Animal-Genome cDNA 20110601C-002510


Search to RefSeqBP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20110601C-002510
         (2005 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_001178084.1| homeobox protein Nkx-3.1 [Bos taurus].            296   6e-80
Alignment   gi|XP_002689825.1| PREDICTED: NK3 homeobox 1-like [Bos taurus].      296   6e-80
Alignment   gi|NP_001180062.1| homeobox protein Nkx-3.2 [Bos taurus].            115   2e-25
Alignment   gi|XP_002688506.1| PREDICTED: NK3 homeobox 2-like [Bos taurus].      115   2e-25
Alignment   gi|NP_001178387.1| NK2 homeobox 1 [Bos taurus].                       89   1e-17
Alignment   gi|NP_001029848.1| homeobox protein Nkx-2.3 [Bos taurus].             89   1e-17
Alignment   gi|XP_002696755.1| PREDICTED: NK2 homeobox 1 isoform 2 [Bos tau...    89   1e-17
Alignment   gi|XP_002696754.1| PREDICTED: NK2 homeobox 1 isoform 1 [Bos tau...    89   1e-17
Alignment   gi|XP_880071.2| PREDICTED: thyroid transcription factor 1 isofo...    89   1e-17
Alignment   gi|NP_001179092.1| homeobox protein Nkx-2.8 [Bos taurus].             88   2e-17

>ref|NP_001178084.1| homeobox protein Nkx-3.1 [Bos taurus].
          Length = 243

 Score =  296 bits (757), Expect = 6e-80
 Identities = 154/239 (64%), Positives = 165/239 (69%)
 Frame = +1

Query: 94  PELRPGEGGTAGCSPRAAPPIQSKPLTSFLIQDILRDRTEQCGGQAGSXXXXXXXXXXXX 273
           PE + G  G AGCSP A PP Q+KPLTSFLIQDILRD  ++ GG AGS            
Sbjct: 5   PEPQLGNAGAAGCSPPAVPPTQTKPLTSFLIQDILRDGADRRGGHAGSPQPQPSRQQYPR 64

Query: 274 XXXXXXXKGGRGSAGAPEDHRXXXXXXXXRXXXXXXXXXXDRHLETYLLDCENTPGALPS 453
                  +G RG A APED +                    RHLETYLLDCEN P AL S
Sbjct: 65  RDPKPEPEGRRGCARAPEDQQSDQPRAGSEEAEKPVETEPGRHLETYLLDCENPPSALQS 124

Query: 454 LPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR 633
           LPP  KQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR
Sbjct: 125 LPPATKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR 184

Query: 634 RYKTKRKQLTSDLGDLEKHPSLPALKEEGFSRASLIAMHHTXXXXXXXXXXXXWSPAFW 810
           RYKTKRKQLTSDLG+LEKH SLPALKEEGFS+ SLI++H+T            WSPAFW
Sbjct: 185 RYKTKRKQLTSDLGNLEKHSSLPALKEEGFSQGSLISVHNTYPYYPYVYCLGGWSPAFW 243


>ref|XP_002689825.1| PREDICTED: NK3 homeobox 1-like [Bos taurus].
          Length = 243

 Score =  296 bits (757), Expect = 6e-80
 Identities = 154/239 (64%), Positives = 165/239 (69%)
 Frame = +1

Query: 94  PELRPGEGGTAGCSPRAAPPIQSKPLTSFLIQDILRDRTEQCGGQAGSXXXXXXXXXXXX 273
           PE + G  G AGCSP A PP Q+KPLTSFLIQDILRD  ++ GG AGS            
Sbjct: 5   PEPQLGNAGAAGCSPPAVPPTQTKPLTSFLIQDILRDGADRRGGHAGSPQPQPSRQQYPR 64

Query: 274 XXXXXXXKGGRGSAGAPEDHRXXXXXXXXRXXXXXXXXXXDRHLETYLLDCENTPGALPS 453
                  +G RG A APED +                    RHLETYLLDCEN P AL S
Sbjct: 65  RDPKPEPEGRRGCARAPEDQQSDQPRAGSEEAEKPVETEPGRHLETYLLDCENPPSALQS 124

Query: 454 LPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR 633
           LPP  KQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR
Sbjct: 125 LPPATKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR 184

Query: 634 RYKTKRKQLTSDLGDLEKHPSLPALKEEGFSRASLIAMHHTXXXXXXXXXXXXWSPAFW 810
           RYKTKRKQLTSDLG+LEKH SLPALKEEGFS+ SLI++H+T            WSPAFW
Sbjct: 185 RYKTKRKQLTSDLGNLEKHSSLPALKEEGFSQGSLISVHNTYPYYPYVYCLGGWSPAFW 243


>ref|NP_001180062.1| homeobox protein Nkx-3.2 [Bos taurus].
          Length = 330

 Score =  115 bits (287), Expect = 2e-25
 Identities = 54/72 (75%), Positives = 62/72 (86%)
 Frame = +1

Query: 457 PPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 636
           P  PK  +KRSRAAFSH QV ELER+F+HQ+YLS PERA LA +LKLTETQVKIWFQNRR
Sbjct: 196 PAAPKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRR 255

Query: 637 YKTKRKQLTSDL 672
           YKTKR+Q+ +DL
Sbjct: 256 YKTKRRQMAADL 267


>ref|XP_002688506.1| PREDICTED: NK3 homeobox 2-like [Bos taurus].
          Length = 330

 Score =  115 bits (287), Expect = 2e-25
 Identities = 54/72 (75%), Positives = 62/72 (86%)
 Frame = +1

Query: 457 PPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 636
           P  PK  +KRSRAAFSH QV ELER+F+HQ+YLS PERA LA +LKLTETQVKIWFQNRR
Sbjct: 196 PAAPKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRR 255

Query: 637 YKTKRKQLTSDL 672
           YKTKR+Q+ +DL
Sbjct: 256 YKTKRRQMAADL 267


>ref|NP_001178387.1| NK2 homeobox 1 [Bos taurus].
          Length = 370

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 152 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 211

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 212 HRYKMKRQ 219


>ref|NP_001029848.1| homeobox protein Nkx-2.3 [Bos taurus].
          Length = 367

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 47/84 (55%), Positives = 57/84 (67%)
 Frame = +1

