLVCSVNGFYPGHIEVRWFWNSHEEEAGVISTGLIQNGDWTFQTMVMLET 181

Query: 661 NLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXRHRS 840
             Q G+VYTC+VEH S  SP+ VEWRAQS+SAQSKM+S                    R+
Sbjct: 182 VPQSGEVYTCQVEHPSRTSPLTVEWRAQSDSAQSKMMSGTGGFALGLLFLVVGLFTHFRN 241

Query: 841 QKG 849
           QKG
Sbjct: 242 QKG 244


>ref|NP_001013618.1| major histocompatibility complex, class II, DO beta [Bos taurus].
          Length = 271

 Score =  255 bits (651), Expect = 6e-68
 Identities = 120/220 (54%), Positives = 154/220 (70%)
 Frame = +1

Query: 115 WTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEEYVRFD 294
           W        + L A V +GRDSP+DFV Q K +CYF NGT++VR V R+++N E+Y RFD
Sbjct: 8   WVVTFLSTALRLDASVTQGRDSPEDFVTQAKADCYFTNGTEKVRFVVRFIFNLEDYARFD 67

Query: 295 SDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPTVTI 474
           SD+G F A+T LG P A+ WN + D+L + RA VD +C+ NY +    T+ RRVQP VT+
Sbjct: 68  SDLGMFVALTELGKPDAERWNNRPDILARSRASVDMLCRRNYYLGAPFTVGRRVQPEVTV 127

Query: 475 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 654
            P K  AL H NLL+C VT FYP  +KV WFRNGQE+  G++ST LIRNGDWT+Q+ VML
Sbjct: 128 YPEKTPALQHRNLLLCLVTGFYPGDIKVTWFRNGQEQREGIMSTGLIRNGDWTFQMTVML 187

Query: 655 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 774
            M  + G+VYTC V+H SL SP+ VEWRAQSE +  K+LS
Sbjct: 188 AMTPELGEVYTCLVDHPSLLSPVSVEWRAQSEYSWRKILS 227


>ref|NP_001077254.1| MHC class II antigen DS beta [Bos taurus].
          Length = 260

 Score =  251 bits (641), Expect = 9e-67
 Identities = 124/230 (53%), Positives = 160/230 (69%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           MV L  P G WT  + V+L+VL   +A   ++   F+ Q K EC+F NGTQ+VR + R++
Sbjct: 1   MVCLWFPPGSWTVILPVILMVLSPLLAWAGNTRTFFMVQGKSECHFSNGTQQVRFLDRYI 60

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           YN+EE V+FDS VGE+RA T +G P A+ WN     L++ RA V   C  NY+     T+
Sbjct: 61  YNREEQVQFDSLVGEYRARTEMGRPAAERWNRWPQALQRARAAVHAFCASNYEFFASRTV 120

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
           QRRVQPTVT+ P K+  L HHNLLVC+V  FYP  ++V+WFRNGQE+ AGVVST LI NG
Sbjct: 121 QRRVQPTVTVYPVKSRPLWHHNLLVCSVNGFYPGHIEVRWFRNGQEKEAGVVSTGLIPNG 180

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 774
           DWT+Q++VMLE+  Q G+VY C VEH S  SP+ VEWRAQ +S+Q KMLS
Sbjct: 181 DWTFQIMVMLEIVPQGGEVYACHVEHPSRMSPVSVEWRAQDKSSQEKMLS 230


  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: 49,248,370
Number of extensions: 1418481
Number of successful extensions: 6244
Number of sequences better than 1.0e-05: 68
Number of HSP's gapped: 6186
Number of HSP's successfully gapped: 68
Length of query: 413
Length of database: 17,681,374
Length adjustment: 105
Effective length of query: 308
Effective length of database: 14,207,134
Effective search space: 4375797272
Effective search space used: 4375797272
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)

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-001845
         (1241 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_001014403.1| major histocompatibility complex, class II, ...   380   e-105
Alignment   gi|NP_001014768.1| DLA class II histocompatibility antigen, DR-...   305   8e-83
Alignment   gi|NP_001041592.1| major histocompatibility complex, class II, ...   266   3e-71
Alignment   gi|XP_849737.1| PREDICTED: similar to HLA class II histocompati...    72   8e-13
Alignment   gi|NP_001011723.1| MHC class II DR alpha chain [Canis lupus fam...    69   9e-12
Alignment   gi|XP_850803.1| PREDICTED: similar to HLA class II histocompati...    68   2e-11
Alignment   gi|XP_536867.2| PREDICTED: similar to Zinc-alpha-2-glycoprotein...    65   2e-10
Alignment   gi|NP_001011726.1| major histocompatibility complex, class II, ...    65   2e-10
Alignment   gi|XP_855624.1| PREDICTED: MHC class Ib [Canis familiaris].           64   3e-10
Alignment   gi|NP_001018646.1| MHC class Ib [Canis lupus familiaris].             64   3e-10

>ref|NP_001014403.1| major histocompatibility complex, class II, DQ beta 1 [Canis lupus
           familiaris].
          Length = 269

 Score =  380 bits (975), Expect = e-105
 Identities = 182/258 (70%), Positives = 211/258 (81%)
 Frame = +1

Query: 76  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVA 255
           MSG + L +PRG WTAAV ++LVVL  PVAEGRDSPQDFV+Q+K ECYF NGT+RVR + 
Sbjct: 1   MSGKMTLCIPRGFWTAAVMMILVVLSIPVAEGRDSPQDFVFQYKAECYFTNGTERVRLLT 60

Query: 256 RWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEG 435
           +++YN+EE+VRFDSDVGEFRAVT LG P A+YWN QKD ++++RAE+D VC+HNY  EE 
Sbjct: 61  KYIYNREEFVRFDSDVGEFRAVTELGRPDAEYWNRQKDEMDRVRAELDTVCRHNYGREEL 120

Query: 436 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 615
           TTLQRRV+PTVTI PSK E LNHHNLLVC+VTDFYP Q+KV+WFRN QE+TAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTIFPSKTEVLNHHNLLVCSVTDFYPGQIKVRWFRNDQEQTAGVVSTPLI 180

Query: 616 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 795
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH+SLQSPI V+WRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHASLQSPITVQWRAQSESAQSKMLSGIGGFVL 240

Query: 796 XXXXXXXXXXXRHRSQKG 849
                      RHRSQKG
Sbjct: 241 GLIFLGLGLIIRHRSQKG 258


>ref|NP_001014768.1| DLA class II histocompatibility antigen, DR-1 beta chain precursor
           [Canis lupus familiaris].
          Length = 266

 Score =  305 bits (780), Expect = 8e-83
 Identities = 149/255 (58%), Positives = 183/255 (71%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           MV L    G W  A+ ++L+VL  P A  RD+P  F+   K ECYF NGT+RVR V R++
Sbjct: 1   MVCLCFLGGSWMTALMLILMVLNPPFAWARDTPPHFLEVAKSECYFTNGTERVRFVERYI 60

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           +N+EE+VRFDSDVGEFRAVT LG P A+ WNGQK++LEQ RA VD  C+HNY + E  T+
Sbjct: 61  HNREEFVRFDSDVGEFRAVTELGRPVAESWNGQKEILEQERATVDTYCRHNYGVIESFTV 120

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
           QRRV+PTVT+ P+K + L HHNLLVC+V  FYP  ++V+W RNGQEE AGVVST LIRNG
Sbjct: 121 QRRVEPTVTVYPTKTQTLQHHNLLVCSVNGFYPGHIEVRWLRNGQEEEAGVVSTGLIRNG 180

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 804
           DWT+Q+LVMLE+  Q G+VYTC+VEH SL SP+ VEWRAQS+SAQSKMLS          
Sbjct: 181 DWTFQILVMLEIVPQSGEVYTCQVEHPSLTSPVTVEWRAQSDSAQSKMLSGIGGFVLGLL 240

Query: 805 XXXXXXXXRHRSQKG 849
                     R+QKG
Sbjct: 241 FLAVGLFIYFRNQKG 255


>ref|NP_001041592.1| major histocompatibility complex, class II, DO beta [Canis lupus
           familiaris].
          Length = 270

 Score =  266 bits (680), Expect = 3e-71
 Identities = 127/247 (51%), Positives = 166/247 (67%)
 Frame = +1

Query: 115 WTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEEYVRFD 294
           W  A+ V +  L + + +GRDSP+DFV Q K +CYF NGT++V+ V R+++N EEY RFD
Sbjct: 8   WMLALLVNVTGLDSSMTQGRDSPEDFVIQAKADCYFINGTEKVQFVVRFIFNLEEYARFD 67

Query: 295 SDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPTVTI 474
           S VG F A+T LG P A+ WN Q  +LE+ RA VD +C+HNY++    T+ R+VQP VT+
Sbjct: 68  SHVGMFVALTELGKPDAELWNSQPGILERSRASVDLLCRHNYELGAPFTVGRKVQPEVTV 127

Query: 475 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 654
            P +  ++ HHNLL+C+VT FYP  +K++WFRNGQEE  GV+ST LIRNGDWT+Q +VML
Sbjct: 128 YPERTPSMQHHNLLLCSVTGFYPGDIKIKWFRNGQEERVGVMSTGLIRNGDWTFQTMVML 187

Query: 655 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXXXXXRH 834
           EM  + GDVYTC V H SL SP+ VEWRAQS  +  KMLS                    
Sbjct: 188 EMTPELGDVYTCLVNHPSLLSPVSVEWRAQSTYSWRKMLSGIAAFLLGLIFLLVGTVICL 247

Query: 835 RSQKGLV 855
           R+QKG V
Sbjct: 248 RAQKGYV 254


>ref|XP_849737.1| PREDICTED: similar to HLA class II histocompatibility antigen, DM
           beta chain precursor (MHC class II antigen DMB) [Canis
           familiaris].
          Length = 263

