>CHR550 (CHR550Q) /CSM/CH/CHR5-C/CHR550Q.Seq.d/
ATTTTTTCAATTTCTTTATATATTGCTCTTAAAGAGTAATAATTGTATATATAATATCAA
AAATGAATAAAGTTGATATGAACGCTTTTGTATCACAAAATCTATTCGACAAATTTCCAC
AAAGAATAGAATGTATTGAACAATGGGAATATAAAGGAAAGAAACATTTATTCATTGGAA
CTACAGAAGGTCATGTTTTAGTATATGATGTTATTGAAAAAGAGAATCAACATGGTAATA
TTCAAGTTTCAGTTATAATTAGAGATACAAAATTAGTATCAAAAAAACCAATTACACAAA
TGAGTATATTTGATGATTATAATAAATTATTAGTATTAACAGATGGTGATTTAAAGGTAT
ATGATTTGATTCAATTTGATGTAACAACAGGAATAACATTAATGAAAGCAAAAGGATGTA
GTACATATGCAGTTAGTTATCAACCTGGTTCATTAAGTTTAGTAGCAGCAGTTAAAAAGA
AATTAGTATTATATGGTTGGGATGGTTCAGATTTCTATGAATTAAAAGAATTCAATATGC
CAGXXXXXXXXXXAAACAAACACCCAAACTCTGCAATTGTACGTGAACCTGGTTTAATAC
CAGCCGGTAAGGAGAGTGGCGAGTTGGGTGAACTTAGAACAAAGATCATTCAATTCTTGG
AAAACTCAAAATACTATTTACCAGAGAAAATGTTGTCACGTTTCCCTTCGAATGATCTCT
ACGAAGAGAGAGCTATCCTATTAAGTAAAATTGGTCGTCACGAGCAAGCATTGGCAATCT
ATGCTCACAAGTTAAAAAATTTCGCCATGGCAGAGGAATATTGCGATCGTCATTACAATA
AGGACTCTGAAGAGAGTAGAGATGTTTATTTATCATTGTTAAATGTTTATTTAAAACCAA
CCGATGCAAATACATCTCCACTATTAGATCCCGCTTTAAAACTTTTAAACAAACATTATC
GTTCAATCAATACTCCAAAAGCATTGTCACTTTTACCTTTAAATACTCCAATCGATCAAC
TCTATCCTTTCTTTGAATCGGTCATTAGAGATAATACCAAAACCAAAAGAGATAATCAAA
TCGTAAAAAATCTTTTCAAATCTGAAAACTTTAAAATCAAAGATGAACTTTCTCAACTTA
AAACTGGTGTCATTAAAATCACTGAAGATTTAACTTGTCCAATTTGTAATAAAATATTTT
TAGGTACTCAGGCTTTTGTTGCTCGTCCCGATGGTACTGCTTTACATTATCATCATAAAA
ANATAAACAACATCAAAGT

ffnffiycs*RVIIVYIISKMNKVDMNAFVSQNLFDKFPQRIECIEQWEYKGKKHLFIGT
TEGHVLVYDVIEKENQHGNIQVSVIIRDTKLVSKKPITQMSIFDDYNKLLVLTDGDLKVY
DLIQFDVTTGITLMKAKGCSTYAVSYQPGSLSLVAAVKKKLVLYGWDGSDFYELKEFNMP
---

---NKHPNSAIVREPGLIPAGKESGELGELRTKIIQFLENSKYYLPEKMLSRFPSNDLYE
ERAILLSKIGRHEQALAIYAHKLKNFAMAEEYCDRHYNKDSEESRDVYLSLLNVYLKPTD
ANTSPLLDPALKLLNKHYRSINTPKALSLLPLNTPIDQLYPFFESVIRDNTKTKRDNQIV
KNLFKSENFKIKDELSQLKTGVIKITEDLTCPICNKIFLGTQAFVARPDGTALHYHHKXI
NNIK

Frame A:
ifsislyialke**lyi*yqk*ikli*tllyhkiystnfhke*nvlnngnikerniysle
lqkvmf*ymmllkkrinmvifkfql*leiqn*yqknqlhk*vylmiiiny*y*qmvi*ry
mi*fnlm*qqe*h**kqkdvvhmqlvinlvh*v**qqlkrn*yymvgmvqismn*knsic
q---

