$ gth -genomic NC_003070.fna.gz -cdna AU236313.gbk.gz
$ GenomeThreader 1.2.3 (2008-11-15 02:38:08)
$ Date run: 2008-11-18 11:32:05
$ Arguments: -genomic NC_003070.fna.gz -cdna AU236313.gbk.gz
********************************************************************************
EST Sequence: file=AU236313.gbk.gz, strand=+, description=AU236313 AU236313 RAFL14 Arabidopsis thaliana cDNA clone RAFL14-87-E12 5',

    1  GCGTGTTGTT AAAGAGCTCA CTAGTTGGGT GATTTATTCA GAGGAGGATC CGGAAGCTCA
   61  ACAAAGATAT TACTATTGGT CTTATCCAGC GTGAGTTGCT TAGCCTAGCG GAGTACAATG
  121  TCCACATGGC GAAGCATCTT GATGGAGGGA GAAACAAGAC CGCAACTGAC TTTGCTATTT
  181  CTCTACTCCA ATCCTTGGTC ACTGAGGAGT CNAGTGTCAT TTNNTAG

Genomic Template: file=NC_003070.fna.gz, strand=+, from=382240, to=383395, description=gi|42592260|ref|NC_003070.5| Arabidopsis thaliana chromosome 1, complete sequence

Predicted gene structure:

 Exon  1   382540   382567 (  28 n);  cDNA      1     28 (  28 n); score: 1.000
  Intron  1   382568   382802 ( 235 n); Pd: 0.050 (s:    0), Pa: 0.050 (s: 0.95)
 Exon  2   382803   382929 ( 127 n);  cDNA     29    156 ( 128 n); score: 0.980
  Intron  2   382930   383029 ( 100 n); Pd: 0.050 (s: 1.00), Pa: 0.050 (s: 1.00)
 Exon  3   383030   383100 (  71 n);  cDNA    157    227 (  71 n); score: 0.944

MATCH	42592260+	AU236313+	0.967	226	0.996	C
PGS_42592260+_AU236313+	(382540  382567,382803  382929,383030  383100)

Alignment (genomic DNA sequence = upper lines):

GCGTGTTGTT AAAGAGCTCA CTAGTTGGGT ATGTTTACAA CCTTTTCAAG ATTTCACTTC      382599
|||||||||| |||||||||| ||||||||                                   
GCGTGTTGTT AAAGAGCTCA CTAGTTGG.. .......... .......... ..........          28


GCTGATGTGC TTTGTTCAGT TACTTCTCCA TTAATTTGTC ACTATTTCTG TCAGAACACA      382659
                                                                 
.......... .......... .......... .......... .......... ..........          28


TAGGATAACA CATATCATAT AAGTGCTAGG TCGAGTCTGT TTCCTGTAGT TGGAGCCTAT      382719
                                                                 
.......... .......... .......... .......... .......... ..........          28


CCTCAACTGG TTATAGATAC TAGATTTGTT TCTTTGGTAT TTTTAGTTAT AATTAATTAT      382779
                                                                 
.......... .......... .......... .......... .......... ..........          28


CTTTCTTCAA ACTTTTGACA CAGGTGATTT ATTCAGAGGA GGAT-CGGAA GCTCAACAAA      382838
                         ||||||| |||||||||| |||| ||||| ||||||||||
.......... .......... ...GTGATTT ATTCAGAGGA GGATCCGGAA GCTCAACAAA          65


GATATTACTA TTGGTCTTAT CCAGCGTGAG TTGCTTAGCC TAGCGGAGTA CAATGTCCAC      382898
|||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
GATATTACTA TTGGTCTTAT CCAGCGTGAG TTGCTTAGCC TAGCGGAGTA CAATGTCCAC         125


ATGGCGAAGC ATCTTGATGG AGGGAGAAAC AGTATGCTGA ATTGCTTAAC CTTTGTTGAT      382958
|||||||||| |||||||||| |||||||||| |                               
ATGGCGAAGC ATCTTGATGG AGGGAGAAAC A......... .......... ..........         156