 Score = 72.4 bits (176), Expect = 8e-13
 Identities = 53/187 (28%), Positives = 82/187 (43%), Gaps = 1/187 (0%)
 Frame = +1

Query: 178 SPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWN 357
           +P+DF Y     C  +N       +  W  ++ + V +     EF  +  L    +DY N
Sbjct: 36  TPKDFTY-----CVSFNKDL----LTCWDPDEAKMVPY-----EFGTLNVLANYLSDYLN 81

Query: 358 GQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDF 537
            Q++ L Q  +   + C  + Q   G+   R   PTV ++ S         +L C V  F
Sbjct: 82  -QQEYLHQRLSNGLQDCATHTQSFWGSLTHRTRPPTVQVAKSTPFNTKESVMLACYVWGF 140

Query: 538 YPSQVKVQWFRNGQEETAGVVSTPLIR-NGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQ 714
           YP+ V + W +NGQ   +   +  + + NGDWTYQ +  L       D YTC VEH    
Sbjct: 141 YPADVTISWRKNGQPVPSHSSALNMAQPNGDWTYQTVSHLATTPSYEDTYTCVVEHIGAP 200

Query: 715 SPILVEW 735
            P+  +W
Sbjct: 201 EPVCEDW 207


>ref|NP_001011723.1| MHC class II DR alpha chain [Canis lupus familiaris].
          Length = 254

 Score = 68.9 bits (167), Expect = 9e-12
 Identities = 59/217 (27%), Positives = 86/217 (39%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           M  L  P+  W  AV    V++ A      D   +F++ F G+  F+   ++       V
Sbjct: 14  MAFLMGPQESW--AVKEEHVIIQAEFYLTPDPSGEFMFDFDGDEIFHVDMEK----KETV 67

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           +  EE+ RF S    F A   L     D            +A +D + K +       T 
Sbjct: 68  WRLEEFGRFAS----FEAQGALANIAVD------------KANLDTMIKRSNH-----TP 106

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
              V P VT+  +    L   N+L+C +  F P  + V W RNG   T GV  T  +   
Sbjct: 107 NTNVPPEVTVLSNTPVELGEPNILICFIDKFSPPVINVTWLRNGNPVTTGVSETIFLPRE 166

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 735
           D  ++    L       DVY C+VEH  L  P+L  W
Sbjct: 167 DHLFRKFHYLPFLPSAEDVYDCKVEHWGLDEPLLKHW 203


>ref|XP_850803.1| PREDICTED: similar to HLA class II histocompatibility antigen, DO
           alpha chain precursor (MHC class II antigen DOA) (MHC DZ
           alpha) (MHC DN-alpha) isoform 11 [Canis familiaris].
          Length = 227

 Score = 67.8 bits (164), Expect = 2e-11
 Identities = 33/104 (31%), Positives = 48/104 (46%)
 Frame = +1

Query: 433 GTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPL 612
           GT L   + P V + P     L   N+L+C V + +P  + + W RNGQ  + GV  T  
Sbjct: 81  GTHLSSPLPPRVAVLPKFRVELGQPNVLICIVDNIFPPVINITWLRNGQIISEGVAQTSF 140

Query: 613 IRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 744
               D  ++    L       D+Y C+VEH  L+ P+L  W  Q
Sbjct: 141 YSQPDHLFRKFCYLTFVPSAEDMYDCKVEHWGLEEPLLRHWEPQ 184


>ref|XP_536867.2| PREDICTED: similar to Zinc-alpha-2-glycoprotein precursor
           (Zn-alpha-2-glycoprotein) (Zn-alpha-2-GP) [Canis
           familiaris].
          Length = 315

 Score = 64.7 bits (156), Expect = 2e-10
 Identities = 47/168 (27%), Positives = 83/168 (49%), Gaps = 8/168 (4%)
 Frame = +1

Query: 256 RWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQ--IE 429
           R+ Y+   ++ F+ ++  +    P  L T   W  ++  +++ +A ++  C    Q  +E
Sbjct: 136 RYAYDGRNFIEFNKEIPAWVPQDPAALNTKKKWEAEEVYVQRAKAYLEEECPVMLQRYLE 195

Query: 430 EGTT-LQRRVQPTVTI-SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFR--NGQEETAGV 597
            G T L R+  P+V+I S    E +     L C V+ FYP ++ + W +  + QE  +G 
Sbjct: 196 YGKTYLDRQEPPSVSITSHGTPEGIQ---TLKCWVSGFYPQEIDLHWIQADDTQETKSGG 252

Query: 598 VSTPLIRNGDWTYQVLVMLEMNLQ--RGDVYTCRVEHSSLQSPILVEW 735
              P   +G+ TYQ  V++  + Q      Y+C V+HSSL  P+ V W
Sbjct: 253 ALLP---SGNNTYQAWVVMSASPQDLASFSYSCLVKHSSLSQPLTVLW 297


>ref|NP_001011726.1| major histocompatibility complex, class II, DQ alpha [Canis lupus
           familiaris].
          Length = 255

 Score = 64.7 bits (156), Expect = 2e-10
 Identities = 30/103 (29%), Positives = 46/103 (44%)
 Frame = +1

Query: 460 PTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQ 639
           P VT+       L   N L+C V + +P  + V W +N    T GV  T     GD ++ 
Sbjct: 113 PEVTVFSKSPVMLGQPNTLICLVDNIFPPVINVTWLKNRHSVTEGVSETSFFAKGDHSFS 172

Query: 640 VLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKM 768
            +  L       D+Y C+VEH  L  P+L  W  +  +  S++
Sbjct: 173 KISYLTFLPSAEDIYDCKVEHWGLDEPLLKHWEPEVPTPMSEL 215


>ref|XP_855624.1| PREDICTED: MHC class Ib [Canis familiaris].
          Length = 381

 Score = 63.9 bits (154), Expect = 3e-10
 Identities = 42/173 (24%), Positives = 71/173 (41%), Gaps = 2/173 (1%)
 Frame = +1

Query: 241 VRGVARWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKH-- 414
           +RG  R  Y+  +Y+    D+  +    P+   T   W+    V E  +  ++  C    
Sbjct: 140 LRGYQRHAYDGLDYITLSEDLRSWIVEDPVAQITRRKWDAAT-VAENRKNFLEGRCLEWL 198

Query: 415 NYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAG 594
              +E G    +R  P  T S ++     H   L C    FYP+++ + W R+G+++T  
Sbjct: 199 RRHLENGRETLQRADPPKT-SVTRRPISEHEVTLKCWALGFYPAEITLTWQRDGEDQTQD 257

Query: 595 VVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSES 753
                    GD T+Q    + +       YTC + H SL  PI + W    +S
Sbjct: 258 TELVETRPGGDGTFQKWAAVVVPSGEEQRYTCHILHKSLPKPITLRWEPPPQS 310


>ref|NP_001018646.1| MHC class Ib [Canis lupus familiaris].
          Length = 381

 Score = 63.9 bits (154), Expect = 3e-10
 Identities = 42/173 (24%), Positives = 71/173 (41%), Gaps = 2/173 (1%)
 Frame = +1

Query: 241 VRGVARWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKH-- 414
           +RG  R  Y+  +Y+    D+  +    P+   T   W+    V E  +  ++  C    
Sbjct: 140 LRGYQRHAYDGLDYITLSEDLRSWIVEDPVAQITRRKWDAAT-VAENRKNFLEGRCLEWL 198

Query: 415 NYQIEEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAG 594
              +E G    +R  P  T S ++     H   L C    FYP+++ + W R+G+++T  
Sbjct: 199 RRHLENGRETLQRADPPKT-SVTRRPISEHEVTLKCWALGFYPAEITLTWQRDGEDQTQD 257

Query: 595 VVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSES 753
                    GD T+Q    + +       YTC + H SL  PI + W    +S
Sbjct: 258 TELVETRPGGDGTFQKWAAVVVPSGEEQRYTCHILHKSLTKPITLRWEPPPQS 310


  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: 51,294,971
Number of extensions: 1449199
Number of successful extensions: 6769
Number of sequences better than 1.0e-05: 23
Number of HSP's gapped: 6709
Number of HSP's successfully gapped: 23
Length of query: 413
Length of database: 18,874,504
Length adjustment: 105
Effective length of query: 308
Effective length of database: 15,374,224
Effective search space: 4735260992
Effective search space used: 4735260992
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)

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-001845
         (1241 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|XP_003120321.1| PREDICTED: HLA class II histocompatibility a...   388   e-108
Alignment   gi|NP_001230891.1| HLA class II histocompatibility antigen, DQ ...   385   e-107
Alignment   gi|NP_002114.3| HLA class II histocompatibility antigen, DQ bet...   362   e-100
Alignment   gi|NP_001230890.1| HLA class II histocompatibility antigen, DQ ...   360   1e-99
Alignment   gi|NP_001185787.1| major histocompatibility complex, class II, ...   335   7e-92
Alignment   gi|NP_002115.2| major histocompatibility complex, class II, DR ...   300   1e-81
Alignment   gi|NP_002112.3| HLA class II histocompatibility antigen, DP bet...   300   2e-81
Alignment   gi|XP_003119340.1| PREDICTED: HLA class II histocompatibility a...   296   2e-80
Alignment   gi|XP_003119339.1| PREDICTED: HLA class II histocompatibility a...   296   2e-80
Alignment   gi|XP_003119308.1| PREDICTED: HLA class II histocompatibility a...   296   2e-80

>ref|XP_003120321.1| PREDICTED: HLA class II histocompatibility antigen, DQ beta 1
           chain-like isoform 2 [Homo sapiens].
          Length = 261

 Score =  388 bits (996), Expect = e-108
 Identities = 191/260 (73%), Positives = 213/260 (81%)
 Frame = +1