Query: 421 DCENTPGALPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLT 600
           DC+    A  S  P P+  +++ R  FS  QV ELER+F  Q+YLSAPER HLA +LKLT
Sbjct: 134 DCK---AAEESERPKPRS-RRKPRVLFSQAQVFELERRFKQQRYLSAPEREHLASSLKLT 189

Query: 601 ETQVKIWFQNRRYKTKRKQLTSDL 672
            TQVKIWFQNRRYK KR++    L
Sbjct: 190 STQVKIWFQNRRYKCKRQRQDKSL 213


>ref|XP_002696755.1| PREDICTED: NK2 homeobox 1 isoform 2 [Bos taurus].
          Length = 400

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 182 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 241

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 242 HRYKMKRQ 249


>ref|XP_002696754.1| PREDICTED: NK2 homeobox 1 isoform 1 [Bos taurus].
          Length = 370

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 152 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 211

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 212 HRYKMKRQ 219


>ref|XP_880071.2| PREDICTED: thyroid transcription factor 1 isoform 4 [Bos taurus].
          Length = 400

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 182 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 241

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 242 HRYKMKRQ 249


>ref|NP_001179092.1| homeobox protein Nkx-2.8 [Bos taurus].
          Length = 237

 Score = 88.2 bits (217), Expect = 2e-17
 Identities = 42/77 (54%), Positives = 52/77 (67%)
 Frame = +1

Query: 421 DCENTPGALPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLT 600
           D    P A P+ P +  + +K+ R  FS  Q +ELER+F  Q+YLSAPER  LA+ L+LT
Sbjct: 65  DSSQRPSARPASPGSDAEKRKKRRVLFSKAQTLELERRFRQQRYLSAPEREQLARLLRLT 124

Query: 601 ETQVKIWFQNRRYKTKR 651
            TQVKIWFQN RYK KR
Sbjct: 125 PTQVKIWFQNHRYKLKR 141


  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: 71,074,971
Number of extensions: 2020215
Number of successful extensions: 9571
Number of sequences better than 1.0e-05: 192
Number of HSP's gapped: 9553
Number of HSP's successfully gapped: 193
Length of query: 668
Length of database: 17,681,374
Length adjustment: 109
Effective length of query: 559
Effective length of database: 14,074,782
Effective search space: 7867803138
Effective search space used: 7867803138
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: 36 (18.5 bits)

Search to RefSeqCP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20110601C-002510
         (2005 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|XP_543240.2| PREDICTED: similar to Homeobox protein Nkx-3.1 ...   230   4e-60
Alignment   gi|XP_545940.2| PREDICTED: similar to bagpipe homeobox 1 [Canis...   115   2e-25
Alignment   gi|XP_852202.1| PREDICTED: similar to NK2 transcription factor ...    92   2e-18
Alignment   gi|NP_001003260.1| thyroid transcription factor 1 [Canis lupus ...    89   1e-17
Alignment   gi|XP_543239.2| PREDICTED: similar to NK2 transcription factor ...    89   2e-17
Alignment   gi|XP_849082.1| PREDICTED: similar to Homeobox protein Nkx-2.4 ...    86   2e-16
Alignment   gi|NP_001010959.1| homeobox protein Nkx-2.5 [Canis lupus famili...    82   2e-15
Alignment   gi|XP_542867.2| PREDICTED: similar to NK2 transcription factor ...    78   3e-14
Alignment   gi|XP_855075.1| PREDICTED: similar to T-cell leukemia homeobox ...    75   2e-13
Alignment   gi|XP_546241.2| PREDICTED: similar to T-cell leukemia homeobox ...    74   4e-13

>ref|XP_543240.2| PREDICTED: similar to Homeobox protein Nkx-3.1 [Canis familiaris].
          Length = 206

 Score =  230 bits (586), Expect = 4e-60
 Identities = 112/139 (80%), Positives = 120/139 (86%)
 Frame = +1

Query: 394 DRHLETYLLDCENTPGALPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERA 573
           +RH ETYLLDCEN+ G+LPSLP T KQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERA
Sbjct: 68  NRHFETYLLDCENSAGSLPSLPQTSKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERA 127

Query: 574 HLAKNLKLTETQVKIWFQNRRYKTKRKQLTSDLGDLEKHPSLPALKEEGFSRASLIAMHH 753
           HLAKNLKLTETQVKIWFQNRRYKTKRKQLTSDLGDLEKH SLPALKEEG  +ASLI+MH+
Sbjct: 128 HLAKNLKLTETQVKIWFQNRRYKTKRKQLTSDLGDLEKHSSLPALKEEGLPQASLISMHN 187

Query: 754 TXXXXXXXXXXXXWSPAFW 810
           +            W+PAFW
Sbjct: 188 SYPYYPYLYCLGGWNPAFW 206


>ref|XP_545940.2| PREDICTED: similar to bagpipe homeobox 1 [Canis familiaris].
          Length = 333

 Score =  115 bits (287), Expect = 2e-25
 Identities = 54/72 (75%), Positives = 62/72 (86%)
 Frame = +1

Query: 457 PPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 636
           P  PK  +KRSRAAFSH QV ELER+F+HQ+YLS PERA LA +LKLTETQVKIWFQNRR
Sbjct: 199 PAAPKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRR 258

Query: 637 YKTKRKQLTSDL 672
           YKTKR+Q+ +DL
Sbjct: 259 YKTKRRQMAADL 270


>ref|XP_852202.1| PREDICTED: similar to NK2 transcription factor related, locus 8
           [Canis familiaris].
          Length = 239

 Score = 91.7 bits (226), Expect = 2e-18
 Identities = 50/103 (48%), Positives = 62/103 (60%)
 Frame = +1

Query: 406 ETYLLDCENTPGALPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAK 585
           ET   D    P A P+ P +  + +K+ R  FS  Q +ELER+F  Q+YLSAPER  LA+
Sbjct: 60  ETSPPDSSQRPSARPASPGSDAEKRKKRRVLFSKAQTLELERRFRQQRYLSAPEREQLAR 119

Query: 586 NLKLTETQVKIWFQNRRYKTKRKQLTSDLGDLEKHPSLPALKE 714
            L+LT TQVKIWFQN RYK KR +     G +E  P L A  E
Sbjct: 120 LLRLTPTQVKIWFQNHRYKLKRARAPGAPGAMEP-PDLAASAE 161


>ref|NP_001003260.1| thyroid transcription factor 1 [Canis lupus familiaris].
          Length = 371

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 152 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 211