---kqtpklcnct*twfntsr*gewrvg*t*nkdhsilgklkilftrenvvtfpfe*slr
resypik*nwssrasignlcsqvkkfrhgrgilrsslq*gl*re*rclfiivkclfktnr
ckyistirsrfktfkqtlsfnqysksivtftfkysnrstlsfl*igh*r*yqnqkr*snr
kksfqi*kl*nqr*tfst*nwch*nh*rfnlsnl**nifrysgfccssrwycftlss*kx
kqhqs

Frame B:
ffqflyilllksnnciynikne*s*yerfcitksirqistknrmy*tmgi*rketfihwn
yrrscfsi*cy*krestw*yssfsyn*rykisikktnytneyi**l**iisinrw*fkgi
*fdsi*cnnrnnineskrm*yics*lstwfikfssss*keisiiwlgwfrfl*ikriqya
---

---NKHPNSAIVREPGLIPAGKESGELGELRTKIIQFLENSKYYLPEKMLSRFPSNDLYE
ERAILLSKIGRHEQALAIYAHKLKNFAMAEEYCDRHYNKDSEESRDVYLSLLNVYLKPTD
ANTSPLLDPALKLLNKHYRSINTPKALSLLPLNTPIDQLYPFFESVIRDNTKTKRDNQIV
KNLFKSENFKIKDELSQLKTGVIKITEDLTCPICNKIFLGTQAFVARPDGTALHYHHKXI
NNIK

Frame C:
ffnffiycs*RVIIVYIISKMNKVDMNAFVSQNLFDKFPQRIECIEQWEYKGKKHLFIGT
TEGHVLVYDVIEKENQHGNIQVSVIIRDTKLVSKKPITQMSIFDDYNKLLVLTDGDLKVY
DLIQFDVTTGITLMKAKGCSTYAVSYQPGSLSLVAAVKKKLVLYGWDGSDFYELKEFNMP
---

---tntqtlqlyvnlv*yqpvrrvaswvnleqrsfnswktqntiyqrkcchvslrmistk
relsy*vklvvtskhwqsmlts*kispwqrniaivitirtlkrvemfiyhc*mfi*nqpm
qihlhy*ipl*nf*tniivqsilqkhchfyl*ilqsinsilslnrsleiipkpkeiiks*
kifsnlktlkskmnflnlklvslkslki*lvqfvikyf*vlrllllvpmvllyiiiikx*
ttsk

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CHR550 (CHR550Q) /CSM/CH/CHR5-C/CHR550Q.Seq.d/                       1994   0.0
VHH455 (VHH455Q) /CSM/VH/VHH4-C/VHH455Q.Seq.d/                       1021   0.0
AHL751 (AHL751Q) /CSM/AH/AHL7-C/AHL751Q.Seq.d/                       1021   0.0
VHE636 (VHE636Q) /CSM/VH/VHE6-B/VHE636Q.Seq.d/                       1019   0.0
CHI877 (CHI877Q) /CSM/CH/CHI8-D/CHI877Q.Seq.d/                       1007   0.0
AHC105 (AHC105Q) /CSM/AH/AHC1-A/AHC105Q.Seq.d/                       1001   0.0
CHP886 (CHP886Q) /CSM/CH/CHP8-D/CHP886Q.Seq.d/                        993   0.0
SHE509 (SHE509Q) /CSM/SH/SHE5-A/SHE509Q.Seq.d/                        985   0.0
AHQ858 (AHQ858Q) /CSM/AH/AHQ8-C/AHQ858Q.Seq.d/                        969   0.0
SHD387 (SHD387Q) /CSM/SH/SHD3-D/SHD387Q.Seq.d/                        963   0.0