Query: 76  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVA 255
           MS   ALR+P GL  A VT+ML +L  PVAEGRDSP+DFVYQFKG CYF NGT+RVR V+
Sbjct: 1   MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS 60

Query: 256 RWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEG 435
           R +YN+EE VRFDSDVGEFRAVT LGLP A+YWN QKD+LE+ RA VDRVC+HNYQ+E  
Sbjct: 61  RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR 120

Query: 436 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 615
           TTLQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KV+WFRNGQEETAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNGQEETAGVVSTPLI 180

Query: 616 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 795
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVL 240

Query: 796 XXXXXXXXXXXRHRSQKGLV 855
                       HRSQKGL+
Sbjct: 241 GLIFLGLGLIIHHRSQKGLL 260


>ref|NP_001230891.1| HLA class II histocompatibility antigen, DQ beta 1 chain isoform 1
           precursor [Homo sapiens].
          Length = 261

 Score =  385 bits (989), Expect = e-107
 Identities = 190/260 (73%), Positives = 212/260 (81%)
 Frame = +1

Query: 76  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVA 255
           MS   ALR+P GL  A VT+ML +L  PVAEGRDSP+DFVYQFKG CYF NGT+RVR V+
Sbjct: 1   MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVS 60

Query: 256 RWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEG 435
           R +YN+EE VRFDSDVGEFRAVT LGLP A+YWN QKD+LE+ RA VDRVC+HNYQ+E  
Sbjct: 61  RSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELR 120

Query: 436 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 615
           TTLQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KV+WFRN QEETAGVVSTPLI
Sbjct: 121 TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLI 180

Query: 616 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 795
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVL 240

Query: 796 XXXXXXXXXXXRHRSQKGLV 855
                       HRSQKGL+
Sbjct: 241 GLIFLGLGLIIHHRSQKGLL 260


>ref|NP_002114.3| HLA class II histocompatibility antigen, DQ beta 1 chain isoform 1
           precursor [Homo sapiens].
          Length = 261

 Score =  362 bits (929), Expect = e-100
 Identities = 178/260 (68%), Positives = 204/260 (78%)
 Frame = +1

Query: 76  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVA 255
           MS   ALR+P  L  A VT+ML +L + +AEGRDSP+DFV+QFKG CYF NGT+RVR V 
Sbjct: 1   MSWKKALRIPGDLRVATVTLMLAMLSSLLAEGRDSPEDFVFQFKGMCYFTNGTERVRLVT 60

Query: 256 RWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEG 435
           R++YN+EEY RFDSDVG +RAVTP G P A+YWN QK+VLE  RAE+D VC+HNY++   
Sbjct: 61  RYIYNREEYARFDSDVGVYRAVTPQGRPDAEYWNSQKEVLEGTRAELDTVCRHNYEVAFR 120

Query: 436 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 615
             LQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYP Q+KV+WFRN QEETAGVVSTPLI
Sbjct: 121 GILQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETAGVVSTPLI 180

Query: 616 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 795
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGVGGFVL 240

Query: 796 XXXXXXXXXXXRHRSQKGLV 855
                      R RSQKGL+
Sbjct: 241 GLIFLGLGLIIRQRSQKGLL 260


>ref|NP_001230890.1| HLA class II histocompatibility antigen, DQ beta 1 chain isoform 2
           precursor [Homo sapiens].
          Length = 269

 Score =  360 bits (924), Expect = 1e-99
 Identities = 177/258 (68%), Positives = 202/258 (78%)
 Frame = +1

Query: 76  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVA 255
           MS   ALR+P  L  A VT+ML +L + +AEGRDSP+DFV+QFKG CYF NGT+RVR V 
Sbjct: 1   MSWKKALRIPGDLRVATVTLMLAMLSSLLAEGRDSPEDFVFQFKGMCYFTNGTERVRLVT 60

Query: 256 RWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEG 435
           R++YN+EEY RFDSDVG +RAVTP G P A+YWN QK+VLE  RAE+D VC+HNY++   
Sbjct: 61  RYIYNREEYARFDSDVGVYRAVTPQGRPDAEYWNSQKEVLEGTRAELDTVCRHNYEVAFR 120

Query: 436 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 615
             LQRRV+PTVTISPS+ EALNHHNLLVC+VTDFYP Q+KV+WFRN QEETAGVVSTPLI
Sbjct: 121 GILQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETAGVVSTPLI 180

Query: 616 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 795
           RNGDWT+Q+LVMLEM  QRGDVYTC VEH SLQSPI VEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGVGGFVL 240

Query: 796 XXXXXXXXXXXRHRSQKG 849
                      R RSQKG
Sbjct: 241 GLIFLGLGLIIRQRSQKG 258


>ref|NP_001185787.1| major histocompatibility complex, class II, DQ beta 2 [Homo
           sapiens].
          Length = 227

 Score =  335 bits (858), Expect = 7e-92
 Identities = 159/217 (73%), Positives = 185/217 (85%)
 Frame = +1

Query: 88  VALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVY 267
           +AL++P G W AAVTVMLV+L  PVAE RD P+DF+ QFKG CYF NGT+RVRGVAR++Y
Sbjct: 1   MALQIPGGFWAAAVTVMLVMLSTPVAEARDFPKDFLVQFKGMCYFTNGTERVRGVARYIY 60

Query: 268 NQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQ 447
           N+EEY RFDSDVGEF+AVT LG    D WN  KD LEQ RA VD+VC+HNY+ E  TTLQ
Sbjct: 61  NREEYGRFDSDVGEFQAVTELGRSIED-WNNYKDFLEQERAAVDKVCRHNYEAELRTTLQ 119

Query: 448 RRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGD 627
           R+V+PTVTISPS+ EALNHHNLLVC+VTDFYP+Q+KV+WFRN QEETAGVVST LIRNGD
Sbjct: 120 RQVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTSLIRNGD 179

Query: 628 WTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWR 738
           WT+Q+LVMLE+  QRGD+YTC+VEH SLQSPI VEWR
Sbjct: 180 WTFQILVMLEITPQRGDIYTCQVEHPSLQSPITVEWR 216


>ref|NP_002115.2| major histocompatibility complex, class II, DR beta 1 precursor
           [Homo sapiens].
          Length = 266

 Score =  300 bits (769), Expect = 1e-81
 Identities = 149/255 (58%), Positives = 184/255 (72%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           MV L+LP G    A+TV L+VL +P+A   D+   F++Q K EC+F+NGT+RVR + R+ 
Sbjct: 1   MVCLKLPGGSCMTALTVTLMVLSSPLALSGDTRPRFLWQPKRECHFFNGTERVRFLDRYF 60

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           YNQEE VRFDSDVGEFRAVT LG P A+YWN QKD+LEQ RA VD  C+HNY + E  T+
Sbjct: 61  YNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVESFTV 120

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
           QRRVQP VT+ PSK + L HHNLLVC+V+ FYP  ++V+WF NGQEE AG+VST LI+NG
Sbjct: 121 QRRVQPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNG 180

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 804
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 805 XXXXXXXXRHRSQKG 849
                     R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255


>ref|NP_002112.3| HLA class II histocompatibility antigen, DP beta 1 chain precursor
           [Homo sapiens].
          Length = 258

 Score =  300 bits (768), Expect = 2e-81
 Identities = 141/230 (61%), Positives = 182/230 (79%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           M+ L++     T A+T +L+VL   V +GR +P+++++Q + ECY +NGTQR   + R++
Sbjct: 1   MMVLQVSAAPRTVALTALLMVLLTSVVQGRATPENYLFQGRQECYAFNGTQRF--LERYI 58

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           YN+EE+ RFDSDVGEFRAVT LG P A+YWN QKD+LE+ RA  DR+C+HNY++    TL
Sbjct: 59  YNREEFARFDSDVGEFRAVTELGRPAAEYWNSQKDILEEKRAVPDRMCRHNYELGGPMTL 118

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
           QRRVQP V +SPSK   L HHNLLVC VTDFYP  ++V+WF NGQEETAGVVST LIRNG
Sbjct: 119 QRRVQPRVNVSPSKKGPLQHHNLLVCHVTDFYPGSIQVRWFLNGQEETAGVVSTNLIRNG 178

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 774
           DWT+Q+LVMLEM  Q+GDVYTC+VEH+SL SP+ VEW+AQS+SA+SK L+
Sbjct: 179 DWTFQILVMLEMTPQQGDVYTCQVEHTSLDSPVTVEWKAQSDSARSKTLT 228


>ref|XP_003119340.1| PREDICTED: HLA class II histocompatibility antigen, DRB1-7 beta
           chain-like isoform 2 [Homo sapiens].
          Length = 266

 Score =  296 bits (759), Expect = 2e-80
 Identities = 145/255 (56%), Positives = 184/255 (72%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           MV L+LP G   AA+TV L+VL +P+A   D+   F++Q K +C+F+NGT+RV+ + R  
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLWQGKYKCHFFNGTERVQFLERLF 60

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           YNQEE+VRFDSDVGE+RAVT LG P A+ WN QKD+LE  R +VD VC+HNY + E  T+
Sbjct: 61  YNQEEFVRFDSDVGEYRAVTELGRPVAESWNSQKDILEDRRGQVDTVCRHNYGVGESFTV 120

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
           QRRV P VT+ P+K + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 804
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 805 XXXXXXXXRHRSQKG 849
                     R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255


>ref|XP_003119339.1| PREDICTED: HLA class II histocompatibility antigen, DRB1-7 beta
           chain-like isoform 1 [Homo sapiens].
          Length = 266

 Score =  296 bits (759), Expect = 2e-80
 Identities = 145/255 (56%), Positives = 184/255 (72%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           MV L+LP G   AA+TV L+VL +P+A   D+   F++Q K +C+F+NGT+RV+ + R  
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLWQGKYKCHFFNGTERVQFLERLF 60