GTCCTTGTGT GGTAACATTC TTTTTTTGTT TTGGCTAGTG AACTTGTTTT AACAAGTTGT      383018
                                                                 
.......... .......... .......... .......... .......... ..........         156


TTGTTACGCA GAGACCGCAA CTGACTTTGC TATTTCTCTA CTCCAATCCT TGGTCACTGA      383078
            ||||||||| |||||||||| |||||||||| |||||||||| ||||||||||
.......... .AGACCGCAA CTGACTTTGC TATTTCTCTA CTCCAATCCT TGGTCACTGA         205


GGAGTCGAGT GTCATTTCAG AG                                               383100
|||||| ||| |||||||    ||
GGAGTCNAGT GTCATTTNNT AG                                                  227


--------------------------------------------------------------------------------

Predicted gene locations (1):


PGL   1 (+ strand):      382540     383100
AGS-1 (382540  382567,382803  382929,383030  383100)
SCR   (e 1.000  d 0.050 a 0.050,e 0.980  d 0.050 a 0.050,e 0.944)

  Exon  1   382540   382567 (  28 n); score: 1.000
    Intron  1   382568   382802 ( 235 n);           Pd: 0.050  Pa: 0.050
  Exon  2   382803   382929 ( 127 n); score: 0.980
    Intron  2   382930   383029 ( 100 n);           Pd: 0.050  Pa: 0.050
  Exon  3   383030   383100 (  71 n); score: 0.944

  PGS (382540  382567,382803  382929,383030  383100)	AU236313+

3-phase translation of AGS-1 (+strand):

          .         .         .        :   .         .         .         
  382540  GCGTGTTGTTAAAGAGCTCACTAGTTGG : GTGATTTATTCAGAGGAGGATCGGAAGCTCAA
           A  C  C  *  R  A  H  *  L   : G  D  L  F  R  G  G  S  E  A  Q 
            R  V  V  K  E  L  T  S  W  :  V  I  Y  S  E  E  D  R  K  L  N
             V  L  L  K  S  S  L  V  G :   *  F  I  Q  R  R  I  G  S  S  


          .         .         .         .         .         .         
  382835  CAAAGATATTACTATTGGTCTTATCCAGCGTGAGTTGCTTAGCCTAGCGGAGTACAATGT
           Q  R  Y  Y  Y  W  S  Y  P  A  *  V  A  *  P  S  G  V  Q  C 
            K  D  I  T  I  G  L  I  Q  R  E  L  L  S  L  A  E  Y  N  V
          T  K  I  L  L  L  V  L  S  S  V  S  C  L  A  *  R  S  T  M  


          .         .         .         .     :      .         .         
  382895  CCACATGGCGAAGCATCTTGATGGAGGGAGAAACA : AGACCGCAACTGACTTTGCTATTTC
           P  H  G  E  A  S  *  W  R  E  K  Q :   D  R  N  *  L  C  Y  F 
            H  M  A  K  H  L  D  G  G  R  N   : K  T  A  T  D  F  A  I  S
          S  T  W  R  S  I  L  M  E  G  E  T  :  R  P  Q  L  T  L  L  F  


          .         .         .         .         .     
  383055  TCTACTCCAATCCTTGGTCACTGAGGAGTCGAGTGTCATTTCAGAG
           S  T  P  I  L  G  H  *  G  V  E  C  H  F  R  
            L  L  Q  S  L  V  T  E  E  S  S  V  I  S  E 
          L  Y  S  N  P  W  S  L  R  S  R  V  S  F  Q   


Maximal non-overlapping open reading frames (>= 64 codons)

>42592260+_PGL-1_AGS-1_PPS_1 (382541  382567,382803  382929,383030  383100)	(frame '1';   225 bp,   75 residues) 
       1  RVVKELTSWV IYSEEDRKLN KDITIGLIQR ELLSLAEYNV HMAKHLDGGR NKTATDFAIS 
      61  LLQSLVTEES SVISE




$ general statistics:
$ 1 chain has been computed
$ 
$ memory statistics:
$ 1 spliced alignments have been stored
$ 1 predicted gene locations have been stored
$ 0 megabytes was the average size of the backtrace matrix
$ 2 backtrace matrices have been allocated
$ 
$ date finished: 2008-11-18 11:32:07