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 212 HRYKMKRQ 219


>ref|XP_543239.2| PREDICTED: similar to NK2 transcription factor related, locus 6
           [Canis familiaris].
          Length = 342

 Score = 89.0 bits (219), Expect = 2e-17
 Identities = 47/80 (58%), Positives = 56/80 (70%), Gaps = 1/80 (1%)
 Frame = +1

Query: 466 PKQPQKRS-RAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYK 642
           PK+ Q+R  R  FS  QV+ LER+F  Q+YLSAPER HLA  L+LT TQVKIWFQNRRYK
Sbjct: 170 PKERQRRRPRVLFSQAQVLALERRFKQQRYLSAPEREHLAGALQLTPTQVKIWFQNRRYK 229

Query: 643 TKRKQLTSDLGDLEKHPSLP 702
            KR++    L +L  HP  P
Sbjct: 230 CKRQRQDKSL-ELAGHPLAP 248


>ref|XP_849082.1| PREDICTED: similar to Homeobox protein Nkx-2.4 (Homeobox protein
           NKX2.4) (Homeobox protein NK-2 homolog D) [Canis
           familiaris].
          Length = 233

 Score = 85.5 bits (210), Expect = 2e-16
 Identities = 42/80 (52%), Positives = 50/80 (62%)
 Frame = +1

Query: 415 LLDCENTPGALPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLK 594
           + D   T   L +       P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + 
Sbjct: 44  IADAAKTLAPLHAAAAAAAAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIH 103

Query: 595 LTETQVKIWFQNRRYKTKRK 654
           LT TQVKIWFQN RYK KR+
Sbjct: 104 LTPTQVKIWFQNHRYKMKRQ 123


>ref|NP_001010959.1| homeobox protein Nkx-2.5 [Canis lupus familiaris].
          Length = 322

 Score = 82.0 bits (201), Expect = 2e-15
 Identities = 39/60 (65%), Positives = 46/60 (76%)
 Frame = +1

Query: 478 QKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 657
           +++ R  FS  QV ELER+F  Q+YLSAPER  LA  LKLT TQVKIWFQNRRYK KR++
Sbjct: 137 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKCKRQR 196


>ref|XP_542867.2| PREDICTED: similar to NK2 transcription factor related, locus 2
           [Canis familiaris].
          Length = 273

 Score = 78.2 bits (191), Expect = 3e-14
 Identities = 36/58 (62%), Positives = 43/58 (74%)
 Frame = +1

Query: 478 QKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 651
           +++ R  FS  Q  ELER+F  Q+YLSAPER HLA  ++LT TQVKIWFQN RYK KR
Sbjct: 128 KRKRRVLFSKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKMKR 185


>ref|XP_855075.1| PREDICTED: similar to T-cell leukemia homeobox protein 2 (Homeobox
           protein Hox-11L1) (Homeobox TLX-2) (PMUR10F) [Canis
           familiaris].
          Length = 284

 Score = 75.5 bits (184), Expect = 2e-13
 Identities = 40/79 (50%), Positives = 53/79 (67%)
 Frame = +1

Query: 457 PPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 636
           PP  K+P    R +FS +QV+ELER+F  QKYL++ ERA LAK L++T+ QVK WFQNRR
Sbjct: 154 PPKRKKP----RTSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 209

Query: 637 YKTKRKQLTSDLGDLEKHP 693
            K +  +     G  E+HP
Sbjct: 210 TKWRGPKAKEPQG--ERHP 226


>ref|XP_546241.2| PREDICTED: similar to T-cell leukemia homeobox protein 3 (Homeobox
           protein Hox-11L2) [Canis familiaris].
          Length = 637

 Score = 74.3 bits (181), Expect = 4e-13
 Identities = 36/66 (54%), Positives = 48/66 (72%)
 Frame = +1

Query: 457 PPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 636
           PP  K+P    R +FS  Q+ ELE++F  QKYL++ ERA LAK+LK+T+ QVK WFQNRR
Sbjct: 509 PPKRKKP----RTSFSRVQICELEKRFHRQKYLASAERAALAKSLKMTDAQVKTWFQNRR 564

Query: 637 YKTKRK 654
            K +R+
Sbjct: 565 TKWRRQ 570


  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: 73,893,220
Number of extensions: 2045663
Number of successful extensions: 9579
Number of sequences better than 1.0e-05: 150
Number of HSP's gapped: 9556
Number of HSP's successfully gapped: 151
Length of query: 668
Length of database: 18,874,504
Length adjustment: 109
Effective length of query: 559
Effective length of database: 15,240,880
Effective search space: 8519651920
Effective search space used: 8519651920
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: 36 (18.5 bits)

Search to RefSeqHP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20110601C-002510
         (2005 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|NP_006158.2| homeobox protein Nkx-3.1 [Homo sapiens].             269   8e-72
Alignment   gi|NP_001180.1| homeobox protein Nkx-3.2 [Homo sapiens].             115   2e-25
Alignment   gi|NP_055175.2| homeobox protein Nkx-2.8 [Homo sapiens].              90   9e-18
Alignment   gi|NP_660328.2| homeobox protein Nkx-2.3 [Homo sapiens].              90   9e-18
Alignment   gi|NP_001129743.2| homeobox protein Nkx-2.6 [Homo sapiens].           89   1e-17
Alignment   gi|NP_003308.1| homeobox protein Nkx-2.1 isoform 2 [Homo sapien...    89   1e-17
Alignment   gi|NP_001073136.1| homeobox protein Nkx-2.1 isoform 1 [Homo sap...    89   1e-17
Alignment   gi|NP_149416.1| homeobox protein Nkx-2.4 [Homo sapiens].              84   5e-16
Alignment   gi|NP_004378.1| homeobox protein Nkx-2.5 isoform 1 [Homo sapien...    84   6e-16
Alignment   gi|NP_002500.1| homeobox protein Nkx-2.2 [Homo sapiens].              78   3e-14

>ref|NP_006158.2| homeobox protein Nkx-3.1 [Homo sapiens].
          Length = 234

 Score =  269 bits (687), Expect = 8e-72
 Identities = 146/239 (61%), Positives = 160/239 (66%)
 Frame = +1

Query: 94  PELRPGEGGTAGCSPRAAPPIQSKPLTSFLIQDILRDRTEQCGGQAGSXXXXXXXXXXXX 273
           PE RPGE    G    AAPP  SKPLTSFLIQDILRD  ++ GG+  S            
Sbjct: 5   PEPRPGEAKAEG----AAPPTPSKPLTSFLIQDILRDGAQRQGGRTSSQRQRDPEPEPEP 60