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           YNQEE+VRFDSDVGE+RAVT LG P A+ WN QKD+LE  R +VD VC+HNY + E  T+
Sbjct: 61  YNQEEFVRFDSDVGEYRAVTELGRPVAESWNSQKDILEDRRGQVDTVCRHNYGVGESFTV 120

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
           QRRV P VT+ P+K + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 804
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 805 XXXXXXXXRHRSQKG 849
                     R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255


>ref|XP_003119308.1| PREDICTED: HLA class II histocompatibility antigen, DRB1-7 beta
           chain-like isoform 2 [Homo sapiens].
          Length = 266

 Score =  296 bits (759), Expect = 2e-80
 Identities = 145/255 (56%), Positives = 184/255 (72%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           MV L+LP G   AA+TV L+VL +P+A   D+   F++Q K +C+F+NGT+RV+ + R  
Sbjct: 1   MVCLKLPGGSCMAALTVTLMVLSSPLALAGDTQPRFLWQGKYKCHFFNGTERVQFLERLF 60

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           YNQEE+VRFDSDVGE+RAVT LG P A+ WN QKD+LE  R +VD VC+HNY + E  T+
Sbjct: 61  YNQEEFVRFDSDVGEYRAVTELGRPVAESWNSQKDILEDRRGQVDTVCRHNYGVGESFTV 120

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
           QRRV P VT+ P+K + L HHNLLVC+V+ FYP  ++V+WFRNGQEE AGVVST LI+NG
Sbjct: 121 QRRVHPEVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG 180

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 804
           DWT+Q LVMLE   + G+VYTC+VEH S+ SP+ VEWRA+SESAQSKMLS          
Sbjct: 181 DWTFQTLVMLETVPRSGEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLL 240

Query: 805 XXXXXXXXRHRSQKG 849
                     R+QKG
Sbjct: 241 FLGAGLFIYFRNQKG 255


  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: 50,312,070
Number of extensions: 1415706
Number of successful extensions: 6438
Number of sequences better than 1.0e-05: 85
Number of HSP's gapped: 6368
Number of HSP's successfully gapped: 85
Length of query: 413
Length of database: 18,297,164
Length adjustment: 105
Effective length of query: 308
Effective length of database: 14,835,944
Effective search space: 4569470752
Effective search space used: 4569470752
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)

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-001845
         (1241 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|NP_996988.2| histocompatibility 2, class II antigen A, beta ...   323   2e-88
Alignment   gi|NP_034512.2| H-2 class II histocompatibility antigen, I-E be...   288   8e-78
Alignment   gi|NP_001029150.1| histocompatibility 2, class II antigen E bet...   263   2e-70
Alignment   gi|NP_034519.2| histocompatibility 2, O region beta locus [Mus ...   242   5e-64
Alignment   gi|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus ...    75   1e-13
Alignment   gi|NP_034517.2| class II histocompatibility antigen, M beta 1 c...    74   2e-13
Alignment   gi|XP_003086107.1| PREDICTED: class II histocompatibility antig...    74   3e-13
Alignment   gi|NP_034508.2| histocompatibility 2, class II antigen A, alpha...    70   3e-12
Alignment   gi|NP_032232.2| histocompatibility 2, O region alpha locus [Mus...    68   1e-11
Alignment   gi|NP_997531.1| histocompatibility 2, Q region locus 6 [Mus mus...    66   6e-11

>ref|NP_996988.2| histocompatibility 2, class II antigen A, beta 1 precursor [Mus
           musculus].
          Length = 265

 Score =  323 bits (828), Expect = 2e-88
 Identities = 163/255 (63%), Positives = 195/255 (76%), Gaps = 1/255 (0%)
 Frame = +1

Query: 88  VALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVY 267
           +AL++P  L +AAV V+L+VL +P  EG DS + FVYQF GECYF NGTQR+R V R++Y
Sbjct: 1   MALQIPSLLLSAAV-VVLMVLSSPGTEGGDSERHFVYQFMGECYFTNGTQRIRYVTRYIY 59

Query: 268 NQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQ-IEEGTTL 444
           N+EEYVR+DSDVGE RAVT LG P A+YWN Q ++LE+ RAE+D VC+HNY+  E  T+L
Sbjct: 60  NREEYVRYDSDVGEHRAVTELGRPDAEYWNSQPEILERTRAELDTVCRHNYEGPETHTSL 119

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
           +R  QP V IS S+ EALNHHN LVC+VTDFYP+++KV+WFRNGQEET GV ST LIRNG
Sbjct: 120 RRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNG 179

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXX 804
           DWT+QVLVMLEM  +RG+VYTC VEH SL+SPI VEWRAQSESA SKMLS          
Sbjct: 180 DWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQSESAWSKMLSGIGGCVLGVI 239

Query: 805 XXXXXXXXRHRSQKG 849
                   RHRSQKG
Sbjct: 240 FLGLGLFIRHRSQKG 254


>ref|NP_034512.2| H-2 class II histocompatibility antigen, I-E beta chain precursor
           [Mus musculus].
          Length = 264

 Score =  288 bits (736), Expect = 8e-78
 Identities = 143/250 (57%), Positives = 176/250 (70%)
 Frame = +1

Query: 100 LPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEE 279
           LPR    AAV ++L VL  PVA  RDS   F+   K EC+FYNGTQRVR + R+ YN EE
Sbjct: 4   LPRVPCVAAVILLLTVLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRLLERYFYNLEE 63

Query: 280 YVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQ 459
            +RFDSDVGEFRAVT LG P A+ WN Q + LEQ RAEVD VC+HNY+I +   ++RRV+
Sbjct: 64  NLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEISDKFLVRRRVE 123

Query: 460 PTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQ 639
           PTVT+ P+K + L HHNLLVC+V+DFYP  ++V+WFRNG+EE  G+VST L+RNGDWT+Q
Sbjct: 124 PTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQ 183

Query: 640 VLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXXXXXXXXXX 819
            LVMLE   Q G+VYTC+VEH SL  P+ VEW+AQS SAQ+KMLS               
Sbjct: 184 TLVMLETVPQSGEVYTCQVEHPSLTDPVTVEWKAQSTSAQNKMLSGVGGFVLGLLFLGAG 243

Query: 820 XXXRHRSQKG 849
                R+QKG
Sbjct: 244 LFIYFRNQKG 253


>ref|NP_001029150.1| histocompatibility 2, class II antigen E beta2 [Mus musculus].
          Length = 287

 Score =  263 bits (672), Expect = 2e-70
 Identities = 129/230 (56%), Positives = 168/230 (73%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           MV+L LPRGL  AAV + L++L  PV   RD    F+ Q K EC+++NG +RV  V R++
Sbjct: 1   MVSLWLPRGLCVAAVILSLMMLTPPVILVRDPRPRFLEQLKAECHYFNGKERVWSVTRFI 60

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           YNQEE+ RF+SD G+F AVT LG P  +Y N QKD+L+  RA VDR C++NY + +   L
Sbjct: 61  YNQEEFARFNSDFGKFLAVTELGRPIVEYLNTQKDMLDNYRASVDR-CRNNYDLVDIFML 119

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
             + +P VT+ P+K + L HHNLLVC+V DFYP  ++V+WFRNG+EE  GVVST LI+N 
Sbjct: 120 NLKAEPKVTVYPAKTQPLEHHNLLVCSVIDFYPGSIEVRWFRNGEEEKTGVVSTGLIQNR 179

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 774
           DWTYQ LVMLEM  + G+VYTC+VEH SL SP+ VEWRA+S SAQ+K+LS
Sbjct: 180 DWTYQTLVMLEMVPRGGEVYTCQVEHPSLTSPVTVEWRARSTSAQNKLLS 229


>ref|NP_034519.2| histocompatibility 2, O region beta locus [Mus musculus].
          Length = 271

 Score =  242 bits (617), Expect = 5e-64
 Identities = 114/223 (51%), Positives = 154/223 (69%)
 Frame = +1

Query: 106 RGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEEYV 285
           R  W  A+ V L+ L + + EGRDSP++FV Q K +CYF NGT++V  + R+++N EEY+
Sbjct: 5   RAPWVVALLVNLMRLDSFMIEGRDSPENFVIQAKADCYFTNGTEKVHLLVRFIFNLEEYL 64

Query: 286 RFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPT 465
            FDSD+G F A+T LG P AD WN + D+LE  RA V+ VC+  Y++    T++R V P 
Sbjct: 65  HFDSDLGMFVALTELGEPDADQWNKRLDLLETSRAAVNMVCRQKYKLGAPFTVERNVPPE 124

Query: 466 VTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVL 645
           VT+ P +   L  HNLL+C+VT FYP  + V+WFRNGQEE +GV+ST L+RNGDWT+Q  
Sbjct: 125 VTVYPERTPLLQQHNLLLCSVTGFYPGDISVKWFRNGQEERSGVMSTGLVRNGDWTFQTT 184

Query: 646 VMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 774
           VMLEM  + GD+Y+C VEH  L  P+ V W AQSE +  K+LS
Sbjct: 185 VMLEMIPELGDIYSCLVEHPGLLRPVSVAWMAQSEYSWKKILS 227


>ref|NP_034518.1| histocompatibility 2, class II, locus Mb2 [Mus musculus].
          Length = 261

 Score = 74.7 bits (182), Expect = 1e-13
 Identities = 49/170 (28%), Positives = 79/170 (46%), Gaps = 13/170 (7%)
 Frame = +1

Query: 265 YNQEEYVRFDSDVG-----EFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIE 429
           +N++    +D DVG     EF  ++ L    ++  N Q+ ++ +++  +     H     
Sbjct: 46  FNKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPFW 105

