>SHH274 (SHH274Q) /CSM/SH/SHH2-D/SHH274Q.Seq.d/
AAATTCACCAAATCAACGTTTAGCAATGAGATCATTTCAAATTTTACGTGGTTTAGAACC
AACTACAACCATTGATTCCCTTACAGAGGTGATGCAAACAATGGGTAAATATATTCAAAA
TAATTCAATTGAAAATTCATTATTTATTTCAGAAATTCAAGAAACGCTTCAAGTCATGAT
AAAATGTATTCATCCTAGTAAATTAATTTTATTCCCACAAATATTTTGGGGTACAGTTGC
AATGTTACATACTGATTTTGAAAATCATTTCATTGGTGCCATCAAGTTGTTATCAATGTT
ATTGGATATCATAAACTTTAGTGACCGTGCAGTTCAAAATGTTTTCTTGGCATCAATGCC
AAAAGATTGGGAAAATTACCATGGTGTTCAACCATTGATTATCAAAGGTTTAATGTCTGT
AAATACTGCACCCTATGCATTGGAATTCCTAAGTAGAATCACGCTTGAACCATGTGATGA
AATATTTCAACCTGAACCAATAAGATTCTTAACCAATTTAATCAGTTTATTACCTTATCT
TTGTTTATCAATTGGTGATGAATCTCCAATGCCACAACAAGTAGCCGAGAATCTATCGGT
TGGTTGTGAAAATCXXXXXXXXXX

NSPNQRLAMRSFQILRGLEPTTTIDSLTEVMQTMGKYIQNNSIENSLFISEIQETLQVMI
KCIHPSKLILFPQIFWGTVAMLHTDFENHFIGAIKLLSMLLDIINFSDRAVQNVFLASMP
KDWENYHGVQPLIIKGLMSVNTAPYALEFLSRITLEPCDEIFQPEPIRFLTNLISLLPYL
CLSIGDESPMPQQVAENLSVGCEN---

Frame A:
kftkstfsneiisnftwfrtnynh*fpyrgdanng*iysk*fn*kfiiyfrnsrnasshd
kmyss**infiptnilgyscnvty*f*ksfhwchqvvinvigyhkl**pcsskcflgina
krlgklpwcstidyqrfnvckyctlcigipk*nha*tm**nist*tnkilnqfnqfitls
lfinw**isnattssresigwl*k---


Frame B:
NSPNQRLAMRSFQILRGLEPTTTIDSLTEVMQTMGKYIQNNSIENSLFISEIQETLQVMI
KCIHPSKLILFPQIFWGTVAMLHTDFENHFIGAIKLLSMLLDIINFSDRAVQNVFLASMP
KDWENYHGVQPLIIKGLMSVNTAPYALEFLSRITLEPCDEIFQPEPIRFLTNLISLLPYL
CLSIGDESPMPQQVAENLSVGCEN---


Frame C:
ihqinv*q*dhfkfyvv*nqlqpliplqr*ckqwvnifkiiqlkihylfqkfkkrfks**
nvfilvn*fyshkyfgvqlqcyililkiislvpsscyqcywis*tlvtvqfkmfswhqcq
kigkitmvfnh*lskv*cl*ilhpmhwns*vesrlnhvmkyfnlnq*ds*pi*svyylif
vyqlvmnlqchnk*priyrlvvk---

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

SHH274 (SHH274Q) /CSM/SH/SHH2-D/SHH274Q.Seq.d/                       1217   0.0
AHF605 (AHF605Q) /CSM/AH/AHF6-A/AHF605Q.Seq.d/                        886   0.0
VHE534 (VHE534Q) /CSM/VH/VHE5-B/VHE534Q.Seq.d/                        878   0.0
AHE252 (AHE252Q) /CSM/AH/AHE2-C/AHE252Q.Seq.d/                        747   0.0
AFE655 (AFE655Q) /CSM/AF/AFE6-C/AFE655Q.Seq.d/                        236   3e-61
VHQ316 (VHQ316Q) /CSM/VH/VHQ3-A/VHQ316Q.Seq.d/                         68   2e-10
AHA814 (AHA814Q) /CSM/AH/AHA8-A/AHA814Q.Seq.d/                         42   0.010
VHA777 (VHA777Q) /CSM/VH/VHA7-D/VHA777Q.Seq.d/                         36   0.61
VFN418 (VFN418Q) /CSM/VF/VFN4-A/VFN418Q.Seq.d/                         36   0.61
SSF272 (SSF272Q) /CSM/SS/SSF2-C/SSF272Q.Seq.d/                         36   0.61