Query: 274 XXXXXXXKGGRGSAGAPEDHRXXXXXXXXRXXXXXXXXXXDRHLETYLLDCENTPGALPS 453
                  +GGR  AGA  D                     +RHL +YLLD ENT GALP 
Sbjct: 61  EP-----EGGRSRAGAQNDQLSTGPRAAPEEAETLAETEPERHLGSYLLDSENTSGALPR 115

Query: 454 LPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR 633
           LP TPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR
Sbjct: 116 LPQTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNR 175

Query: 634 RYKTKRKQLTSDLGDLEKHPSLPALKEEGFSRASLIAMHHTXXXXXXXXXXXXWSPAFW 810
           RYKTKRKQL+S+LGDLEKH SLPALKEE FSRASL++++++            WSPAFW
Sbjct: 176 RYKTKRKQLSSELGDLEKHSSLPALKEEAFSRASLVSVYNSYPYYPYLYCVGSWSPAFW 234


>ref|NP_001180.1| homeobox protein Nkx-3.2 [Homo sapiens].
          Length = 333

 Score =  115 bits (287), Expect = 2e-25
 Identities = 54/72 (75%), Positives = 62/72 (86%)
 Frame = +1

Query: 457 PPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 636
           P  PK  +KRSRAAFSH QV ELER+F+HQ+YLS PERA LA +LKLTETQVKIWFQNRR
Sbjct: 199 PAAPKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRR 258

Query: 637 YKTKRKQLTSDL 672
           YKTKR+Q+ +DL
Sbjct: 259 YKTKRRQMAADL 270


>ref|NP_055175.2| homeobox protein Nkx-2.8 [Homo sapiens].
          Length = 239

 Score = 89.7 bits (221), Expect = 9e-18
 Identities = 45/83 (54%), Positives = 54/83 (65%)
 Frame = +1

Query: 403 LETYLLDCENTPGALPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLA 582
           LET   D    P A P+ P +  + +K+ R  FS  Q +ELER+F  Q+YLSAPER  LA
Sbjct: 59  LETSPPDSSQRPSARPASPGSDAEKRKKRRVLFSKAQTLELERRFRQQRYLSAPEREQLA 118

Query: 583 KNLKLTETQVKIWFQNRRYKTKR 651
             L+LT TQVKIWFQN RYK KR
Sbjct: 119 SLLRLTPTQVKIWFQNHRYKLKR 141


>ref|NP_660328.2| homeobox protein Nkx-2.3 [Homo sapiens].
          Length = 364

 Score = 89.7 bits (221), Expect = 9e-18
 Identities = 50/94 (53%), Positives = 61/94 (64%)
 Frame = +1

Query: 421 DCENTPGALPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLT 600
           DC+    A  S  P P+  +++ R  FS  QV ELER+F  Q+YLSAPER HLA +LKLT
Sbjct: 133 DCK---AAEESERPKPRS-RRKPRVLFSQAQVFELERRFKQQRYLSAPEREHLASSLKLT 188

Query: 601 ETQVKIWFQNRRYKTKRKQLTSDLGDLEKHPSLP 702
            TQVKIWFQNRRYK KR++    L +L  H   P
Sbjct: 189 STQVKIWFQNRRYKCKRQRQDKSL-ELGAHAPPP 221


>ref|NP_001129743.2| homeobox protein Nkx-2.6 [Homo sapiens].
          Length = 301

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 47/80 (58%), Positives = 55/80 (68%), Gaps = 1/80 (1%)
 Frame = +1

Query: 466 PKQPQKRS-RAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYK 642
           PK  Q+R  R  FS  QV+ LER+F  Q+YLSAPER HLA  L+LT TQVKIWFQNRRYK
Sbjct: 127 PKARQRRKPRVLFSQAQVLALERRFKQQRYLSAPEREHLASALQLTSTQVKIWFQNRRYK 186

Query: 643 TKRKQLTSDLGDLEKHPSLP 702
            KR++    L +L  HP  P
Sbjct: 187 CKRQRQDKSL-ELAGHPLTP 205


>ref|NP_003308.1| homeobox protein Nkx-2.1 isoform 2 [Homo sapiens].
          Length = 371

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 152 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 211

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 212 HRYKMKRQ 219


>ref|NP_001073136.1| homeobox protein Nkx-2.1 isoform 1 [Homo sapiens].
          Length = 401

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 182 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 241

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 242 HRYKMKRQ 249


>ref|NP_149416.1| homeobox protein Nkx-2.4 [Homo sapiens].
          Length = 354

 Score = 84.0 bits (206), Expect = 5e-16
 Identities = 39/60 (65%), Positives = 45/60 (75%)
 Frame = +1

Query: 475 PQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 654
           P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN RYK KR+
Sbjct: 188 PRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 247


>ref|NP_004378.1| homeobox protein Nkx-2.5 isoform 1 [Homo sapiens].
          Length = 324

 Score = 83.6 bits (205), Expect = 6e-16
 Identities = 45/78 (57%), Positives = 53/78 (67%), Gaps = 2/78 (2%)
 Frame = +1

Query: 478 QKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 657
           +++ R  FS  QV ELER+F  Q+YLSAPER  LA  LKLT TQVKIWFQNRRYK KR++
Sbjct: 138 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKCKRQR 197

Query: 658 --LTSDLGDLEKHPSLPA 705
              T +L  L   P  PA
Sbjct: 198 QDQTLELVGLPPPPPPPA 215


>ref|NP_002500.1| homeobox protein Nkx-2.2 [Homo sapiens].
          Length = 273

 Score = 78.2 bits (191), Expect = 3e-14
 Identities = 36/58 (62%), Positives = 43/58 (74%)
 Frame = +1

Query: 478 QKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 651
           +++ R  FS  Q  ELER+F  Q+YLSAPER HLA  ++LT TQVKIWFQN RYK KR
Sbjct: 128 KRKRRVLFSKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKMKR 185


  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: 72,168,477
Number of extensions: 1990587
Number of successful extensions: 9033
Number of sequences better than 1.0e-05: 153
Number of HSP's gapped: 9019
Number of HSP's successfully gapped: 153
Length of query: 668
Length of database: 18,297,164
Length adjustment: 109
Effective length of query: 559
Effective length of database: 14,704,088
Effective search space: 8219585192
Effective search space used: 8219585192
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: 36 (18.5 bits)