Query: 430 EGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------EE 585
           +  T + R  P+V ++ +         +L C V  FYP+ V + W +NGQ        E+
Sbjct: 106 DVLTHRTRA-PSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEK 164

Query: 586 TAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 735
           TA         NGDWTYQ +  L +    GDVYTC V+HS    PI  +W
Sbjct: 165 TAQP-------NGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


>ref|NP_034517.2| class II histocompatibility antigen, M beta 1 chain precursor [Mus
           musculus].
          Length = 261

 Score = 73.9 bits (180), Expect = 2e-13
 Identities = 60/231 (25%), Positives = 93/231 (40%), Gaps = 23/231 (9%)
 Frame = +1

Query: 112 LWTAAVTVMLVVLGAP----------VAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARW 261
           LW   + + L  +GA           V +   +PQDF Y                     
Sbjct: 4   LWLLLLVLSLDCMGAGGFVAHVESTCVLDDAGTPQDFTYCVS------------------ 45

Query: 262 VYNQEEYVRFDSDVG-----EFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQI 426
            +N++    +D DVG     EF  + P     +   N ++ +L++++  +     H    
Sbjct: 46  -FNKDLLACWDPDVGKIVPCEFGVLYPWAENFSRILNKEESLLQRLQNGLLDCASHTQPF 104

Query: 427 EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------E 582
               T + R  P+V ++ +         +L C V  FYP+ V + W +NGQ        E
Sbjct: 105 WNALTHRTRA-PSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKE 163

Query: 583 ETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 735
           +TA         NGDWTYQ +  L +    GDVYTC V+HS    PI  +W
Sbjct: 164 KTAQP-------NGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


>ref|XP_003086107.1| PREDICTED: class II histocompatibility antigen, M beta 1 chain-like
           [Mus musculus].
          Length = 261

 Score = 73.6 bits (179), Expect = 3e-13
 Identities = 60/231 (25%), Positives = 93/231 (40%), Gaps = 23/231 (9%)
 Frame = +1

Query: 112 LWTAAVTVMLVVLGAP----------VAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARW 261
           LW   + + L  +GA           V +   +PQDF Y                     
Sbjct: 4   LWLLLLVLSLDCMGAGGFVAHVESTCVLDDAGTPQDFTYCVS------------------ 45

Query: 262 VYNQEEYVRFDSDVG-----EFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQI 426
            +N++    +D DVG     EF  + P     +   N ++ +L++++  +     H    
Sbjct: 46  -FNKDLLACWDPDVGKIVPCEFGVLYPWAENFSRILNKEESLLQRLQNGLLDCASHTQPF 104

Query: 427 EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ--------E 582
               T + R  P+V ++ +         +L C V  FYP+ V + W +NGQ        E
Sbjct: 105 WNALTHRTR-PPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKE 163

Query: 583 ETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 735
           +TA         NGDWTYQ +  L +    GDVYTC V+HS    PI  +W
Sbjct: 164 KTAQP-------NGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDW 207


>ref|NP_034508.2| histocompatibility 2, class II antigen A, alpha precursor [Mus
           musculus].
          Length = 256

 Score = 70.1 bits (170), Expect = 3e-12
 Identities = 35/125 (28%), Positives = 55/125 (44%), Gaps = 3/125 (2%)
 Frame = +1

Query: 403 VCKHNYQI---EEGTTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRN 573
           V KHN  +      +T      P  T+ P     L   N L+C V + +P  + + W RN
Sbjct: 92  VVKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRN 151

Query: 574 GQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSES 753
            +    GV  T    N D+++  L  L       D+Y C+VEH  L+ P+L  W  +  +
Sbjct: 152 SKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPEIPA 211

Query: 754 AQSKM 768
             S++
Sbjct: 212 PMSEL 216


>ref|NP_032232.2| histocompatibility 2, O region alpha locus [Mus musculus].
          Length = 250

 Score = 68.2 bits (165), Expect = 1e-11
 Identities = 34/97 (35%), Positives = 45/97 (46%)
 Frame = +1

Query: 454 VQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWT 633
           V P VT+ P     L   N+L+C V D +P  + V W RN Q  T GV  T      +  
Sbjct: 111 VPPRVTVLPKTRVELGKPNVLICIVDDIFPPVINVTWLRNSQPITKGVAQTSFYSQPNHR 170

Query: 634 YQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 744
           ++    L       DVY C+VEH  L +P+L  W  Q
Sbjct: 171 FRKFHYLTFVPSAEDVYDCKVEHWGLDTPLLQHWEPQ 207


>ref|NP_997531.1| histocompatibility 2, Q region locus 6 [Mus musculus].
          Length = 326

 Score = 65.9 bits (159), Expect = 6e-11
 Identities = 43/170 (25%), Positives = 71/170 (41%), Gaps = 5/170 (2%)
 Frame = +1

Query: 241 VRGVARWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNY 420
           +RG  ++ Y   +Y+  + D+  + A       T   W  Q  + E+ RA ++  C  + 
Sbjct: 131 LRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITLHKWE-QAGIAERDRAYLEGACVQSL 189

Query: 421 QIEEGTTLQRRVQPTVTISPSKAEALNHHN-----LLVCAVTDFYPSQVKVQWFRNGQEE 585
           +      LQ R +  +   P KA   +H        L C    FYP+ + + W  NG+E 
Sbjct: 190 R----RYLQLRKETLLCTDPPKAHVTHHPRSYGAVTLRCWALGFYPADITLTWQLNGEEL 245

Query: 586 TAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 735
           T  +        GD T+Q    + + L +   YTC V H  L  P+ + W
Sbjct: 246 TQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCHVNHEGLPEPLTLRW 295


  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: 42,429,244
Number of extensions: 1178760
Number of successful extensions: 5153
Number of sequences better than 1.0e-05: 98
Number of HSP's gapped: 5013
Number of HSP's successfully gapped: 98
Length of query: 413
Length of database: 15,617,559
Length adjustment: 104
Effective length of query: 309
Effective length of database: 12,493,815
Effective search space: 3860588835
Effective search space used: 3860588835
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)

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-001845
         (1241 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|NP_001107166.1| SLA class II histocompatibility antigen, DQ ...   469   e-132
Alignment   gi|NP_001107167.1| MHC class II histocompatibility antigen SLA-...   303   1e-82
Alignment   gi|XP_003128397.1| PREDICTED: DLA class II histocompatibility a...   288   4e-78
Alignment   gi|XP_003128372.1| PREDICTED: DLA class II histocompatibility a...   281   4e-76
Alignment   gi|XP_003128376.1| PREDICTED: HLA class II histocompatibility a...   259   2e-69
Alignment   gi|NP_001107536.2| MHC class II, DO beta [Sus scrofa].               258   5e-69
Alignment   gi|NP_998933.1| MHC class I antigen 7 [Sus scrofa].                   78   1e-14
Alignment   gi|NP_001107179.1| MHC class II, DM beta [Sus scrofa].                77   2e-14
Alignment   gi|NP_001172072.1| src-like-adapter [Sus scrofa].                     72   5e-13
Alignment   gi|NP_001107176.1| MHC class I antigen 6 [Sus scrofa].                70   3e-12

>ref|NP_001107166.1| SLA class II histocompatibility antigen, DQ haplotype C beta chain
           precursor [Sus scrofa].
          Length = 261

 Score =  469 bits (1207), Expect = e-132
 Identities = 232/261 (88%), Positives = 239/261 (91%)
 Frame = +1

Query: 76  MSGMVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVA 255
           MSGMVALRLPRGLWTAA+TVMLVVLGAPVAEGRDSPQDFV+QFKGECYFYNGTQRVRGVA
Sbjct: 1   MSGMVALRLPRGLWTAALTVMLVVLGAPVAEGRDSPQDFVFQFKGECYFYNGTQRVRGVA 60

Query: 256 RWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEG 435
           R++YNQEE++RFDSDVGEFRAVTPLG P AD WN QKDVLEQMRAEVDRVCKHNYQIEEG
Sbjct: 61  RYIYNQEEHLRFDSDVGEFRAVTPLGRPEADSWNSQKDVLEQMRAEVDRVCKHNYQIEEG 120

Query: 436 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 615
           TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI
Sbjct: 121 TTLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLI 180

Query: 616 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLSXXXXXXX 795
           RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQ+PILVEWRAQSESAQSKMLS       
Sbjct: 181 RNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQNPILVEWRAQSESAQSKMLSGVGGFVL 240

Query: 796 XXXXXXXXXXXRHRSQKGLVR 858
                      RHRSQKGLVR
Sbjct: 241 GLIFLGLGLFIRHRSQKGLVR 261


>ref|NP_001107167.1| MHC class II histocompatibility antigen SLA-DRB1 [Sus scrofa].
          Length = 266

 Score =  303 bits (777), Expect = 1e-82
 Identities = 145/230 (63%), Positives = 177/230 (76%)
 Frame = +1

Query: 85  MVALRLPRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWV 264
           M+ L   RG W AA+TVMLVVL  P+A  RD+P  F++  K EC+F+NGT+RVR + +  
Sbjct: 1   MLHLCFSRGFWMAALTVMLVVLSPPLALARDTPPHFLFLVKDECHFFNGTERVRLLQKQY 60

Query: 265 YNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTL 444
           YN EE+VRFDSDVGE+RAVT LG P A YWN QKD+LEQMRA VD  C+HNY+I +   +
Sbjct: 61  YNGEEHVRFDSDVGEYRAVTELGRPDAKYWNSQKDLLEQMRAAVDTYCRHNYRILDTFLV 120

Query: 445 QRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNG 624
            RR +PTVT+ P+K + L HHNLLVC+VT FYP  V+V+WFRNGQEE AGVVST LI NG
Sbjct: 121 PRRAEPTVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNG 180