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

AC006738|AC006738.1 Caenorhabditis elegans clone Y37E11a, *** SEQUENCING IN PROGRESS***, 4 unordered pieces.    42   0.14   8
AC127217|AC127217.3 Rattus norvegicus clone CH230-11M5, *** SEQUENCING IN PROGRESS ***, 3 unordered pieces.    38   0.31   7
BU777752|BU777752.1 SJEDNF04 SJE Schistosoma japonicum cDNA, mRNA sequence.    48   0.46   1
AC104485|AC104485.2 Sus scrofa clone RP44-73K12, WORKING DRAFT SEQUENCE, 4 ordered pieces.    48   0.46   1
CT179860|CT179860.1 Sus scrofa genomic clone PigE-180P6, genomic survey sequence.    48   0.46   1
AC111398|AC111398.4 Rattus norvegicus clone CH230-237J10, *** SEQUENCING IN PROGRESS ***, 2 unordered pieces.    42   0.51   6
AE017308|AE017308.1 Mycoplasma mobile 163K complete genome.        38   0.67   15
AC168396|AC168396.2 Strongylocentrotus purpuratus clone R3-4002M14, WORKING DRAFT SEQUENCE, 36 unordered pieces.    42   1.2    4
AC006281|AC006281.8 Plasmodium falciparum chromosome 12 clone 3D7, *** SEQUENCING IN PROGRESS ***, 2 unordered pieces.    36   1.2    8
AC155044|AC155044.2 Bos taurus clone CH240-35E19, *** SEQUENCING IN PROGRESS ***, 28 unordered pieces.    46   1.8    1

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CR859168_1(CR859168|pid:none) Pongo abelii mRNA; cDNA DKFZp469J2...   190   1e-46
AB028844_1(AB028844|pid:none) Mus musculus mRNA for mVAM6, compl...   189   2e-46
AK042253_1(AK042253|pid:none) Mus musculus 3 days neonate thymus...   189   2e-46
AK141424_1(AK141424|pid:none) Mus musculus 12 days embryo spinal...   189   2e-46
AM393769_1(AM393769|pid:none) Synthetic construct Homo sapiens c...   188   3e-46
AM392538_1(AM392538|pid:none) Synthetic construct Homo sapiens c...   188   3e-46
EF446162_1(EF446162|pid:none) Danio rerio vesicle fusion protein...   184   7e-45
AK128403_1(AK128403|pid:none) Homo sapiens cDNA FLJ46546 fis, cl...   167   9e-40
AK084743_1(AK084743|pid:none) Mus musculus 13 days embryo heart ...   147   1e-33
AE017348_329(AE017348|pid:none) Cryptococcus neoformans var. neo...   126   2e-27

 psg: 0.58  gvh: 0.31  alm: 0.43  top: 0.53  tms: 0.00  mit: 0.28  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.50  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 %: nuclear
	 36.0 %: cytoplasmic
	  8.0 %: mitochondrial
	  4.0 %: plasma membrane
	  4.0 %: extracellular, including cell wall
	  4.0 %: endoplasmic reticulum

>> prediction for CHR550 is nuc

>CHR550F.Seq
ATTTTTTCAATTTCTTTATATATTGCTCTTAAAGAGTAATAATTGTATATATAATATCAA
AAATGAATAAAGTTGATATGAACGCTTTTGTATCACAAAATCTATTCGACAAATTTCCAC
AAAGAATAGAATGTATTGAACAATGGGAATATAAAGGAAAGAAACATTTATTCATTGGAA
CTACAGAAGGTCATGTTTTAGTATATGATGTTATTGAAAAAGAGAATCAACATGGTAATA
TTCAAGTTTCAGTTATAATTAGAGATACAAAATTAGTATCAAAAAAACCAATTACACAAA
TGAGTATATTTGATGATTATAATAAATTATTAGTATTAACAGATGGTGATTTAAAGGTAT
ATGATTTGATTCAATTTGATGTAACAACAGGAATAACATTAATGAAAGCAAAAGGATGTA
GTACATATGCAGTTAGTTATCAACCTGGTTCATTAAGTTTAGTAGCAGCAGTTAAAAAGA
AATTAGTATTATATGGTTGGGATGGTTCAGATTTCTATGAATTAAAAGAATTCAATATGC
CAGNNNNNNNNNN

