>SHA231 (SHA231Q) /CSM/SH/SHA2-B/SHA231Q.Seq.d/
CGTGCAAATCGCTTGTCTAACTTGGGTATAGGGGCGAAAGACTAATCGAACAACCTAGTA
GCTGGTTCCTTCCGAAGTTTCCCTCAGGATAGCTGGAGCAGTATTCTAGTTCCATCTTGT
AAAGACAATGATTAGCAGTTTCGGGGGCGTAATGCTCTCAGCTGATTCTCAAACTCTGAA
CGGGTGGGTATCATTTTAATTCACTTAATTGGATTTTAAAATTAAATTGCACATGTGCAA
TGAAAAATAGGAGCTCTTAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGTGGGTTGA
ACCAAATATTGGGATAAGACGTCTAACATTCACTAATAGATACCACAAAAGGTGTTAGTT
CATTAAGACAGCAGGACGGTGGCCATGGAAGTCGGTATCCGCTAAGGAGTGTGTAACAAC
TCACCTGCCAAATGGACTAGCCCTGAAAATGGATGACGCTAGCAGTGGATGGTCGATGCC
CAATXXXXXXXXXXCGCAAACCAAATGCTTTAGAGTGTGAATGTTGTAGGTAACATTAGG
TTGTTGGTGGGGGACCACTTTCAACTTTAAACCATATGATTAATCGCTGTTACACTGCAG
TTTCCTTCCGGTTATTGTGGTGGGTGGCTAAATTCTAATTTATATCCTCGTTCCGCTCAA
CTCTTCGATTGTAGACGACTATCAAATGAACTAGGTGCTGTAAGCTTCCGAGTAGCGTTC
AGTTACGAGGGGTTGAGGCTTTTCCATTAGTTCTTAATAATTTCCGATAACATCACAATA
TGGGTAAGCCAAATGGTTTAAAAACAGCTAGAAAGCTTAGAAATCACAGAAGAGTCCAAA
GATGGAACGATAAACTCTACAAAAAGGCTCATTTCGGTACTGCTCTTAAAGCCAATCCAT
TCGGTGGTGCCTCCCATGCCTCTGGTATCGTCGTAAGCAGACTTGGTATCGAAGCCAAAC
AACCAAATTCTGCCATCCGTAAATGTGTCAGAGTTCAATTAAAAAAGAACGGTAAAAAGA
TCACTGCTTTCGTTCCAAACGATGGTTGTTTAAATTACATCCAAGAAAATGACAAAGTTT
TAGTTGCTGGTCTCGGTCGTTCAGGTCACTCTGTCGGTGATATTCCAGGCGTCCGTTTCA
AGGTTGTCAAAGTTTCATCCGTCTCCCTCATTGCCATCTACCGGGTATCAAAGATAACCA
AACGTATAAATAAATAT

vqiacltwv*grktnrtt**lvpsevslriagavf*fhlvktmissfggvmlsadsqtln
gwvsf*ft*ldfkiklhmcnek*ellvghfw*aelamwvepnigirrltftnryhkrc*F
IKTAGRWPWKSVSAKECVTTHLPNGLALKMDDASSGWSMPN---

---RKPNALECECCR*h*vvgggplstlnhminrcytavsfrllwwvakf*fissfrstl
rl*ttik*trccklpssvqlrgveafplvlnnfr*hhnmgkpnglktarklrnhrrvqrw
ndklykkahfgtalkanpfggashasgivvsrlgieakqpnsairkcvrvqlkkngkkit
afvpndgclnyiqendkvlvaglgrsghsvgdipgvrfkvvkvssvsliaiyrvskitkr
inky

Frame A:
ranrlsnlgigakd*snnlvagsfrsfpqdswssilvpsckdnd*qfrgrnals*fsnse
rvgiilihligf*n*iahvq*kigalsgpflvsrtgdvg*tkywdktsnih**ipqkvlv
h*dsrtvamevgir*gvcnnspakwtspeng*r*qwmvdaq---