Query: 625 DWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 774
           DWT+Q +VMLE   Q G+VY+CRVEH SL SP+ VEWRA+SESAQ KM+S
Sbjct: 181 DWTFQTMVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRARSESAQGKMMS 230


>ref|XP_003128397.1| PREDICTED: DLA class II histocompatibility antigen, DR-1 beta
           chain-like [Sus scrofa].
          Length = 321

 Score =  288 bits (737), Expect = 4e-78
 Identities = 135/223 (60%), Positives = 171/223 (76%)
 Frame = +1

Query: 103 PRGLWTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEEY 282
           P   WT  +TV+L+VL  P+A   D+   F+ Q K EC+F NGTQ+VR + R++YN++E 
Sbjct: 7   PGSSWTVFLTVILMVLSPPLAWAGDTRPVFMIQGKSECHFSNGTQQVRFLDRYIYNRDEL 66

Query: 283 VRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQP 462
           VRFDSDVGE+RAVTP+G P A YWN QKD+L+++RA VD  C+ NY+  E  T+QRRV+P
Sbjct: 67  VRFDSDVGEYRAVTPMGQPAAKYWNSQKDILKRVRAAVDTFCRSNYEFFESCTVQRRVKP 126

Query: 463 TVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQV 642
           TVT+ P+K + L HHNLLVC+VT FYP  V+V+WFRNGQEE AGVVST LI NGDWT+Q 
Sbjct: 127 TVTVYPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQT 186

Query: 643 LVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKML 771
           +VMLE   Q G+VY+CRVEH SL SP+ VEWRAQ +S+Q KML
Sbjct: 187 MVMLETVPQSGEVYSCRVEHPSLTSPVTVEWRAQHDSSQGKML 229


>ref|XP_003128372.1| PREDICTED: DLA class II histocompatibility antigen, DR-1 beta
           chain-like [Sus scrofa].
          Length = 261

 Score =  281 bits (720), Expect = 4e-76
 Identities = 137/220 (62%), Positives = 166/220 (75%)
 Frame = +1

Query: 115 WTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEEYVRFD 294
           W AA+TV L++   P+A  RD P  F++QFK EC F NGT+RVR +AR++YN EE V FD
Sbjct: 6   WMAALTVTLMLWSPPLACARDIPPVFMHQFKCECQFSNGTERVRFLARYIYNTEEDVHFD 65

Query: 295 SDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPTVTI 474
           SD+GEFRA+T LG P A+YWN QK  LEQMR +VD +C+ NY       +QRRV+P VT+
Sbjct: 66  SDLGEFRALTELGRPDAEYWNQQKGFLEQMRTKVDTMCRSNYLGIGSLMMQRRVKPRVTV 125

Query: 475 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 654
            P+K + L HHNLLVC+VT FYP  V+V+WFRNGQEE AGVVST LI NGDWT+Q +VML
Sbjct: 126 YPAKTQPLQHHNLLVCSVTGFYPGHVEVRWFRNGQEEAAGVVSTGLIPNGDWTFQTMVML 185

Query: 655 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 774
           E   Q G+VY+CRVEH SL SP+ VEWRA SESAQ KMLS
Sbjct: 186 ETVPQSGEVYSCRVEHPSLTSPVTVEWRAWSESAQGKMLS 225


>ref|XP_003128376.1| PREDICTED: HLA class II histocompatibility antigen, DO beta
           chain-like [Sus scrofa].
          Length = 277

 Score =  259 bits (663), Expect = 2e-69
 Identities = 116/219 (52%), Positives = 163/219 (74%)
 Frame = +1

Query: 115 WTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEEYVRFD 294
           W  A+ VM++ L + + +GRD P+DFV Q K +CYF NGTQRV+ V R+++N EE+VRFD
Sbjct: 21  WVVALLVMVIRLDSSMTQGRDPPEDFVIQAKADCYFTNGTQRVQFVVRFIFNLEEFVRFD 80

Query: 295 SDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPTVTI 474
           SD+G+F A+T LG P A+ WN + D+LE  RA VD +C+ NY +    T++R+VQP VT+
Sbjct: 81  SDLGKFVALTELGQPDAELWNSRPDILESSRASVDVLCRRNYWLGAPLTVERKVQPEVTV 140

Query: 475 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 654
            P +  +L   NLL+C+VT FYP  ++++WFRNGQE+  GV++T L+RNGDWT+Q +VML
Sbjct: 141 HPERTPSLQLRNLLLCSVTGFYPGAIEIRWFRNGQEQREGVLATGLVRNGDWTFQTVVML 200

Query: 655 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKML 771
           EM  + GDVYTC V+H SL SP+ VEWRAQS+ + +K+L
Sbjct: 201 EMTPELGDVYTCLVDHPSLLSPVSVEWRAQSDCSWTKLL 239


>ref|NP_001107536.2| MHC class II, DO beta [Sus scrofa].
          Length = 277

 Score =  258 bits (659), Expect = 5e-69
 Identities = 117/219 (53%), Positives = 162/219 (73%)
 Frame = +1

Query: 115 WTAAVTVMLVVLGAPVAEGRDSPQDFVYQFKGECYFYNGTQRVRGVARWVYNQEEYVRFD 294
           W  A+ V ++ L + + +GRDSP+DFV Q K +CYF NGTQRV+ V R+++N EE VRFD
Sbjct: 21  WVVALLVTVIRLDSSMTQGRDSPEDFVIQAKADCYFTNGTQRVQFVVRFIFNLEELVRFD 80

Query: 295 SDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPTVTI 474
           SD+G+F A+T LG P A+ WN + D+LE  RA VD +C+ NY +    T++R+VQP VT+
Sbjct: 81  SDLGKFVALTELGQPDAELWNSRPDILESSRASVDVLCRRNYWLGAPLTVERKVQPEVTV 140

Query: 475 SPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVML 654
            P +  +L   NLL+C+VT FYP  ++++WFRNGQE+  GV++T LIRNGDWT+Q +VML
Sbjct: 141 HPERTPSLQLRNLLLCSVTGFYPGAIEIRWFRNGQEQREGVLATGLIRNGDWTFQTVVML 200

Query: 655 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKML 771
           EM  + GDVYTC V+H SL SP+ VEWRAQS+ + +K+L
Sbjct: 201 EMTPELGDVYTCLVDHPSLLSPVSVEWRAQSDCSWTKLL 239


>ref|NP_998933.1| MHC class I antigen 7 [Sus scrofa].
          Length = 401

 Score = 77.8 bits (190), Expect = 1e-14
 Identities = 52/185 (28%), Positives = 83/185 (44%), Gaps = 5/185 (2%)
 Frame = +1

Query: 196 YQFKGECYFYNGTQRVRGVARWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVL 375
           YQ+   CY     + +RG +++ Y+  +Y+  + D+  + AV      T   W  ++ V 
Sbjct: 116 YQWLCGCYVARDGRLLRGYSQFAYDGADYIVLNEDLRSWTAVGMAAQITRRKWE-EETVA 174

Query: 376 EQMRAEVDRVCK---HNYQIEEGTTLQRRVQPT--VTISPSKAEALNHHNLLVCAVTDFY 540
           EQ RA ++  C    H Y      TLQR   P   VT  PS    +     L C    FY
Sbjct: 175 EQSRAYLEVACVQSLHRYLANGKETLQRSDPPKTHVTRHPSSDNKVT----LRCWALGFY 230

Query: 541 PSQVKVQWFRNGQEETAGVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSP 720
           P ++ + W + GQ+++  V       +GD T++    L +       YTC V+H  LQ P
Sbjct: 231 PKEISLTWQQEGQDQSQDVEVVETRPSGDGTFRKWAALVVPPGEEQSYTCHVQHEGLQEP 290

Query: 721 ILVEW 735
           + + W
Sbjct: 291 LTLRW 295


>ref|NP_001107179.1| MHC class II, DM beta [Sus scrofa].
          Length = 272

 Score = 77.0 bits (188), Expect = 2e-14
 Identities = 48/160 (30%), Positives = 74/160 (46%), Gaps = 4/160 (2%)
 Frame = +1

Query: 307 EFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKHNYQIEEGTTLQRRVQPTVTISPSK 486
           EF A+  L    + Y N Q+ +L+++   +     H     +  T  R   P+V ++ + 
Sbjct: 74  EFGALNALATYFSVYLNQQEKLLQRLSNGLQNCATHTQPFWKSLT-HRTQPPSVQVAKTT 132

Query: 487 AEALNHHNLLVCAVTDFYPSQVKVQWFRNGQ----EETAGVVSTPLIRNGDWTYQVLVML 654
                   +L C V  FYP+ V + W +NGQ       A +++ P   NGDWTYQ +  L
Sbjct: 133 PFNTRESVMLACYVWGFYPADVIITWRKNGQPVLPHGKAHMITQP---NGDWTYQTVSHL 189

Query: 655 EMNLQRGDVYTCRVEHSSLQSPILVEWRAQSESAQSKMLS 774
                 GD YTC VEH  +  PIL +W +     Q+  +S
Sbjct: 190 ATTPSYGDTYTCVVEHIGVPEPILQDWTSGLSPVQTVKIS 229


>ref|NP_001172072.1| src-like-adapter [Sus scrofa].
          Length = 250

 Score = 72.4 bits (176), Expect = 5e-13
 Identities = 34/102 (33%), Positives = 46/102 (45%)
 Frame = +1

Query: 439 TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETAGVVSTPLIR 618
           T    V P VT+ P    AL   N+L+C V + +P  + + W  NGQ  T GV  T    
Sbjct: 106 TRATNVPPRVTVLPKSPVALGQPNVLICIVDNIFPPVINITWLHNGQTVTEGVTQTSFYA 165

Query: 619 NGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEWRAQ 744
             D +++    L      GD Y C+VEH  L  P+   W  Q
Sbjct: 166 QPDHSFRKFHYLTFVPSAGDFYDCKVEHWGLDEPLFTHWEPQ 207