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

AC116305|AC116305.2 Dictyostelium discoideum chromosome 2 map 1005175-1418323 strain AX4, complete sequence.  1209   0.0    1
AX510404|AX510404.1 Sequence 5099 from Patent WO0216655.           40   0.087  2
L34770|L34770.1 Arabidopsis thaliana RNA polymerase II third largest subunit (RPB35.5A) gene, complete cds.    40   0.20   2
AC115612|AC115612.2 Dictyostelium discoideum chromosome 2 map 6245135-6357017 strain AX4, complete sequence.    42   0.72   5
AF435076|AF435076.2 Tetrahymena thermophila anlagen stage induced 1 protein (ASI1) and anlagen stage induced 2 protein (ASI2) genes, complete cds.    34   1.4    4
DV188815|DV188815.1 BCT031_D05_BCT031_3700_90.ab1 C. tentans, embryo midgut Chironomus tentans cDNA, mRNA sequence.    40   1.6    2
CR855357|CR855357.6 Zebrafish DNA sequence *** SEQUENCING IN PROGRESS *** from clone DKEY-147L18.    34   1.8    2
CR759807|CR759807.8 Zebrafish DNA sequence from clone CH211-176L1.    34   1.9    2
AC084435|AC084435.2 Homo sapiens chromosome 3 clone RP11-91G3 map 3, WORKING DRAFT SEQUENCE, 4 unordered pieces.    34   2.4    5
AC006920|AC006920.11 Arabidopsis thaliana chromosome 2 clone F26H6 map mi398, complete sequence.    40   2.7    2

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC116305_18(AC116305|pid:none) Dictyostelium discoideum chromoso...   410   e-113
AK118154_1(AK118154|pid:none) Arabidopsis thaliana At5g15680 mRN...   149   5e-35
AM920436_2090(AM920436|pid:none) Penicillium chrysogenum Wiscons...    97   5e-19
AL807577_1(AL807577|pid:none) Aspergillus fumigatus BAC AFA12F2.       91   2e-17
AM270176_10(AM270176|pid:none) Aspergillus niger contig An08c021...    91   3e-17
AP007157_465(AP007157|pid:none) Aspergillus oryzae RIB40 genomic...    88   2e-16
CU638744_310(CU638744|pid:none) Podospora anserina genomic DNA c...    87   3e-16
CR382126_200(CR382126|pid:none) Kluyveromyces lactis strain NRRL...    85   2e-15
DQ116822_1(DQ116822|pid:none) Saccharomyces cerevisiae strain YJ...    83   7e-15
DQ116815_1(DQ116815|pid:none) Saccharomyces cerevisiae strain YJ...    83   7e-15

 psg: 0.73  gvh: 0.36  alm: 0.32  top: 0.53  tms: 0.00  mit: 0.42  mip: 0.04
 nuc: 0.00  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 0.00  tyr: 0.00  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 1.00 

	 44.0 %: mitochondrial
	 32.0 %: nuclear
	 20.0 %: cytoplasmic
	  4.0 %: cytoskeletal

>> prediction for SHH274 is mit

>SHH274F.Seq
AAATTCACCAAATCAACGTTTAGCAATGAGATCATTTCAAATTTTACGTGGTTTAGAACC
AACTACAACCATTGATTCCCTTACAGAGGTGATGCAAACAATGGGTAAATATATTCAAAA
TAATTCAATTGAAAATTCATTATTTATTTCAGAAATTCAAGAAACGCTTCAAGTCATGAT
AAAATGTATTCATCCTAGTAAATTAATTTTATTCCCACAAATATTTTGGGGTACAGTTGC
AATGTTACATACTGATTTTGAAAATCATTTCATTGGTGCCATCAAGTTGTTATCAATGTT
ATTGGATATCATAAACTTTAGTGACCGTGCAGTTCAAAATGTTTTCTTGGCATCAATGCC
AAAAGATTGGGAAAATTACCATGGTGTTCAACCATTGATTATCAAAGGTTTAATGTCTGT
AAATACTGCACCCTATGCATTGGAATTCCTAAGTAGAATCACGCTTGAACCATGTGATGA
AATATTTCAACCTGAACCAATAAGATTCTTAACCAATTTAATCAGTTTATTACCTTATCT
TTGTTTATCAATTGGTGATGAATCTCCAATGCCACAACAAGTAGCCGAGAATCTATCGGT
TGGTTGTGAAAATCNNNNNNNNNN