Search to RefSeqMP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20110601C-002510
         (2005 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_035051.1| homeobox protein Nkx-3.1 [Mus musculus].             231   2e-60
Alignment   gi|NP_031550.2| homeobox protein Nkx-3.2 [Mus musculus].             115   2e-25
Alignment   gi|NP_035050.2| homeobox protein Nkx-2.6 [Mus musculus].              92   2e-18
Alignment   gi|NP_032725.1| homeobox protein Nkx-2.3 [Mus musculus].              89   1e-17
Alignment   gi|NP_001139670.1| homeobox protein Nkx-2.1 [Mus musculus].           89   1e-17
Alignment   gi|NP_033411.3| homeobox protein Nkx-2.1 [Mus musculus].              89   1e-17
Alignment   gi|NP_075993.1| homeobox protein Nkx-2.4 [Mus musculus].              84   4e-16
Alignment   gi|NP_032726.1| homeobox protein Nkx-2.5 [Mus musculus].              83   9e-16
Alignment   gi|NP_032727.2| homeobox protein Nkx-2.8 [Mus musculus].              81   3e-15
Alignment   gi|NP_001071100.1| homeobox protein Nkx-2.2 isoform 2 [Mus musc...    78   2e-14

>ref|NP_035051.1| homeobox protein Nkx-3.1 [Mus musculus].
          Length = 237

 Score =  231 bits (588), Expect = 2e-60
 Identities = 132/230 (57%), Positives = 146/230 (63%), Gaps = 2/230 (0%)
 Frame = +1

Query: 127 GCSPRAAPPIQSKPLTSFLIQDILRDRTEQCGGQAGSXXXXXXXXXXXXXXXXXXXKGGR 306
           G SP AAPP QSK LTSFLIQDILRDR E+ GG +G+                    GGR
Sbjct: 16  GRSPWAAPPTQSKRLTSFLIQDILRDRAERHGGHSGNPQHSPDPRRDSAPEPDKA--GGR 73

Query: 307 GSAGAPEDHRXXXXXXXXRXXXXXXXXXXDRHLETYLLDCENTPGALPSLPPTPKQPQKR 486
           G A  PED                     D H ETYLLDCE+ PG L S P   KQPQKR
Sbjct: 74  GVA--PED----PPSIRHSPAETPTEPESDAHFETYLLDCEHNPGDLASAPQVTKQPQKR 127

Query: 487 SRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLTS 666
           SRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL+ 
Sbjct: 128 SRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSE 187

Query: 667 DLGDLEKHP--SLPALKEEGFSRASLIAMHHTXXXXXXXXXXXXWSPAFW 810
           DLG LEK+   SLPALK++     SL++++ +            W P+FW
Sbjct: 188 DLGVLEKNSPLSLPALKDDSLPSTSLVSVYTSYPYYPYLYCLGSWHPSFW 237


>ref|NP_031550.2| homeobox protein Nkx-3.2 [Mus musculus].
          Length = 333

 Score =  115 bits (287), Expect = 2e-25
 Identities = 54/72 (75%), Positives = 62/72 (86%)
 Frame = +1

Query: 457 PPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 636
           P  PK  +KRSRAAFSH QV ELER+F+HQ+YLS PERA LA +LKLTETQVKIWFQNRR
Sbjct: 199 PAAPKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRR 258

Query: 637 YKTKRKQLTSDL 672
           YKTKR+Q+ +DL
Sbjct: 259 YKTKRRQMAADL 270


>ref|NP_035050.2| homeobox protein Nkx-2.6 [Mus musculus].
          Length = 289

 Score = 91.7 bits (226), Expect = 2e-18
 Identities = 45/80 (56%), Positives = 57/80 (71%)
 Frame = +1

Query: 463 TPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYK 642
           T  +PQ++SR  FS  QV+ LER+F  Q+YL+APER HLA  L+LT TQVKIWFQNRRYK
Sbjct: 118 TRTRPQRKSRVLFSQAQVLALERRFKQQRYLTAPEREHLASALQLTSTQVKIWFQNRRYK 177

Query: 643 TKRKQLTSDLGDLEKHPSLP 702
           +K ++    L +L  HP  P
Sbjct: 178 SKSQRQDQTL-ELAGHPLAP 196


>ref|NP_032725.1| homeobox protein Nkx-2.3 [Mus musculus].
          Length = 362

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 46/81 (56%), Positives = 56/81 (69%)
 Frame = +1

Query: 460 PTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRY 639
           P P+  +++ R  FS  QV ELER+F  Q+YLSAPER HLA +LKLT TQVKIWFQNRRY
Sbjct: 140 PKPRS-RRKPRVLFSQAQVFELERRFKQQRYLSAPEREHLASSLKLTSTQVKIWFQNRRY 198

Query: 640 KTKRKQLTSDLGDLEKHPSLP 702
           K KR++    L +L  H   P
Sbjct: 199 KCKRQRQDKSL-ELGTHAPPP 218


>ref|NP_001139670.1| homeobox protein Nkx-2.1 [Mus musculus].
          Length = 372

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 152 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 211

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 212 HRYKMKRQ 219


>ref|NP_033411.3| homeobox protein Nkx-2.1 [Mus musculus].
          Length = 372

 Score = 89.4 bits (220), Expect = 1e-17
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 152 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 211

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 212 HRYKMKRQ 219


>ref|NP_075993.1| homeobox protein Nkx-2.4 [Mus musculus].
          Length = 354

 Score = 84.0 bits (206), Expect = 4e-16
 Identities = 39/60 (65%), Positives = 45/60 (75%)
 Frame = +1

Query: 475 PQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 654
           P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN RYK KR+
Sbjct: 187 PRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 246


>ref|NP_032726.1| homeobox protein Nkx-2.5 [Mus musculus].
          Length = 318

 Score = 82.8 bits (203), Expect = 9e-16
 Identities = 45/87 (51%), Positives = 55/87 (63%), Gaps = 6/87 (6%)
 Frame = +1

Query: 478 QKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 657
           +++ R  FS  QV ELER+F  Q+YLSAPER  LA  LKLT TQVKIWFQNRRYK KR++
Sbjct: 137 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKCKRQR 196

Query: 658 LTSDLGDLEKHP------SLPALKEEG 720
               L  L   P      ++P L  +G
Sbjct: 197 QDQTLELLGPPPPPARRIAVPVLVRDG 223


