>AFN629 (AFN629Q) /CSM/AF/AFN6-B/AFN629Q.Seq.d/
XXXXXXXXXXCNNNNNNNNNNNCNNNGNANNCAGNNTNNNNNCCANNNCCNCNNACATCA
TCATCATCATCATCATCAAATGTTACATCACCCACCATTTCCTACAACTACAACTACAAC
AACAACAACAACAAATAACAATGAAACTTTACAATCTACATCAACACCACCAACATTCCA
AACTCTAACTTCTTCAGTAATTGAAACTTTTACAATTAAAAATCCAAAGAAAGTCTTTGA
AAAACATCCAAATTTAATTAGTAGAGTTGTAGAACTTTTAAGTCATTCACATCAATCAAT
TCAATTATTATCAATTCAAATTTTATCAACACTCTCAAAATCTTCTCAAAAATTAAGAAT
TACAATTTGTCATTATCCAGGATTAGTTAGACATTTAATTAATTTATTAACACATAAACC
AACTGGAGAGAATGCAGAAATTTCAAAAAGAGCAGCAAGTTTATTATCACGT

---XXXXXXQXXXXXXXHHHHHHHQMLHHPPFPTTTTTTTTTTNNNETLQSTSTPPTFQT
LTSSVIETFTIKNPKKVFEKHPNLISRVVELLSHSHQSIQLLSIQILSTLSKSSQKLRIT
ICHYPGLVRHLINLLTHKPTGENAEISKRAASLLSR

Frame A:
---xxxxxxxxxxxxxxxiiiiiiikcyithhflqlqlqqqqqqitmklynlhqhhqhsk
l*llq*lkllqlkiqrkslkniqi*lvel*nf*vihinqfnyyqfkfyqhsqnllkn*el
qfviiqd*ldi*liy*hinqlermqkfqkeqqvyyh


Frame B:
---xxxxxxxxxxpxpxtsssssssnvtsptisynynynnnnnk*q*nftiyinttnipn
snffsn*nfyn*kskesl*ktskfn**scrtfksftsinsiiinsnfintlkifskikny
nlslsris*tfn*fint*tnwrecrnfkksskfiit


Frame C:
---XXXXXXQXXXXXXXHHHHHHHQMLHHPPFPTTTTTTTTTTNNNETLQSTSTPPTFQT
LTSSVIETFTIKNPKKVFEKHPNLISRVVELLSHSHQSIQLLSIQILSTLSKSSQKLRIT
ICHYPGLVRHLINLLTHKPTGENAEISKRAASLLSR

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

SLE201 (SLE201Q) /CSM/SL/SLE2-A/SLE201Q.Seq.d/                        656   0.0
AFN629 (AFN629Q) /CSM/AF/AFN6-B/AFN629Q.Seq.d/                        656   0.0
AFD128 (AFD128Q) /CSM/AF/AFD1-B/AFD128Q.Seq.d/                        331   6e-90
VFA220 (VFA220Q) /CSM/VF/VFA2-A/VFA220Q.Seq.d/                         42   0.007
SSJ714 (SSJ714Q) /CSM/SS/SSJ7-A/SSJ714Q.Seq.d/                         38   0.12
SFJ642 (SFJ642Q) /CSM/SF/SFJ6-B/SFJ642Q.Seq.d/                         38   0.12
SFJ263 (SFJ263Q) /CSM/SF/SFJ2-C/SFJ263Q.Seq.d/                         38   0.12
SFD776 (SFD776Q) /CSM/SF/SFD7-D/SFD776Q.Seq.d/                         38   0.12
CHA332 (CHA332Q) /CSM/CH/CHA3-B/CHA332Q.Seq.d/                         38   0.12
AHQ247 (AHQ247Q) /CSM/AH/AHQ2-B/AHQ247Q.Seq.d/                         38   0.12

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

AY243492|AY243492.1 Stylonychia lemnae FED-a1 macronuclear DNA polymerase catalytic subunit alpha gene, partial cds.    46  0.12  3
BF295676|BF295676.1 026PbH07 Pb cDNA #17, Tommaso Pace, Marta Ponzi, and Clara Frontali Plasmodium berghei cDNA 5', mRNA sequence.    46  0.37  1
CB560367|CB560367.1 AGENCOURT_13327215 NICHD_XGC_Tad1 Xenopus laevis cDNA clone IMAGE:6880593 3', mRNA sequence.    34  0.50  3
AC116988|AC116988.2 Dictyostelium discoideum chromosome 2 map 6445720-6776760 strain AX4, complete sequence.    34  0.61  11
AC131732|AC131732.2 Mus musculus chromosome UNK clone RP23-119H3, WORKING DRAFT SEQUENCE, 8 unordered pieces.    36  0.66  4
AC090055|AC090055.1 Oryza sativa chromosome 9 clone PAC0651G05, *** SEQUENCING IN PROGRESS ***, 9 ordered pieces.    38  0.76  4
CC453824|CC453824.1 BARC-Sat_291 Size-selected soybean genomic Glycine max genomic, DNA sequence.    28  0.94  4
AC003984|AC003984.2 Homo sapiens clone RP4-566F10, complete sequence.    38  1.0  3
AF068711|AF068711.1 Caenorhabditis elegans cosmid R09A1.    40  1.3  3
AL731623|AL731623.3 Oryza sativa genomic DNA, chromosome 4, BAC clone: OSJNBa0083D01.    44  1.5  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: 3039690
Number of Hits to DB: 417,001,641

 psg: 0.87  gvh: 0.47  alm: 0.45  top: 0.77  tms: 0.00  mit: 0.36  mip: 0.00
 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
	 12.0 %: cytoplasmic
	  8.0 %: cytoskeletal
	  4.0 %: endoplasmic reticulum

>> prediction for AFN629 is mit

>AFN629Z.Seq
----------CNNNNNNNNNNNCNNNGNANNCAGNNTNNNNNCCANNNCCNCNNACATCA
TCATCATCATCATCATCAAATGTTACATCACCCACCATTTCCTACAACTACAACTACAAC
AACAACAACAACAAATAACAATGAAACTTTACAATCTACATCAACACCACCAACATTCCA
AACTCTAACTTCTTCAGTAATTGAAACTTTTACAATTAAAAATCCAAAGAAAGTCTTTGA
AAAACATCCAAATTTAATTAGTAGAGTTGTAGAACTTTTAAGTCATTCACATCAATCAAT
TCAATTATTATCAATTCAAATTTTATCAACACTCTCAAAATCTTCTCAAAAATTAAGAAT
TACAATTTGTCATTATCCAGGATTAGTTAGACATTTAATTAATTTATTAACACATAAACC
AACTGGAGAGAATGCAGAAATTTCAAAAAGAGCAGCAAGTTTATTATCACGT