>VHF173 (VHF173Q) /CSM/VH/VHF1-D/VHF173Q.Seq.d/
GTTTCAAAATCTTCTCTGCTCAATTGGCCCCTGGTGCTTCATCAGTACCAACTGTCGCTT
CACCAACCACTCCAACTGGTGTTGTCACTGGTGTCTCTTCACCAAGTGTCAATGGTGGCG
GTGCTGGTAGTGGTGCTTCAACTGTTGGTACAAACATTGCCAATAACACTACTACCTCTG
TAAATGGAATTAGTAGTAATAGCTCAACACCTGAACCATCAAAACATGCCGATAAAATCG
TTGGTCTTTTAGAGTTCTCTTCACCAGCTAATGCAATCGATGCTTTGGTACTTTTAAATA
ACTCTGTTTTACCAAATTCAAATCATATGGGTTTAAGACTTTCATTTAGTAACTCTACAG
TTTTACCAAAATCTTCAACAAGTAATAATAATAATAATAATACTAATAACACCACCACCA
CTTCCACCAACACCAATAATAATAATAGCAACAATATCGCCTCACCACAACAACCACAAC
AATTNCAACAACCACAACAACCACAACAACAATCTCCAACAACTCAAAAACTTTTTTAAA
TTTTCTGTCTCAAATTTTTTTTTTTXXXXXXXXXX

FKIFSAQLAPGASSVPTVASPTTPTGVVTGVSSPSVNGGGAGSGASTVGTNIANNTTTSV
NGISSNSSTPEPSKHADKIVGLLEFSSPANAIDALVLLNNSVLPNSNHMGLRLSFSNSTV
LPKSSTSNNNNNNTNNTTTTSTNTNNNNSNNIASPQQPQQXQQPQQPQQQSPTTQKLF*i
fclkfff---

Frame A:
vskssllnwplvlhqyqlslhqplqlvlslvslhqvsmvavlvvvlqllvqtlpitllpl
*melvviaqhlnhqnmpikslvf*sslhqlmqsmlwyf*itlfyqiqiiwv*dfhlvtlq
fyqnlqqviiiiiilitppplpptpiiiiatisphhnnhnnxnnhnnhnnnlqqlknffk
fsvsnfff---


Frame B:
fqnllcsigpwcfistncrftnhsnwcchwclftkcqwwrcw*wcfncwykhcq*hyylc
kwn****lnt*tiktcr*nrwsfrvlfts*cnrcfgtfk*lcftkfksygfktfi**lys
ftkifnk******y**hhhhfhqhq****qqyrlttttttixttttttttisnnsktfln
flsqiff---


Frame C:
FKIFSAQLAPGASSVPTVASPTTPTGVVTGVSSPSVNGGGAGSGASTVGTNIANNTTTSV
NGISSNSSTPEPSKHADKIVGLLEFSSPANAIDALVLLNNSVLPNSNHMGLRLSFSNSTV
LPKSSTSNNNNNNTNNTTTTSTNTNNNNSNNIASPQQPQQXQQPQQPQQQSPTTQKLF*i
fclkfff---

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

VHF173 (VHF173Q) /CSM/VH/VHF1-D/VHF173Q.Seq.d/                        757   0.0
CHR264 (CHR264Q) /CSM/CH/CHR2-C/CHR264Q.Seq.d/                        615   e-175
CHH184 (CHH184Q) /CSM/CH/CHH1-D/CHH184Q.Seq.d/                        147   2e-34
SLB243 (SLB243Q) /CSM/SL/SLB2-B/SLB243Q.Seq.d/                         46   6e-04
VHE852 (VHE852Q) /CSM/VH/VHE8-C/VHE852Q.Seq.d/                         38   0.14
SFJ295 (SFJ295Q) /CSM/SF/SFJ2-D/SFJ295Q.Seq.d/                         38   0.14
CHM652 (CHM652Q) /CSM/CH/CHM6-C/CHM652Q.Seq.d/                         38   0.14
AFI348 (AFI348Q) /CSM/AF/AFI3-B/AFI348Q.Seq.d/                         38   0.14
VSK258 (VSK258Q) /CSM/VS/VSK2-C/VSK258Q.Seq.d/                         36   0.57
VHO671 (VHO671Q) /CSM/VH/VHO6-C/VHO671Q.Seq.d/                         36   0.57

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

AC210986|AC210986.1 Zea mays chromosome 3 clone CH201-464E2; ZMMBBc0464E02, *** SEQUENCING IN PROGRESS ***, 29 unordered pieces.    44   0.091  3
AC127548|AC127548.4 Mus musculus BAC clone RP24-505K1 from chromosome unknown, complete sequence.    42   4.1    2
AC132301|AC132301.4 Mus musculus chromosome UNK clone RP24-277F20, complete sequence.    42   4.5    2
CR932984|CR932984.9 Zebrafish DNA sequence *** SEQUENCING CANCELLED *** from clone  CH211-99D17.    44   4.7    1
AC201020|AC201020.1 Strongylocentrotus purpuratus clone R3-12H3, WORKING DRAFT SEQUENCE, 16 unordered pieces.    44   4.7    1
AC179357|AC179357.1 Strongylocentrotus purpuratus clone R3-59F5, WORKING DRAFT SEQUENCE, 19 unordered pieces.    44   4.7    1
AC178863|AC178863.1 Strongylocentrotus purpuratus clone R3-28K23, WORKING DRAFT SEQUENCE, 21 unordered pieces.    44   4.7    1
AC178853|AC178853.1 Strongylocentrotus purpuratus clone R3-26H21, WORKING DRAFT SEQUENCE, 37 unordered pieces.    44   4.7    1
AC177958|AC177958.1 Strongylocentrotus purpuratus clone R3-3049E17, WORKING DRAFT SEQUENCE, 16 unordered pieces.    44   4.7    1
AC168727|AC168727.2 Strongylocentrotus purpuratus clone R3-3010L3, WORKING DRAFT SEQUENCE, 34 unordered pieces.    44   4.7    1

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

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: 3236559
Number of Hits to DB: 525,633,373

 psg: 0.75  gvh: 0.64  alm: 0.40  top: 0.53  tms: 0.00  mit: 0.41  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  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 

	 40.0 %: mitochondrial
	 36.0 %: nuclear
	 12.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: extracellular, including cell wall
	  4.0 %: peroxisomal

>> prediction for VHF173 is mit

>VHF173F.Seq
GTTTCAAAATCTTCTCTGCTCAATTGGCCCCTGGTGCTTCATCAGTACCAACTGTCGCTT
CACCAACCACTCCAACTGGTGTTGTCACTGGTGTCTCTTCACCAAGTGTCAATGGTGGCG
GTGCTGGTAGTGGTGCTTCAACTGTTGGTACAAACATTGCCAATAACACTACTACCTCTG
TAAATGGAATTAGTAGTAATAGCTCAACACCTGAACCATCAAAACATGCCGATAAAATCG
TTGGTCTTTTAGAGTTCTCTTCACCAGCTAATGCAATCGATGCTTTGGTACTTTTAAATA
ACTCTGTTTTACCAAATTCAAATCATATGGGTTTAAGACTTTCATTTAGTAACTCTACAG
TTTTACCAAAATCTTCAACAAGTAATAATAATAATAATAATACTAATAACACCACCACCA
CTTCCACCAACACCAATAATAATAATAGCAACAATATCGCCTCACCACAACAACCACAAC
AATTNCAACAACCACAACAACCACAACAACAATCTCCAACAACTCAAAAACTTTTTTAAA
TTTTCTGTCTCAAATTTTTTTTTTTNNNNNNNNNN