>CHR550Z.Seq
NNNNNNNNNNAAACAAACACCCAAACTCTGCAATTGTACGTGAACCTGGTTTAATACCAG
CCGGTAAGGAGAGTGGCGAGTTGGGTGAACTTAGAACAAAGATCATTCAATTCTTGGAAA
ACTCAAAATACTATTTACCAGAGAAAATGTTGTCACGTTTCCCTTCGAATGATCTCTACG
AAGAGAGAGCTATCCTATTAAGTAAAATTGGTCGTCACGAGCAAGCATTGGCAATCTATG
CTCACAAGTTAAAAAATTTCGCCATGGCAGAGGAATATTGCGATCGTCATTACAATAAGG
ACTCTGAAGAGAGTAGAGATGTTTATTTATCATTGTTAAATGTTTATTTAAAACCAACCG
ATGCAAATACATCTCCACTATTAGATCCCGCTTTAAAACTTTTAAACAAACATTATCGTT
CAATCAATACTCCAAAAGCATTGTCACTTTTACCTTTAAATACTCCAATCGATCAACTCT
ATCCTTTCTTTGAATCGGTCATTAGAGATAATACCAAAACCAAAAGAGATAATCAAATCG
TAAAAAATCTTTTCAAATCTGAAAACTTTAAAATCAAAGATGAACTTTCTCAACTTAAAA
CTGGTGTCATTAAAATCACTGAAGATTTAACTTGTCCAATTTGTAATAAAATATTTTTAG
GTACTCAGGCTTTTGTTGCTCGTCCCGATGGTACTGCTTTACATTATCATCATAAAAANA
TAAACAACATCAAAGT

>CHR550P.Seq
ATTTTTTCAATTTCTTTATATATTGCTCTTAAAGAGTAATAATTGTATATATAATATCAA
AAATGAATAAAGTTGATATGAACGCTTTTGTATCACAAAATCTATTCGACAAATTTCCAC
AAAGAATAGAATGTATTGAACAATGGGAATATAAAGGAAAGAAACATTTATTCATTGGAA
CTACAGAAGGTCATGTTTTAGTATATGATGTTATTGAAAAAGAGAATCAACATGGTAATA
TTCAAGTTTCAGTTATAATTAGAGATACAAAATTAGTATCAAAAAAACCAATTACACAAA
TGAGTATATTTGATGATTATAATAAATTATTAGTATTAACAGATGGTGATTTAAAGGTAT
ATGATTTGATTCAATTTGATGTAACAACAGGAATAACATTAATGAAAGCAAAAGGATGTA
GTACATATGCAGTTAGTTATCAACCTGGTTCATTAAGTTTAGTAGCAGCAGTTAAAAAGA
AATTAGTATTATATGGTTGGGATGGTTCAGATTTCTATGAATTAAAAGAATTCAATATGC
CAG----------AAACAAACACCCAAACTCTGCAATTGTACGTGAACCTGGTTTAATAC
CAGCCGGTAAGGAGAGTGGCGAGTTGGGTGAACTTAGAACAAAGATCATTCAATTCTTGG
AAAACTCAAAATACTATTTACCAGAGAAAATGTTGTCACGTTTCCCTTCGAATGATCTCT
ACGAAGAGAGAGCTATCCTATTAAGTAAAATTGGTCGTCACGAGCAAGCATTGGCAATCT
ATGCTCACAAGTTAAAAAATTTCGCCATGGCAGAGGAATATTGCGATCGTCATTACAATA
AGGACTCTGAAGAGAGTAGAGATGTTTATTTATCATTGTTAAATGTTTATTTAAAACCAA
CCGATGCAAATACATCTCCACTATTAGATCCCGCTTTAAAACTTTTAAACAAACATTATC
GTTCAATCAATACTCCAAAAGCATTGTCACTTTTACCTTTAAATACTCCAATCGATCAAC
TCTATCCTTTCTTTGAATCGGTCATTAGAGATAATACCAAAACCAAAAGAGATAATCAAA
TCGTAAAAAATCTTTTCAAATCTGAAAACTTTAAAATCAAAGATGAACTTTCTCAACTTA
AAACTGGTGTCATTAAAATCACTGAAGATTTAACTTGTCCAATTTGTAATAAAATATTTT
TAGGTACTCAGGCTTTTGTTGCTCGTCCCGATGGTACTGCTTTACATTATCATCATAAAA
ANATAAACAACATCAAAGT