---RKPNALECECCR*h*vvgggplstlnhminrcytavsfrllwwvakf*fissfrstl
rl*ttik*trccklpssvqlrgveafplvlnnfr*hhnmgkpnglktarklrnhrrvqrw
ndklykkahfgtalkanpfggashasgivvsrlgieakqpnsairkcvrvqlkkngkkit
afvpndgclnyiqendkvlvaglgrsghsvgdipgvrfkvvkvssvsliaiyrvskitkr
inky

Frame B:
vqiacltwv*grktnrtt**lvpsevslriagavf*fhlvktmissfggvmlsadsqtln
gwvsf*ft*ldfkiklhmcnek*ellvghfw*aelamwvepnigirrltftnryhkrc*F
IKTAGRWPWKSVSAKECVTTHLPNGLALKMDDASSGWSMPN---

---anqml*svnvvgnirllvgdhfql*ti*liavtlqfpsgycggwlnsnlyprsaqlf
dcrrlsnelgavsfrvafsyeglrlfh*fliisdnitiwvsqmv*kqlesleiteeskdg
tinstkrlisvlllkpihsvvppmplvss*adlvskpnnqilpsvnvsefn*krtvkrsl
lsfqtmvv*itskkmtkf*llvsvvqvtlsvifqasvsrlskfhpspslpstgyqr*pnv
*in

Frame C:
ckslv*lgyrgerlieqpsswflpkfpsg*leqysssil*rq*lavsga*csqlilkl*t
ggyhfnslnwilklnctcamknrss*waifgkqnwrcglnqilg*dv*hslidttkgvss
lrqqdgghgsryplrsv*qltcqmd*p*kwmtlavdgrcp---

---qtkcfrv*ml*vtlgcwwgttfnfkpyd*sllhcsflpvivvgg*iliyilvplnss
ivddyqmn*vl*ase*rsvtrg*gfsiss**fpitsqyg*akwfkns*ka*ksqkspkme
r*tlqkgsfrycs*sqsirwclpclwyrrkqtwyrsqttkfchp*mcqssikker*kdhc
frskrwlfklhprk*qsfscwsrsfrslcr*ysrrpfqgcqsfirlphchlpgikdnqty
k*i

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

SHA231 (SHA231Q) /CSM/SH/SHA2-B/SHA231Q.Seq.d/                       2353   0.0
VHJ843 (VHJ843Q) /CSM/VH/VHJ8-B/VHJ843Q.Seq.d/                       1253   0.0
VHM752 (VHM752Q) /CSM/VH/VHM7-C/VHM752Q.Seq.d/                        959   0.0
VHC518 (VHC518Q) /CSM/VH/VHC5-A/VHC518Q.Seq.d/                        959   0.0
SHH833 (SHH833Q) /CSM/SH/SHH8-B/SHH833Q.Seq.d/                        959   0.0
SHG223 (SHG223Q) /CSM/SH/SHG2-A/SHG223Q.Seq.d/                        959   0.0
CHJ111 (CHJ111Q) /CSM/CH/CHJ1-A/CHJ111Q.Seq.d/                        959   0.0
AHD244 (AHD244Q) /CSM/AH/AHD2-B/AHD244Q.Seq.d/                        959   0.0
VHE787 (VHE787Q) /CSM/VH/VHE7-D/VHE787Q.Seq.d/                        940   0.0
VHC345 (VHC345Q) /CSM/VH/VHC3-B/VHC345Q.Seq.d/                        938   0.0

