------------------------------
ARAGORN v1.2.41   Dean Laslett
------------------------------

Please reference the following paper if you use this
program as part of any published research.

Laslett, D. and Canback, B. (2004) ARAGORN, a
program for the detection of transfer RNA and
transfer-messenger RNA genes in nucleotide sequences.
Nucleic Acids Research, 32;11-16.


Searching for tRNA genes with introns in anticodon loop
Intron length from 0 to 3000 bases
Searching for tmRNA genes
Assuming circular topology, search wraps around ends
Searching both strands
Using standard genetic code


Mycobacterium phage Filch complete sequence, 75692 bp including 9-base 3' overhang (CGCTTGTCA), Cluster E
75692 nucleotides in sequence
Mean G+C content = 62.9%
 
1.
 
 
                c
               a
             g-c
             a c
             c-g
             a-t
             c-g
             c-g
            ag-c     tg
            g   gctcc  g
      c    g    !!  !  g
     g agat     cgcag  c
     g !!:+      t   tt
     t tcgg       g
      g    a       t
            g-cc    a
            g-c g    c
            c-g  g    g
            g-c   c    t
            g-c    g    g
           c   g    a    t
           t   a     g    a
            gcc       t   g
                       t   c
                        c  a
                         a g
    tRNA-Gly(gcc)         t
    93 bases, %GC = 67.7
    Sequence c[60319,60966]
 

Intron from tRNA-Gly(gcc)
1   .   10    .   20    .   30    .   40    .   50
ggtgcccatggcctgggccatgatcaggagttcgtagaccaccgtggggt
cgtgcccctcggccattcgggtttcctgggcggcggagagggcggtgtcg
gcgcccagccatgccagtacccggatgtcgccgggaatgggctcgctcat
gcgatccgatccacgaagccgtaacgcagggcctcgtcggagtccaacca
ccagtcggtgcgcttccatcccgcgtcgaactcctcggcggtgatcttgc
ccccggcgcggtggacgaagaccttggcgatgcgcgcgcacaggtggcgg
taccagcccaccatgtcctcaatctcgccgatcttgccgcccgtgcccgc
cgaaatctcgtggatcatcaggtacgcctcggggccgatgatgcgctcgt
ccaccgactgcagcaggatgccgcccatggaggccgccatgccgcgcaca
gtcatcgtggtcttgtgcgtgcccttgggacggtcagaggtgtcccacgg
ccgcgtcgagtaggccgcgatctggtcgaacaggtgcatgcccgcgatga
cgctg

Intron Length: 555
Intron Insertion Position(36-37): gccag-Intron-ccgcc

 
2.
 
                 c
                c
               g
             a-t
             t.t
             g-c
             g-c
             c-g
             c-g
             c-g
             g-c     ta
            t   gggcc  a
    tga    a    !!!!!  a
   c   ctcg     cccgg  c
   a   !!!!     c    tt
   g   gagc      t
    gta           g
            a-tt   c
            g-c g  t
            c-g  gt
            c-g
            t+g
           t   c
           c   g
            ctt
 
 
    tRNA-Lys(ctt)
    81 bases, %GC = 64.2
    Sequence [62188,62271]
 

Intron from tRNA-Lys(ctt)
1   .   10    .   20    .   30    .   40    .   50
gcc

Intron Length: 3
Intron Insertion Position(33-34): gcctt-Intron-ccttg

 
3.
 
 
                c
               t
             g-c
             c-g
             g-c
             c-g
             c-g
             c-g
             g-c     tg
            t   tgtcc  a
    taag   g    +!!!!  g
    t   ctg     gcagg  c
    g   !!!     t    tt
    g   gac     a
     aaa   t    t
            c-gt
            c-g
            t-a
            g-c
            g-c
           c   c
           t   a
            tcc
 
 
 
    tRNA-Gly(tcc)
    73 bases, %GC = 61.6
    Sequence [62274,62346]
 



Number of tRNA genes with no introns = 1
Number of tRNA genes with C-loop introns = 2
tRNA GC range = 61.6% to 67.7%
Number of tmRNA genes = 0