>ref|NP_032727.2| homeobox protein Nkx-2.8 [Mus musculus].
          Length = 235

 Score = 81.3 bits (199), Expect = 3e-15
 Identities = 41/83 (49%), Positives = 51/83 (61%)
 Frame = +1

Query: 403 LETYLLDCENTPGALPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLA 582
           LET   D           P +  + +++ R  FS  Q +ELER+F  Q+YLSAPER  LA
Sbjct: 56  LETSPADSSQLASLRRESPGSDPEKRRKRRVLFSKAQTLELERRFRQQRYLSAPEREQLA 115

Query: 583 KNLKLTETQVKIWFQNRRYKTKR 651
           + L+LT TQVKIWFQN RYK KR
Sbjct: 116 RLLRLTPTQVKIWFQNHRYKLKR 138


>ref|NP_001071100.1| homeobox protein Nkx-2.2 isoform 2 [Mus musculus].
          Length = 248

 Score = 78.2 bits (191), Expect = 2e-14
 Identities = 36/58 (62%), Positives = 43/58 (74%)
 Frame = +1

Query: 478 QKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 651
           +++ R  FS  Q  ELER+F  Q+YLSAPER HLA  ++LT TQVKIWFQN RYK KR
Sbjct: 128 KRKRRVLFSKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKMKR 185


  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: 60,674,515
Number of extensions: 1643799
Number of successful extensions: 7357
Number of sequences better than 1.0e-05: 135
Number of HSP's gapped: 7345
Number of HSP's successfully gapped: 135
Length of query: 668
Length of database: 15,617,559
Length adjustment: 108
Effective length of query: 560
Effective length of database: 12,373,671
Effective search space: 6929255760
Effective search space used: 6929255760
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: 36 (18.5 bits)

Search to RefSeqSP_Rel49

BLASTX 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20110601C-002510
         (2005 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Alignment   gi|XP_003356908.1| PREDICTED: homeobox protein Nkx-3.2-like [Su...   115   1e-25
Alignment   gi|XP_003359369.1| PREDICTED: LOW QUALITY PROTEIN: homeobox pro...    89   7e-18
Alignment   gi|XP_001925552.2| PREDICTED: thyroid transcription factor 1-li...    89   7e-18
Alignment   gi|XP_003356737.1| PREDICTED: thyroid transcription factor 1-li...    89   7e-18
Alignment   gi|XP_001925375.2| PREDICTED: homeobox protein Nkx-2.8-like [Su...    88   2e-17
Alignment   gi|XP_003134089.1| PREDICTED: homeobox protein Nkx-2.5-like [Su...    84   4e-16
Alignment   gi|XP_003359963.1| PREDICTED: homeobox protein Nkx-2.2-like [Su...    78   2e-14
Alignment   gi|XP_003125043.1| PREDICTED: t-cell leukemia homeobox protein ...    77   4e-14
Alignment   gi|XP_003134109.2| PREDICTED: t-cell leukemia homeobox protein ...    74   2e-13
Alignment   gi|XP_001928044.1| PREDICTED: homeobox protein HMX3 [Sus scrofa].     74   3e-13

>ref|XP_003356908.1| PREDICTED: homeobox protein Nkx-3.2-like [Sus scrofa].
          Length = 337

 Score =  115 bits (287), Expect = 1e-25
 Identities = 54/72 (75%), Positives = 62/72 (86%)
 Frame = +1

Query: 457 PPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 636
           P  PK  +KRSRAAFSH QV ELER+F+HQ+YLS PERA LA +LKLTETQVKIWFQNRR
Sbjct: 203 PAAPKPRKKRSRAAFSHAQVFELERRFNHQRYLSGPERADLAASLKLTETQVKIWFQNRR 262

Query: 637 YKTKRKQLTSDL 672
           YKTKR+Q+ +DL
Sbjct: 263 YKTKRRQMAADL 274


>ref|XP_003359369.1| PREDICTED: LOW QUALITY PROTEIN: homeobox protein Nkx-2.3-like [Sus
           scrofa].
          Length = 367

 Score = 89.4 bits (220), Expect = 7e-18
 Identities = 47/84 (55%), Positives = 57/84 (67%)
 Frame = +1

Query: 421 DCENTPGALPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLT 600
           DC+    A  S  P P+  +++ R  FS  QV ELER+F  Q+YLSAPER HLA +LKLT
Sbjct: 134 DCK---AAEESERPKPRS-RRKPRVLFSQAQVFELERRFKQQRYLSAPEREHLASSLKLT 189

Query: 601 ETQVKIWFQNRRYKTKRKQLTSDL 672
            TQVKIWFQNRRYK KR++    L
Sbjct: 190 STQVKIWFQNRRYKCKRQRQDKSL 213


>ref|XP_001925552.2| PREDICTED: thyroid transcription factor 1-like isoform 1 [Sus
           scrofa].
          Length = 369

 Score = 89.4 bits (220), Expect = 7e-18
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 152 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 211

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 212 HRYKMKRQ 219


>ref|XP_003356737.1| PREDICTED: thyroid transcription factor 1-like isoform 2 [Sus
           scrofa].
          Length = 369

 Score = 89.4 bits (220), Expect = 7e-18
 Identities = 41/68 (60%), Positives = 49/68 (72%)
 Frame = +1

Query: 451 SLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 630
           ++ P P  P+++ R  FS  QV ELER+F  QKYLSAPER HLA  + LT TQVKIWFQN
Sbjct: 152 NMAPLPSAPRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 211

Query: 631 RRYKTKRK 654
            RYK KR+
Sbjct: 212 HRYKMKRQ 219


>ref|XP_001925375.2| PREDICTED: homeobox protein Nkx-2.8-like [Sus scrofa].
          Length = 241

 Score = 87.8 bits (216), Expect = 2e-17
 Identities = 42/77 (54%), Positives = 52/77 (67%)
 Frame = +1

Query: 421 DCENTPGALPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLT 600
           D    P A P+ P +  + +K+ R  FS  Q +ELER+F  Q+YLSAPER  LA+ L+LT
Sbjct: 65  DSSQRPSAGPASPSSDAEKRKKRRVLFSKAQTLELERRFRQQRYLSAPEREQLARLLRLT 124

Query: 601 ETQVKIWFQNRRYKTKR 651
            TQVKIWFQN RYK KR
Sbjct: 125 PTQVKIWFQNHRYKLKR 141


>ref|XP_003134089.1| PREDICTED: homeobox protein Nkx-2.5-like [Sus scrofa].
          Length = 323

