$ gth -species arabidopsis -genomic NC_003070.fna.gz -cdna AU236313.gbk.gz -v
$ GenomeThreader 1.2.3 (2008-11-15 02:38:08)
$ Date run: 2008-11-18 11:32:07
$ Arguments: -species arabidopsis -genomic NC_003070.fna.gz -cdna AU236313.gbk.gz -v
$ make sure all necessary indices exist
$ make sure the necessary indices of all genomic input files exist
$ check the following file for index:
$ NC_003070.fna.gz
$ index exists
$ make sure the necessary indices off all reference input files exist
$ check the following file for index:
$ AU236313.gbk.gz
$ index exists
$ invoking similarity filter
$ compute direct matches
$ call vmatch to compute matches
# args=-d -v -l 20 -seedlength 18 -exdrop 2 -q AU236313.gbk.gz.dna /Users/gordon/work/genometools/doc/gthmanual/NC_003070.fna.gz.dna
$ file=NC_003070.fna.gz 30867397 30432563
$ databaselength=30432562
$ alphabet "aAcCgGtTuUnsywrkvbdhmNSYWRKVBDHM" (size 32) mapped to "acgtn" (size 5)
$ NC_003070.fna.gz.dna.tis read
$ NC_003070.fna.gz.dna.suf read
$ NC_003070.fna.gz.dna.lcp read
$ NC_003070.fna.gz.dna.llv read
$ NC_003070.fna.gz.dna.sti1 read
$ NC_003070.fna.gz.dna.bck read
$ file=AU236313.gbk.gz 2488 227
$ databaselength=226
$ alphabet "aAcCgGtTuUnsywrkvbdhmNSYWRKVBDHM" (size 32) mapped to "acgtn" (size 5)
$ AU236313.gbk.gz.dna.tis read
$ AU236313.gbk.gz.dna.des read
$ AU236313.gbk.gz.dna.sds read
$ AU236313.gbk.gz.dna.ssp read
# matches are reported in the following way
# l(S) n(S) r(S) t l(Q) n(Q) r(Q) d e s i
# where:
# l = length
# n = sequence number
# r = relative position
# t = type (D=direct, P=palindromic)
# d = distance value (negative=hamming distance, 0=exact, positive=edit distance)
# e = E-value
# s = score value (negative=hamming score, positive=edit score)
# i = percent identity
# (S) = in Subject
# (Q) = in Query
$ find direct substring matches against query (maximal exact matches)
$ overall space peak: main=58.05 MB (2.00 bytes/symbol), secondary=214.19 MB (7.38 bytes/symbol)
$ d=+, compute chains for bucket 1/1 (matches in bucket=4)
$ sort global chains according to reference sequence coverage
$ calculate spliced alignment for every chain
$ d=+, compute spliced alignment, genseq=+, chain=1/1, refseq=+
$ compute palindromic matches
$ call vmatch to compute matches
# args=-p -v -l 20 -seedlength 18 -exdrop 2 -q AU236313.gbk.gz.dna /Users/gordon/work/genometools/doc/gthmanual/NC_003070.fna.gz.dna
$ file=NC_003070.fna.gz 30867397 30432563
$ databaselength=30432562
$ alphabet "aAcCgGtTuUnsywrkvbdhmNSYWRKVBDHM" (size 32) mapped to "acgtn" (size 5)
$ NC_003070.fna.gz.dna.tis read
$ NC_003070.fna.gz.dna.suf read
$ NC_003070.fna.gz.dna.lcp read
$ NC_003070.fna.gz.dna.llv read
$ NC_003070.fna.gz.dna.sti1 read
$ NC_003070.fna.gz.dna.bck read
$ file=AU236313.gbk.gz 2488 227
$ databaselength=226
$ alphabet "aAcCgGtTuUnsywrkvbdhmNSYWRKVBDHM" (size 32) mapped to "acgtn" (size 5)
$ AU236313.gbk.gz.dna.tis read
$ AU236313.gbk.gz.dna.des read
$ AU236313.gbk.gz.dna.sds read
$ AU236313.gbk.gz.dna.ssp read
# matches are reported in the following way
# l(S) n(S) r(S) t l(Q) n(Q) r(Q) d e s i
# where:
# l = length
# n = sequence number
# r = relative position
# t = type (D=direct, P=palindromic)
# d = distance value (negative=hamming distance, 0=exact, positive=edit distance)
# e = E-value
# s = score value (negative=hamming score, positive=edit score)
# i = percent identity
# (S) = in Subject
# (Q) = in Query
$ find palindromic substring matches against query
$ overall space peak: main=58.06 MB (2.00 bytes/symbol), secondary=214.19 MB (7.38 bytes/symbol)
$ calculate spliced alignment for every chain
$ output spliced alignments
********************************************************************************
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: 0.985 (s:    0), Pa: 0.999 (s: 0.95)
 Exon  2   382803   382929 ( 127 n);  cDNA     29    156 ( 128 n); score: 0.980
  Intron  2   382930   383029 ( 100 n); Pd: 0.956 (s: 1.00), Pa: 0.983 (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


$ compute predicted gene locations
$ output predicted gene locations
--------------------------------------------------------------------------------

Predicted gene locations (1):


PGL   1 (+ strand):      382540     383100
AGS-1 (382540  382567,382803  382929,383030  383100)
SCR   (e 1.000  d 0.985 a 0.999,e 0.980  d 0.956 a 0.983,e 0.944)

  Exon  1   382540   382567 (  28 n); score: 1.000
    Intron  1   382568   382802 ( 235 n);           Pd: 0.985  Pa: 0.999
  Exon  2   382803   382929 ( 127 n); score: 0.980
    Intron  2   382930   383029 ( 100 n);           Pd: 0.956  Pa: 0.983
  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
$ 1 backtrace matrix has been allocated
$ 
$ date finished: 2008-11-18 11:32:09