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

AY171066|AY171066.1 Dictyostelium discoideum extrachromosomal palindromic ribosomal RNA gene sequence, central segment.   959   0.0    2
X00601|X00601.1 Dictyostelium discoideum ribosomal RNA gene.      959   0.0    1
AC114265|AC114265.2 Dictyostelium discoideum chromosome 2 map 4520461-4544940 strain AX4, complete sequence.   438   0.0    6
DQ273839|DQ273839.1 Chytriomyces spinosus isolate AFTOL-ID 1540 28S ribosomal RNA gene, partial sequence.   190   3e-97  3
AJ645166|AJ645166.1 Populus tremula x P. tremuloides/Amanita muscaria mixed EST library  EST, clone ptamabc210057a10.   188   7e-94  3
AJ643225|AJ643225.1 Populus tremula x P. tremuloides/Amanita muscaria mixed EST library  EST, clone ptamabc210030f08.   188   1e-93  3
AJ641069|AJ641069.1 Populus tremula x P. tremuloides/Amanita muscaria mixed EST library  EST, clone ptamabc210070d11.   188   1e-93  3
DQ273828|DQ273828.1 Glomus intraradices isolate AFTOL-ID 845 28S ribosomal RNA gene, partial sequence.   206   1e-93  3
AJ644039|AJ644039.1 Populus tremula x P. tremuloides/Amanita muscaria mixed EST library  EST, clone ptamabc210041e06.   188   1e-93  3
AY561910|AY561910.1 Rhizaxinella sp. G319653 28S large subunit ribosomal RNA gene, partial sequence.   165   5e-93  3

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC114265_6(AC114265|pid:none) Dictyostelium discoideum chromosom...   228   2e-58
BT058308_1(BT058308|pid:none) Salmo salar clone Contig3653 40S r...   220   9e-56
AB258536_7(AB258536|pid:none) Oncorhynchus mykiss Onmy-LDA gene ...   218   4e-55
BC088894_1(BC088894|pid:none) Xenopus tropicalis ribosomal prote...   217   7e-55
AB291576_1(AB291576|pid:none) Solea senegalensis rpS23 mRNA for ...   216   9e-55
(Q90YQ1) RecName: Full=40S ribosomal protein S23;  &AF402831_1(A...   214   4e-54
EU124946_1(EU124946|pid:none) Arenicola marina ribosomal protein...   214   4e-54
(P62266) RecName: Full=40S ribosomal protein S23;  &(P62267) Rec...   214   5e-54
BC077634_1(BC077634|pid:none) Xenopus laevis MGC86316 protein, m...   214   5e-54
AK012574_1(AK012574|pid:none) Mus musculus 11 days embryo whole ...   214   6e-54

 psg: 0.68  gvh: 0.37  alm: 0.53  top: 0.53  tms: 0.00  mit: 0.40  mip: 0.03
 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 

	 64.0 %: mitochondrial
	 16.0 %: cytoplasmic
	 12.0 %: nuclear
	  4.0 %: cytoskeletal
	  4.0 %: peroxisomal

>> prediction for SHA231 is mit

>SHA231F.Seq
CGTGCAAATCGCTTGTCTAACTTGGGTATAGGGGCGAAAGACTAATCGAACAACCTAGTA
GCTGGTTCCTTCCGAAGTTTCCCTCAGGATAGCTGGAGCAGTATTCTAGTTCCATCTTGT
AAAGACAATGATTAGCAGTTTCGGGGGCGTAATGCTCTCAGCTGATTCTCAAACTCTGAA
CGGGTGGGTATCATTTTAATTCACTTAATTGGATTTTAAAATTAAATTGCACATGTGCAA
TGAAAAATAGGAGCTCTTAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGTGGGTTGA
ACCAAATATTGGGATAAGACGTCTAACATTCACTAATAGATACCACAAAAGGTGTTAGTT
CATTAAGACAGCAGGACGGTGGCCATGGAAGTCGGTATCCGCTAAGGAGTGTGTAACAAC
TCACCTGCCAAATGGACTAGCCCTGAAAATGGATGACGCTAGCAGTGGATGGTCGATGCC
CAATNNNNNNNNNN