>ref|NP_001107176.1| MHC class I antigen 6 [Sus scrofa].
          Length = 369

 Score = 69.7 bits (169), Expect = 3e-12
 Identities = 43/168 (25%), Positives = 81/168 (48%), Gaps = 3/168 (1%)
 Frame = +1

Query: 241 VRGVARWVYNQEEYVRFDSDVGEFRAVTPLGLPTADYWNGQKDVLEQMRAEVDRVCKH-- 414
           +RG  ++ Y+ ++Y+  + D+  + A++ +       W  +  V EQ RA ++  C    
Sbjct: 159 LRGYEQFSYDGDDYIVLNEDLRSWTAISTVAQIIRRKWEAE-GVAEQYRAYLEIECVEWL 217

Query: 415 NYQIEEGT-TLQRRVQPTVTISPSKAEALNHHNLLVCAVTDFYPSQVKVQWFRNGQEETA 591
              +E+G   LQR V P   ++  +    ++   L C    FYP ++ + W R+G+++T 
Sbjct: 218 RKYLEKGKDVLQRAVPPKTHVT--RHPFYDNKVTLRCWALGFYPKEISLTWQRDGEDQTQ 275

Query: 592 GVVSTPLIRNGDWTYQVLVMLEMNLQRGDVYTCRVEHSSLQSPILVEW 735
            +       +GD T+Q    L +       YTC+V+H  LQ P+ + W
Sbjct: 276 DMELVETRPSGDGTFQKWAALVVPSGEEQSYTCQVQHEGLQEPLTLRW 323


  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: 31,939,265
Number of extensions: 936346
Number of successful extensions: 4051
Number of sequences better than 1.0e-05: 34
Number of HSP's gapped: 4023
Number of HSP's successfully gapped: 34
Length of query: 413
Length of database: 11,343,932
Length adjustment: 101
Effective length of query: 312
Effective length of database: 8,829,335
Effective search space: 2754752520
Effective search space used: 2754752520
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)

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-001845
         (1241 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_Chr07                                                         729   0.0  
gb|GL896569.1| Sus scrofa unplaced genomic scaffold chrU_scaffol...   109   4e-21
gb|GL895823.1| Sus scrofa unplaced genomic scaffold chrU_scaffol...    68   1e-08

>Sscrofa_Chr07 
||          Length = 134764511

 Score =  729 bits (368), Expect = 0.0
 Identities = 371/372 (99%)
 Strand = Plus / Minus

                                                                            
Query: 847      gggctcgtgcgctgaatcctgaagatactttggggttggtttttgctcttcttaaatgtc 906
                |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |
Sbjct: 29180905 gggctcgtgcgctgaatcctgaagatactttggggttggtttttgctcttcttaaatgcc 29180846

                                                                            
Query: 907      tgtctgttcttgcctggaattcccatcccccctgccagcttgtcctctctgaggtcagat 966
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29180845 tgtctgttcttgcctggaattcccatcccccctgccagcttgtcctctctgaggtcagat 29180786

                                                                            
Query: 967      cctacagtgactctgatgcagtcaccagggcgcttcctgtgatccccacctcaaggctct 1026
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29180785 cctacagtgactctgatgcagtcaccagggcgcttcctgtgatccccacctcaaggctct 29180726

                                                                            
Query: 1027     ggctgtgaagcttcttcctgaactgaccccagcgcctctgcctgagtgcagccagctgtg 1086
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29180725 ggctgtgaagcttcttcctgaactgaccccagcgcctctgcctgagtgcagccagctgtg 29180666

                                                                            
Query: 1087     tctactcagaccacaagggattttcctgttcctatttcccctcaacagactgtgcaagag 1146
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29180665 tctactcagaccacaagggattttcctgttcctatttcccctcaacagactgtgcaagag 29180606

                                                                            
Query: 1147     aagcacattgaaaccatttaactggctatagagtgctttttttaaaatcataattaaaca 1206
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29180605 aagcacattgaaaccatttaactggctatagagtgctttttttaaaatcataattaaaca 29180546

                            
Query: 1207     tgattatgagtt 1218
                ||||||||||||
Sbjct: 29180545 tgattatgagtt 29180534



 Score =  557 bits (281), Expect = e-156
 Identities = 284/285 (99%)
 Strand = Plus / Minus

                                                                            
Query: 453      agtgcaacctacagtgactatctccccatccaaggcagaggctctaaaccaccacaacct 512
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29182980 agtgcaacctacagtgactatctccccatccaaggcagaggctctaaaccaccacaacct 29182921

                                                                            
Query: 513      gctggtctgtgcggtgacagatttctatccaagccaggtgaaagtccagtggttccggaa 572
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29182920 gctggtctgtgcggtgacagatttctatccaagccaggtgaaagtccagtggttccggaa 29182861

                                                                            
Query: 573      tggccaggaggagacagctggcgttgtgtccactcctcttattaggaacggagactggac 632
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29182860 tggccaggaggagacagctggcgttgtgtccactcctcttattaggaacggagactggac 29182801

                                                                            
Query: 633      ctaccaggtgctcgtgatgctagagatgaatctccagcgaggagatgtctacacctgccg 692
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29182800 ctaccaggtgctcgtgatgctagagatgaatctccagcgaggagatgtctacacctgccg 29182741

                                                             
Query: 693      cgtggagcactccagcctccagagccccatcttggtggagtggcg 737
                ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct: 29182740 cgtggagcactccagcctccagaaccccatcttggtggagtggcg 29182696



 Score =  480 bits (242), Expect = e-133
 Identities = 263/270 (97%)
 Strand = Plus / Minus

                                                                            
Query: 185      aggatttcgtgtaccagtttaagggcgagtgctacttctacaacggaacgcagcgggtgc 244
                |||||||||||||||||||||||  |||||||||||||| ||||||||||||||||||||
Sbjct: 29187230 aggatttcgtgtaccagtttaagttcgagtgctacttcttcaacggaacgcagcgggtgc 29187171

                                                                            
Query: 245      ggggcgtggccaggtgggtctacaaccaggaggagtacgtgcgcttcgacagcgacgtgg 304
                ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Sbjct: 29187170 ggggcgtggccaggtgggtctacaaccaggaggagcacgtgcgcttcgacagcgacgtgg 29187111

                                                                            
Query: 305      gggagttccgggcggtgaccccgctggggctgccgaccgccgactactggaacggccaga 364
                |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct: 29187110 gggagttccgggcggtgaccccgctggggcggccgaccgccgactactggaacggccaga 29187051

                                                                            
Query: 365      aggacgtcctggagcagatgcgggccgaggtggacagggtgtgcaaacacaactaccaga 424
                |||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||
Sbjct: 29187050 aggacgtcctggagcagaagcgggccgaggtggacacggtgtgcaaacacaactaccaga 29186991

                                              
Query: 425      tagaggaaggcacgaccctgcagcggcgag 454
                ||||||||||||||||||||||||||||||
Sbjct: 29186990 tagaggaaggcacgaccctgcagcggcgag 29186961



 Score =  341 bits (172), Expect = 6e-91
 Identities = 181/184 (98%)
 Strand = Plus / Minus

                                                                            
Query: 1        ctctgaaggggggataccagaaccactgagtgggagctgtgttgactaccattacttctt 60
                ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29188763 ctctgaaggggggatacgagaaccactgagtgggagctgtgttgactaccattacttctt 29188704

                                                                            
Query: 61       cgtttgtcctcaattatgtctgggatggtggctctgcggctccccagaggcctttggaca 120
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29188703 cgtttgtcctcaattatgtctgggatggtggctctgcggctccccagaggcctttggaca 29188644

                                                                            
Query: 121      gcggccgtgacggtgatgctggtggtgctgggtgctccggtggctgagggcagagactct 180
                |||||| ||||||||||||||||||||||||||||||| |||||||||||||||||||||
Sbjct: 29188643 gcggccttgacggtgatgctggtggtgctgggtgctccagtggctgagggcagagactct 29188584

                    
Query: 181      ccac 184
                ||||
Sbjct: 29188583 ccac 29188580



 Score =  222 bits (112), Expect = 4e-55
 Identities = 112/112 (100%)
 Strand = Plus / Minus

                                                                            
Query: 737      gggcacagtctgaatctgcccagagcaagatgctgagcggtgtcgggggcttcgtgctgg 796
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29182204 gggcacagtctgaatctgcccagagcaagatgctgagcggtgtcgggggcttcgtgctgg 29182145

                                                                    
Query: 797      ggctgatcttcctcgggctgggccttttcatccgtcacaggagtcagaaggg 848
                ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 29182144 ggctgatcttcctcgggctgggccttttcatccgtcacaggagtcagaaggg 29182093



 Score =  119 bits (60), Expect = 4e-24
 Identities = 126/148 (85%)
 Strand = Plus / Minus

                                                                            
Query: 274      gaggagtacgtgcgcttcgacagcgacgtgggggagttccgggcggtgaccccgctgggg 333
                ||||||| | |||||||||||||||||||||| |||| |||||||||||||  |||||||
Sbjct: 29118000 gaggagttcctgcgcttcgacagcgacgtgggcgagtaccgggcggtgaccgagctgggg 29117941

                                                                            
Query: 334      ctgccgaccgccgactactggaacggccagaaggacgtcctggagcagatgcgggccgag 393
                | |||   |||| |  |||||||| ||||||||||| |||||||||||| |||||| |||
Sbjct: 29117940 cggccagacgccaaggactggaacagccagaaggacctcctggagcagaggcgggcggag 29117881

                                            
Query: 394      gtggacagggtgtgcaaacacaactacc 421
                ||||||| |   |||| |||||||||||
Sbjct: 29117880 gtggacacgtactgcagacacaactacc 29117853