 Score = 83.6 bits (205), Expect = 4e-16
 Identities = 45/78 (57%), Positives = 53/78 (67%), Gaps = 2/78 (2%)
 Frame = +1

Query: 478 QKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 657
           +++ R  FS  QV ELER+F  Q+YLSAPER  LA  LKLT TQVKIWFQNRRYK KR++
Sbjct: 137 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKCKRQR 196

Query: 658 --LTSDLGDLEKHPSLPA 705
              T +L  L   P  PA
Sbjct: 197 QDQTLELVGLPPPPPPPA 214


>ref|XP_003359963.1| PREDICTED: homeobox protein Nkx-2.2-like [Sus scrofa].
          Length = 273

 Score = 78.2 bits (191), Expect = 2e-14
 Identities = 36/58 (62%), Positives = 43/58 (74%)
 Frame = +1

Query: 478 QKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 651
           +++ R  FS  Q  ELER+F  Q+YLSAPER HLA  ++LT TQVKIWFQN RYK KR
Sbjct: 128 KRKRRVLFSKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKMKR 185


>ref|XP_003125043.1| PREDICTED: t-cell leukemia homeobox protein 2-like [Sus scrofa].
          Length = 284

 Score = 77.0 bits (188), Expect = 4e-14
 Identities = 40/78 (51%), Positives = 56/78 (71%)
 Frame = +1

Query: 457 PPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 636
           PP  K+P    R +FS +QV+ELER+F  QKYL++ ERA LAK L++T+ QVK WFQNRR
Sbjct: 154 PPKRKKP----RTSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 209

Query: 637 YKTKRKQLTSDLGDLEKH 690
            K +R+  T++  + E+H
Sbjct: 210 TKWRRQ--TAEEREAERH 225


>ref|XP_003134109.2| PREDICTED: t-cell leukemia homeobox protein 3-like [Sus scrofa].
          Length = 291

 Score = 74.3 bits (181), Expect = 2e-13
 Identities = 36/66 (54%), Positives = 48/66 (72%)
 Frame = +1

Query: 457 PPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 636
           PP  K+P    R +FS  Q+ ELE++F  QKYL++ ERA LAK+LK+T+ QVK WFQNRR
Sbjct: 163 PPKRKKP----RTSFSRVQICELEKRFHRQKYLASAERAALAKSLKMTDAQVKTWFQNRR 218

Query: 637 YKTKRK 654
            K +R+
Sbjct: 219 TKWRRQ 224


>ref|XP_001928044.1| PREDICTED: homeobox protein HMX3 [Sus scrofa].
          Length = 357

 Score = 73.9 bits (180), Expect = 3e-13
 Identities = 44/86 (51%), Positives = 55/86 (63%), Gaps = 6/86 (6%)
 Frame = +1

Query: 433 TPGA------LPSLPPTPKQPQKRSRAAFSHTQVIELERKFSHQKYLSAPERAHLAKNLK 594
           TPGA        S    P   +K++R  FS +QV +LE  F  ++YLS+ ERA LA +L 
Sbjct: 206 TPGAEDWKKGAESPEKKPACRKKKTRTVFSRSQVFQLESTFDMKRYLSSSERAGLAASLH 265

Query: 595 LTETQVKIWFQNRRYKTKRKQLTSDL 672
           LTETQVKIWFQNRR K KR QL ++L
Sbjct: 266 LTETQVKIWFQNRRNKWKR-QLAAEL 290


  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: 46,372,806
Number of extensions: 1364145
Number of successful extensions: 6132
Number of sequences better than 1.0e-05: 120
Number of HSP's gapped: 6125
Number of HSP's successfully gapped: 120
Length of query: 668
Length of database: 11,343,932
Length adjustment: 106
Effective length of query: 562
Effective length of database: 8,704,850
Effective search space: 4892125700
Effective search space used: 4892125700
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 35 (18.1 bits)

Search to Sscrofa10_2

BLASTN 2.2.24 [Aug-08-2010]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= 20110601C-002510
         (2005 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_Chr14                                                        2625   0.0  

>Sscrofa_Chr14 
||          Length = 153851969

 Score = 2625 bits (1324), Expect = 0.0
 Identities = 1338/1345 (99%)
 Strand = Plus / Minus

                                                                           
Query: 391     ccagataggcaccttgagacttatctgctggactgtgaaaacactccaggcgccttgccg 450
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8628547 ccagataggcaccttgagacttatctgctggactgtgaaaacactccaggcgccttgccg 8628488

                                                                           
Query: 451     agcctgcccccaacccccaagcagccgcagaagcgctcccgggccgccttctcccacact 510
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8628487 agcctgcccccaacccccaagcagccgcagaagcgctcccgggccgccttctcccacact 8628428

                                                                           
Query: 511     caggtcatagagttagagaggaagttcagccaccagaagtatctgtcggcccccgaaagg 570
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8628427 caggtcatagagttagagaggaagttcagccaccagaagtatctgtcggcccccgaaagg 8628368

                                                                           
Query: 571     gctcacctggccaagaacctcaagctcacggagacccaagtgaaaatatggttccaaaat 630
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8628367 gctcacctggccaagaacctcaagctcacggagacccaagtgaaaatatggttccaaaat 8628308

                                                                           
Query: 631     agacgctataaaaccaagcggaagcagctcacctcggacctgggggacctggagaagcac 690
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8628307 agacgctataaaaccaagcggaagcagctcacctcggacctgggggacctggagaagcac 8628248

                                                                           
Query: 691     ccctccttgccggctctgaaggaggaaggcttctctcgggcctccctcatcgccatgcat 750
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8628247 ccctccttgccggctctgaaggaggaaggcttctctcgggcctccctcatcgccatgcat 8628188

                                                                           
Query: 751     cacacgtacccttactacccctacctttactgcttgggaggctggagcccagctttctgg 810
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8628187 cacacgtacccttactacccctacctttactgcttgggaggctggagcccagctttctgg 8628128

                                                                           
Query: 811     taacaacgccggctcagacaaccatgtgtgatcaaaagctgccttcccctggtggtccct 870
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8628127 taacaacgccggctcagacaaccatgtgtgatcaaaagctgccttcccctggtggtccct 8628068

