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Output list from 'trnascan'
Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Name tRNA # Begin End Type Codon Begin End Score -------- ------ ---- ------ ---- ----- ----- ---- ------ X54421_X00886_X02819_X15738 1 2857 2929 Lys TTT 0 0 55.35 X54421_X00886_X02819_X15738 2 3060 3130 Asn GTT 0 0 59.85 X54421_X00886_X02819_X15738 3 4591 4665 Met CAT 0 0 41.54 X54421_X00886_X02819_X15738 4 9818 9888 Arg TCT 0 0 57.70 X54421_X00886_X02819_X15738 5 9920 9992 Thr TGT 0 0 60.78 X54421_X00886_X02819_X15738 6 14081 14153 Met CAT 0 0 32.31 X54421_X00886_X02819_X15738 7 14159 14230 Phe GAA 0 0 52.45 X54421_X00886_X02819_X15738 8 14394 14476 Pseudo TAA 0 0 35.85 X54421_X00886_X02819_X15738 9 14492 14563 Pseudo CCA 0 0 44.39 X54421_X00886_X02819_X15738 10 14596 14669 Leu TAG 0 0 46.47 X54421_X00886_X02819_X15738 11 15551 15622 His GTG 0 0 50.77 X54421_X00886_X02819_X15738 12 16662 16734 Ile GAT 0 0 47.73 X54421_X00886_X02819_X15738 13 17166 17238 Val TAC 0 0 54.52 X54421_X00886_X02819_X15738 14 17460 17532 Arg TCG 0 0 49.97 X54421_X00886_X02819_X15738 15 17542 17613 Met CAT 0 0 43.02 X54421_X00886_X02819_X15738 16 17635 17716 Ser TGA 0 0 56.97 X54421_X00886_X02819_X15738 17 18404 18475 Glu TTC 0 0 50.22 |
Statistics results by 'trnascan'
tRNAscan-SE v.1.23 (April 2002) scan results (on host organism)
Started: Sun Mar 14 00:31:06 MET 2004
------------------------------------------------------------
Sequence file(s) to search: Spombe_972_mtDNA.fsa
Search Mode: Eukaryotic
Results written to: Standard output
Output format: Tabular
Searching with: tRNAscan + EufindtRNA -> Cove
Covariance model: TRNA2-euk.cm
tRNAscan parameters: Strict
EufindtRNA parameters: Relaxed (Int Cutoff= -32.1)
Search statistics saved in: Spombe_972_mtDNA.trna.stat
------------------------------------------------------------
First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read: 1
Seqs w/at least 1 hit: 1
Bases read: 19431 (x2 for both strands)
Bases in tRNAs: 1254
tRNAs predicted: 17
Av. tRNA length: 73
Script CPU time: 0.03 s
Scan CPU time: 0.09 s
Scan speed: 431.8 Kbp/sec
First pass search(es) ended: Sun Mar 14 00:31:06 MET 2004
Cove Stats:
-----------
Candidate tRNAs read: 17
Cove-confirmed tRNAs: 17
Bases scanned by covels: 1492
% seq scanned by covels: 3.8 %
Script CPU time: 0.11 s
Cove CPU time: 8.85 s
Scan speed: 168.6 bp/sec
Cove analysis of tRNAs ended: Sun Mar 14 00:31:18 MET 2004
Summary
--------
Overall scan speed: 4280.0 bp/sec
tRNAs decoding Standard 20 AA: 15
Selenocysteine tRNAs (TCA): 0
Possible suppressor tRNAs (CTA,TTA): 0
tRNAs with undetermined/unknown isotypes: 0
Predicted pseudogenes: 2
-------
Total tRNAs: 17
tRNAs with introns: 0
|
Isotype / Anticodon Counts:
Ala : 0 AGC: GGC: CGC: TGC:
Gly : 0 ACC: GCC: CCC: TCC:
Pro : 0 AGG: GGG: CGG: TGG:
Thr : 1 AGT: GGT: CGT: TGT: 1
Val : 1 AAC: GAC: CAC: TAC: 1
Ser : 1 AGA: GGA: CGA: TGA: 1 ACT: GCT:
Arg : 2 ACG: GCG: CCG: TCG: 1 CCT: TCT: 1
Leu : 1 AAG: GAG: CAG: TAG: 1 CAA: TAA:
Phe : 1 AAA: GAA: 1
Asn : 1 ATT: GTT: 1
Lys : 1 CTT: TTT: 1
Asp : 0 ATC: GTC:
Glu : 1 CTC: TTC: 1
His : 1 ATG: GTG: 1
Gln : 0 CTG: TTG:
Ile : 1 AAT: GAT: 1 TAT:
Met : 3 CAT: 3
Tyr : 0 ATA: GTA:
Supres: 0 CTA: TTA:
Cys : 0 ACA: GCA:
Trp : 0 CCA:
SelCys: 0 TCA:
|
CORRESPONDENCE:
Scientific questions: David W. Ussery
Peter Fischer Hallin
