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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 -------- ------ ---- ------ ---- ----- ----- ---- ------ CP000013 1 46379 46450 Gly TCC 0 0 50.44 CP000013 2 202268 202340 Cys GCA 0 0 69.14 CP000013 3 205930 206002 Phe GAA 0 0 78.84 CP000013 4 206023 206095 Phe GAA 0 0 77.30 CP000013 5 217290 217363 Met CAT 0 0 88.53 CP000013 6 255077 255163 Leu GAG 0 0 51.29 CP000013 7 444915 444988 Ile GAT 0 0 71.67 CP000013 8 483406 483494 Ser GCT 0 0 51.84 CP000013 9 483551 483637 Ser TGA 0 0 67.23 CP000013 10 484443 484516 Arg GCG 0 0 72.81 CP000013 11 484533 484619 Ser GGA 0 0 68.51 CP000013 12 638080 638152 His GTG 0 0 64.57 CP000013 13 638176 638249 Arg TCG 0 0 69.91 CP000013 14 638329 638409 Leu TAG 0 0 53.67 CP000013 15 638415 638486 Gly GCC 0 0 66.76 CP000013 16 650409 650482 Met CAT 0 0 82.28 CP000013 17 658879 658950 Asn GTT 0 0 76.04 CP000013 18 746829 746902 Thr TGT 0 0 80.38 CP000013 19 746907 746988 Tyr GTA 0 0 57.25 CP000013 20 803728 803811 Leu TAA 0 0 65.47 CP000013 21 825030 825101 Gln TTG 0 0 59.77 CP000013 22 791200 791127 Arg TCT 0 0 75.09 CP000013 23 791119 791047 Pro TGG 0 0 68.55 CP000013 24 732507 732434 Val TAC 0 0 85.81 CP000013 25 665077 665004 Asp GTC 0 0 79.20 CP000013 26 645152 645080 Met CAT 0 0 80.18 CP000013 27 586110 586027 Leu CAA 0 0 65.10 CP000013 28 549950 549878 Lys CTT 0 0 70.67 CP000013 29 549767 549695 Lys TTT 0 0 77.18 CP000013 30 549689 549618 Pseudo TTC 0 0 36.94 CP000013 31 446598 446525 Ala TGC 0 0 91.03 CP000013 32 409127 409055 Thr GGT 0 0 78.49 CP000013 33 408839 408767 Trp CCA 0 0 58.17 |
Statistics results by 'trnascan'
tRNAscan-SE v.1.23 (April 2002) scan results (on host cell)
Started: Mon Mar 13 02:06:54 MET 2006
------------------------------------------------------------
Sequence file(s) to search: Bgarinii_PBi_Main.fsa
Search Mode: Bacterial
Results written to: Standard output
Output format: Tabular
Searching with: tRNAscan + EufindtRNA -> Cove
Covariance model: TRNA2-bact.cm
tRNAscan parameters: Strict
EufindtRNA parameters: Relaxed (Int Cutoff= -36)
Search statistics saved in: Bgarinii_PBi_Main.trna.stat
------------------------------------------------------------
First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read: 1
Seqs w/at least 1 hit: 1
Bases read: 904246 (x2 for both strands)
Bases in tRNAs: 3853
tRNAs predicted: 45
Av. tRNA length: 85
Script CPU time: 0.67 s
Scan CPU time: 2.85 s
Scan speed: 634.6 Kbp/sec
First pass search(es) ended: Mon Mar 13 02:07:00 MET 2006
Cove Stats:
-----------
Candidate tRNAs read: 45
Cove-confirmed tRNAs: 33
Bases scanned by covels: 4483
% seq scanned by covels: 0.2 %
Script CPU time: 0.58 s
Cove CPU time: 23.44 s
Scan speed: 191.3 bp/sec
Cove analysis of tRNAs ended: Mon Mar 13 02:07:27 MET 2006
Summary
--------
Overall scan speed: 65667.8 bp/sec
tRNAs decoding Standard 20 AA: 32
Selenocysteine tRNAs (TCA): 0
Possible suppressor tRNAs (CTA,TTA): 0
tRNAs with undetermined/unknown isotypes: 0
Predicted pseudogenes: 1
-------
Total tRNAs: 33
tRNAs with introns: 0
|
Isotype / Anticodon Counts:
Ala : 1 AGC: GGC: CGC: TGC: 1
Gly : 2 ACC: GCC: 1 CCC: TCC: 1
Pro : 1 AGG: GGG: CGG: TGG: 1
Thr : 2 AGT: GGT: 1 CGT: TGT: 1
Val : 1 AAC: GAC: CAC: TAC: 1
Ser : 3 AGA: GGA: 1 CGA: TGA: 1 ACT: GCT: 1
Arg : 3 ACG: GCG: 1 CCG: TCG: 1 CCT: TCT: 1
Leu : 4 AAG: GAG: 1 CAG: TAG: 1 CAA: 1 TAA: 1
Phe : 2 AAA: GAA: 2
Asn : 1 ATT: GTT: 1
Lys : 2 CTT: 1 TTT: 1
Asp : 1 ATC: GTC: 1
Glu : 0 CTC: TTC:
His : 1 ATG: GTG: 1
Gln : 1 CTG: TTG: 1
Ile : 1 AAT: GAT: 1 TAT:
Met : 3 CAT: 3
Tyr : 1 ATA: GTA: 1
Supres: 0 CTA: TTA:
Cys : 1 ACA: GCA: 1
Trp : 1 CCA: 1
SelCys: 0 TCA:
|
CORRESPONDENCE:
Scientific questions: David W. Ussery
Peter Fischer Hallin