 Score =  109 bits (55), Expect = 4e-21
 Identities = 130/155 (83%)
 Strand = Plus / Plus

                                                                            
Query: 220      ttctacaacggaacgcagcgggtgcggggcgtggccaggtgggtctacaaccaggaggag 279
                |||| |||||||||||||| |||||||  | ||| ||| |   ||||||||| ||| |||
Sbjct: 29363788 ttctccaacggaacgcagcaggtgcggttcctggacagatacatctacaaccgggacgag 29363847

                                                                            
Query: 280      tacgtgcgcttcgacagcgacgtgggggagttccgggcggtgaccccgctggggctgccg 339
                |  |||||||||||||||||||||||||||| | |||||||||||||  |||||| ||||
Sbjct: 29363848 ttggtgcgcttcgacagcgacgtgggggagtacagggcggtgaccccaatggggcagccg 29363907

                                                   
Query: 340      accgccgactactggaacggccagaaggacgtcct 374
                 | ||| | ||||||||| ||||||||||| ||||
Sbjct: 29363908 gctgccaagtactggaacagccagaaggacatcct 29363942



 Score =  103 bits (52), Expect = 2e-19
 Identities = 97/112 (86%)
 Strand = Plus / Plus

                                                                            
Query: 263      tctacaaccaggaggagtacgtgcgcttcgacagcgacgtgggggagttccgggcggtga 322
                ||||||||| ||| ||||  |||||||||||||||||||||||||||| | |||||||||
Sbjct: 29210380 tctacaaccgggacgagttggtgcgcttcgacagcgacgtgggggagtacagggcggtga 29210439

                                                                    
Query: 323      ccccgctggggctgccgaccgccgactactggaacggccagaaggacgtcct 374
                ||||  |||||| |||| | ||| | ||||||||| ||||||||||| ||||
Sbjct: 29210440 ccccaatggggcagccggctgccaagtactggaacagccagaaggacatcct 29210491



 Score = 99.6 bits (50), Expect = 4e-18
 Identities = 93/106 (87%), Gaps = 1/106 (0%)
 Strand = Plus / Minus

                                                                            
Query: 275      aggagtacgtgcgcttcgacagcgacgtgggggagttccgggcggtgaccccgctggggc 334
                ||||||||||||||||||||||||||||||| |||||||||| |||||||  ||| ||||
Sbjct: 29098707 aggagtacgtgcgcttcgacagcgacgtgggcgagttccgggtggtgacctagct-gggc 29098649

                                                              
Query: 335      tgccgaccgccgactactggaacggccagaaggacgtcctggagca 380
                 |||  | ||| | ||||||||| ||||||||||| ||||||||||
Sbjct: 29098648 ggccttcagccaagtactggaacagccagaaggacatcctggagca 29098603



 Score = 77.8 bits (39), Expect = 1e-11
 Identities = 168/211 (79%)
 Strand = Plus / Minus

                                                                            
Query: 199      cagtttaagggcgagtgctacttctacaacggaacgcagcgggtgcggggcgtggccagg 258
                ||||||||| |||||||  | |||| |||||| ||| |||||||| ||  | ||||||| 
Sbjct: 29062694 cagtttaagtgcgagtgtcaattctccaacgggacggagcgggtgaggttcttggccaga 29062635

                                                                            
Query: 259      tgggtctacaaccaggaggagtacgtgcgcttcgacagcgacgtgggggagttccgggcg 318
                |   ||||||||  ||||||| | |||| ||||||||||||| ||||||||||| |||| 
Sbjct: 29062634 tacatctacaacacggaggaggatgtgcacttcgacagcgacttgggggagttcagggcc 29062575

                                                                            
Query: 319      gtgaccccgctggggctgccgaccgccgactactggaacggccagaaggacgtcctggag 378
                 ||||   |||||||| |||   ||| || |||||||||   ||||||| | || |||||
Sbjct: 29062574 ctgactgagctggggcggccagacgctgagtactggaaccagcagaagggcttcttggag 29062515

                                               
Query: 379      cagatgcgggccgaggtggacagggtgtgca 409
                ||||||||| || ||||||||| | ||||||
Sbjct: 29062514 cagatgcggaccaaggtggacacgatgtgca 29062484



 Score = 67.9 bits (34), Expect = 1e-08
 Identities = 46/50 (92%)
 Strand = Plus / Minus

                                                                  
Query: 274      gaggagtacgtgcgcttcgacagcgacgtgggggagttccgggcggtgac 323
                ||||||| ||||||||||||||||||| |||| |||| ||||||||||||
Sbjct: 29083002 gaggagttcgtgcgcttcgacagcgacttgggtgagtaccgggcggtgac 29082953



 Score = 60.0 bits (30), Expect = 3e-06
 Identities = 48/54 (88%)
 Strand = Plus / Minus

                                                                      
Query: 354      gaacggccagaaggacgtcctggagcagatgcgggccgaggtggacagggtgtg 407
                ||||| |||||||||  |||||||||||| |||||  |||||||||||||||||
Sbjct: 29082936 gaacgaccagaaggatttcctggagcagaagcgggtggaggtggacagggtgtg 29082883



 Score = 60.0 bits (30), Expect = 3e-06
 Identities = 60/70 (85%)
 Strand = Plus / Minus

                                                                            
Query: 737      gggcacagtctgaatctgcccagagcaagatgctgagcggtgtcgggggcttcgtgctgg 796
                |||||| |||||||||||| ||| |||||||| |||| || || ||||||||||| ||||
Sbjct: 29094966 gggcacggtctgaatctgctcagggcaagatgatgagtggggttgggggcttcgtcctgg 29094907

                          
Query: 797      ggctgatctt 806
                | ||| ||||
Sbjct: 29094906 gtctgctctt 29094897



 Score = 60.0 bits (30), Expect = 3e-06
 Identities = 60/70 (85%)
 Strand = Plus / Minus

                                                                            
Query: 737      gggcacagtctgaatctgcccagagcaagatgctgagcggtgtcgggggcttcgtgctgg 796
                |||||| |||||||||||| ||| |||||||| |||| ||  ||||||||||||| ||||
Sbjct: 29114144 gggcacggtctgaatctgctcagggcaagatgatgagtgggatcgggggcttcgtcctgg 29114085

                          
Query: 797      ggctgatctt 806
                | ||| ||||
Sbjct: 29114084 gtctgctctt 29114075



 Score = 60.0 bits (30), Expect = 3e-06
 Identities = 60/70 (85%)
 Strand = Plus / Minus

                                                                            
Query: 737      gggcacagtctgaatctgcccagagcaagatgctgagcggtgtcgggggcttcgtgctgg 796
                ||||||||||||||||||||| |||||||| || ||| ||  | ||||||   |||||||
Sbjct: 29237638 gggcacagtctgaatctgcccggagcaagacgccgagtggaattgggggccctgtgctgg 29237579

                          
Query: 797      ggctgatctt 806
                ||||||||||
Sbjct: 29237578 ggctgatctt 29237569



 Score = 60.0 bits (30), Expect = 3e-06
 Identities = 60/70 (85%)
 Strand = Plus / Minus

                                                                            
Query: 737      gggcacagtctgaatctgcccagagcaagatgctgagcggtgtcgggggcttcgtgctgg 796
                ||||||||||||||||||||| |||||||| || ||| ||  | ||||||   |||||||
Sbjct: 29392012 gggcacagtctgaatctgcccggagcaagacgccgagtggaattgggggccctgtgctgg 29391953

                          
Query: 797      ggctgatctt 806
                ||||||||||
Sbjct: 29391952 ggctgatctt 29391943


>gb|GL896569.1| Sus scrofa unplaced genomic scaffold chrU_scaffold897
          Length = 986

 Score =  109 bits (55), Expect = 4e-21
 Identities = 100/115 (86%)
 Strand = Plus / Plus

                                                                       
Query: 286 cgcttcgacagcgacgtgggggagttccgggcggtgaccccgctggggctgccgaccgcc 345
           |||||||||||||||||||| |||| |||||||||||||  |||||||| |||   ||||
Sbjct: 1   cgcttcgacagcgacgtgggcgagtaccgggcggtgaccgagctggggcggccagacgcc 60

                                                                  
Query: 346 gactactggaacggccagaaggacgtcctggagcagatgcgggccgaggtggaca 400
            |  |||||||| ||||||||||| |||||||||||| |||||| ||||||||||
Sbjct: 61  aaggactggaacagccagaaggacctcctggagcagaggcgggcggaggtggaca 115


>gb|GL895823.1| Sus scrofa unplaced genomic scaffold chrU_scaffold435
          Length = 2580

 Score = 67.9 bits (34), Expect = 1e-08
 Identities = 46/50 (92%)
 Strand = Plus / Plus

                                                             
Query: 274 gaggagtacgtgcgcttcgacagcgacgtgggggagttccgggcggtgac 323
           ||||||| ||||||||||||||||||| |||| |||| ||||||||||||
Sbjct: 599 gaggagttcgtgcgcttcgacagcgacttgggtgagtaccgggcggtgac 648



 Score = 60.0 bits (30), Expect = 3e-06
 Identities = 48/54 (88%)
 Strand = Plus / Plus

                                                                 
Query: 354 gaacggccagaaggacgtcctggagcagatgcgggccgaggtggacagggtgtg 407
           ||||| |||||||||  |||||||||||| |||||  |||||||||||||||||
Sbjct: 665 gaacgaccagaaggatttcctggagcagaagcgggtggaggtggacagggtgtg 718


  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: 34,169,734
Number of extensions: 308
Number of successful extensions: 308
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 305
Number of HSP's successfully gapped: 19
Length of query: 1241
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 1220
Effective length of database: 2,808,413,156
Effective search space: 3426264050320
Effective search space used: 3426264050320
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)