                                                                           
Query: 871     ctggaaggcagaagggcccggggtcagggaggactgggccgcaagagacctgcagactga 930
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8628067 ctggaaggcagaagggcccggggtcagggaggactgggccgcaagagacctgcagactga 8628008

                                                                           
Query: 931     aagcactggaggtttgcttggaaatcccagattcttcactggtgtgccaatgaaagacct 990
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8628007 aagcactggaggtttgcttggaaatcccagattcttcactggtgtgccaatgaaagacct 8627948

                                                                           
Query: 991     gggacaggaaataacttaagagccaaataggtnnnnnnntccacgggaatgtaggtcatt 1050
               ||||||||||||||||||||||||||||||||       |||||||||||||||||||||
Sbjct: 8627947 gggacaggaaataacttaagagccaaataggtccccccctccacgggaatgtaggtcatt 8627888

                                                                           
Query: 1051    tttgctttgagagacccgcttgaagtggggcgggatacagccaagtgctgtttccagcat 1110
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627887 tttgctttgagagacccgcttgaagtggggcgggatacagccaagtgctgtttccagcat 8627828

                                                                           
Query: 1111    tacttgtggaggctgcccacatcacctgtgagaattctccgcctccagctccatcctctt 1170
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627827 tacttgtggaggctgcccacatcacctgtgagaattctccgcctccagctccatcctctt 8627768

                                                                           
Query: 1171    ttgtgactgagcatccgctcctcctgaagggggtgtgggggaggggaggagagctaagat 1230
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627767 ttgtgactgagcatccgctcctcctgaagggggtgtgggggaggggaggagagctaagat 8627708

                                                                           
Query: 1231    gagatgtcacctccagaattaaactgaaggtcagacgcctctcattggccttggagtatg 1290
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627707 gagatgtcacctccagaattaaactgaaggtcagacgcctctcattggccttggagtatg 8627648

                                                                           
Query: 1291    accacgggttgctctccatccctgggggagagcaggaagcacagggtcccacagagaagc 1350
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627647 accacgggttgctctccatccctgggggagagcaggaagcacagggtcccacagagaagc 8627588

                                                                           
Query: 1351    ctgtggtgctcagggcaggttggcacaggatacagagatgggtaggaggagatgaaaata 1410
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627587 ctgtggtgctcagggcaggttggcacaggatacagagatgggtaggaggagatgaaaata 8627528

                                                                           
Query: 1411    taagcttcttattcttccttttaaaataataggccaactgaagtatttacagggtggccc 1470
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627527 taagcttcttattcttccttttaaaataataggccaactgaagtatttacagggtggccc 8627468

                                                                           
Query: 1471    aagcagaacaagaagaactcactgtggttttaagacaagctgtctaaacagaaactttcc 1530
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627467 aagcagaacaagaagaactcactgtggttttaagacaagctgtctaaacagaaactttcc 8627408

                                                                           
Query: 1531    ctcaagaggtgggctggggccggaagaatctccccgtgtccaagacagtggcttaaggag 1590
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627407 ctcaagaggtgggctggggccggaagaatctccccgtgtccaagacagtggcttaaggag 8627348

                                                                           
Query: 1591    aagtccccacgcatgctgctgcggggggcctcgcatgtctttattagcaaaaggaccttt 1650
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627347 aagtccccacgcatgctgctgcggggggcctcgcatgtctttattagcaaaaggaccttt 8627288

                                                                           
Query: 1651    ttgccctgggcctgagaatttagaatgagaaggttcctggagttttcaggctgtaattca 1710
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627287 ttgccctgggcctgagaatttagaatgagaaggttcctggagttttcaggctgtaattca 8627228

                                        
Query: 1711    tacaacaccatgacaggtaacataa 1735
               |||||||||||||||||||||||||
Sbjct: 8627227 tacaacaccatgacaggtaacataa 8627203



 Score =  521 bits (263), Expect = e-145
 Identities = 321/347 (92%), Gaps = 12/347 (3%)
 Strand = Plus / Minus

                                                                           
Query: 3       aagtggtgcggccgcagccggcgcagcctgggcgcagatgcccgggcctctgctcaggcg 62
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8630186 aagtggtgcggccgcagccggcgcagcctgggcgcagatgcccgggcctctgctcaggcg 8630127

                                                                           
Query: 63      ccggtgctgagccgccaggatgctccgggctcccgagctacggccnnnnnnnnnnnnnac 122
               | |||||||||||||||||||||||||||||||||||||||||||             ||
Sbjct: 8630126 cgggtgctgagccgccaggatgctccgggctcccgagctacggccgggggagggggggac 8630067

                                                                           
Query: 123     ggcaggctgcagcccccgcgccgcaccacccatccagtccaagccgcttacctccttcct 182
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8630066 ggcaggctgcagcccccgcgccgcaccacccatccagtccaagccgcttacctccttcct 8630007

                                                                           
Query: 183     catccaggacatcctacgggaccgcacggagcagtgcggaggccaagcgggcagcccgca 242
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8630006 catccaggacatcctacgggaccgcacggagcagtgcggaggccaagcgggcagcccgca 8629947

                                                                           
Query: 243     gccgc------------agccccggcgccagccagaccagaggcgagaccctgagccgga 290
               |||||            |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8629946 gccgcagccaccgccgcagccccggcgccagccagaccagaggcgagaccctgagccgga 8629887

                                                              
Query: 291     gcccaagggaggaagaggcagcgccggggcgcctgaggaccatagga 337
               |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8629886 gcccaagggaggaagaggcagcgccggggcgcctgaggaccatagga 8629840



 Score =  161 bits (81), Expect = 2e-36
 Identities = 83/84 (98%)
 Strand = Plus / Minus

                                                                           
Query: 1780    ccacagcanggcttcttttcagtccagacttttagtctgactgcacctaacttatgcctt 1839
               |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8627158 ccacagcagggcttcttttcagtccagacttttagtctgactgcacctaacttatgcctt 8627099

                                       
Query: 1840    ccttatttagcctgatccctagtc 1863
               ||||||||||||||||||||||||
Sbjct: 8627098 ccttatttagcctgatccctagtc 8627075


  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: 51,851,893
Number of extensions: 490
Number of successful extensions: 490
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 489
Number of HSP's successfully gapped: 6
Length of query: 2005
Length of database: 2,808,509,378
Length adjustment: 22
Effective length of query: 1983
Effective length of database: 2,808,408,574
Effective search space: 5569074202242
Effective search space used: 5569074202242
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)