>SHA231Z.Seq
NNNNNNNNNNCGCAAACCAAATGCTTTAGAGTGTGAATGTTGTAGGTAACATTAGGTTGT
TGGTGGGGGACCACTTTCAACTTTAAACCATATGATTAATCGCTGTTACACTGCAGTTTC
CTTCCGGTTATTGTGGTGGGTGGCTAAATTCTAATTTATATCCTCGTTCCGCTCAACTCT
TCGATTGTAGACGACTATCAAATGAACTAGGTGCTGTAAGCTTCCGAGTAGCGTTCAGTT
ACGAGGGGTTGAGGCTTTTCCATTAGTTCTTAATAATTTCCGATAACATCACAATATGGG
TAAGCCAAATGGTTTAAAAACAGCTAGAAAGCTTAGAAATCACAGAAGAGTCCAAAGATG
GAACGATAAACTCTACAAAAAGGCTCATTTCGGTACTGCTCTTAAAGCCAATCCATTCGG
TGGTGCCTCCCATGCCTCTGGTATCGTCGTAAGCAGACTTGGTATCGAAGCCAAACAACC
AAATTCTGCCATCCGTAAATGTGTCAGAGTTCAATTAAAAAAGAACGGTAAAAAGATCAC
TGCTTTCGTTCCAAACGATGGTTGTTTAAATTACATCCAAGAAAATGACAAAGTTTTAGT
TGCTGGTCTCGGTCGTTCAGGTCACTCTGTCGGTGATATTCCAGGCGTCCGTTTCAAGGT
TGTCAAAGTTTCATCCGTCTCCCTCATTGCCATCTACCGGGTATCAAAGATAACCAAACG
TATAAATAAATAT

>SHA231P.Seq
CGTGCAAATCGCTTGTCTAACTTGGGTATAGGGGCGAAAGACTAATCGAACAACCTAGTA
GCTGGTTCCTTCCGAAGTTTCCCTCAGGATAGCTGGAGCAGTATTCTAGTTCCATCTTGT
AAAGACAATGATTAGCAGTTTCGGGGGCGTAATGCTCTCAGCTGATTCTCAAACTCTGAA
CGGGTGGGTATCATTTTAATTCACTTAATTGGATTTTAAAATTAAATTGCACATGTGCAA
TGAAAAATAGGAGCTCTTAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGTGGGTTGA
ACCAAATATTGGGATAAGACGTCTAACATTCACTAATAGATACCACAAAAGGTGTTAGTT
CATTAAGACAGCAGGACGGTGGCCATGGAAGTCGGTATCCGCTAAGGAGTGTGTAACAAC
TCACCTGCCAAATGGACTAGCCCTGAAAATGGATGACGCTAGCAGTGGATGGTCGATGCC
CAAT----------CGCAAACCAAATGCTTTAGAGTGTGAATGTTGTAGGTAACATTAGG
TTGTTGGTGGGGGACCACTTTCAACTTTAAACCATATGATTAATCGCTGTTACACTGCAG
TTTCCTTCCGGTTATTGTGGTGGGTGGCTAAATTCTAATTTATATCCTCGTTCCGCTCAA
CTCTTCGATTGTAGACGACTATCAAATGAACTAGGTGCTGTAAGCTTCCGAGTAGCGTTC
AGTTACGAGGGGTTGAGGCTTTTCCATTAGTTCTTAATAATTTCCGATAACATCACAATA
TGGGTAAGCCAAATGGTTTAAAAACAGCTAGAAAGCTTAGAAATCACAGAAGAGTCCAAA
GATGGAACGATAAACTCTACAAAAAGGCTCATTTCGGTACTGCTCTTAAAGCCAATCCAT
TCGGTGGTGCCTCCCATGCCTCTGGTATCGTCGTAAGCAGACTTGGTATCGAAGCCAAAC
AACCAAATTCTGCCATCCGTAAATGTGTCAGAGTTCAATTAAAAAAGAACGGTAAAAAGA
TCACTGCTTTCGTTCCAAACGATGGTTGTTTAAATTACATCCAAGAAAATGACAAAGTTT
TAGTTGCTGGTCTCGGTCGTTCAGGTCACTCTGTCGGTGATATTCCAGGCGTCCGTTTCA
AGGTTGTCAAAGTTTCATCCGTCTCCCTCATTGCCATCTACCGGGTATCAAAGATAACCA
AACGTATAAATAAATAT