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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 -------- ------ ---- ------ ---- ----- ----- ---- ------ NC_003424 1 375379 375450 Pro TGG 0 0 71.02 NC_003424 2 456224 456295 Val CAC 0 0 73.06 NC_003424 3 967407 967478 Glu TTC 0 0 62.18 NC_003424 4 1106593 1106690 Ser CGA 1106630 1106645 77.58 NC_003424 5 1106698 1106769 Met CAT 0 0 69.52 NC_003424 6 1413311 1413383 Cys GCA 0 0 70.58 NC_003424 7 1696744 1696826 Lys CTT 1696783 1696790 75.47 NC_003424 8 1738626 1738709 Tyr GTA 1738664 1738673 68.70 NC_003424 9 1764458 1764531 Ile AAT 0 0 63.37 NC_003424 10 2425219 2425290 Thr AGT 0 0 75.01 NC_003424 11 2434134 2434208 Lys TTT 0 0 75.86 NC_003424 12 2502709 2502781 Cys GCA 0 0 68.46 NC_003424 13 2570597 2570695 Ile TAT 2570635 2570659 59.62 NC_003424 14 3078481 3078563 Lys CTT 3078520 3078527 74.69 NC_003424 15 3435226 3435315 Arg CCG 3435262 3435279 40.63 NC_003424 16 3584119 3584215 Leu TAG 3584156 3584173 53.30 NC_003424 17 3692836 3692908 Cys GCA 0 0 70.58 NC_003424 18 3693727 3693799 Phe GAA 0 0 69.56 NC_003424 19 3728691 3728763 Arg ACG 0 0 75.46 NC_003424 20 3760461 3760534 Ile AAT 0 0 66.44 NC_003424 21 3768939 3769010 Glu CTC 0 0 74.15 NC_003424 22 3769363 3769436 Ala AGC 0 0 67.24 NC_003424 23 4226350 4226446 Ser TGA 4226387 4226401 78.71 NC_003424 24 4226454 4226525 Met CAT 0 0 69.52 NC_003424 25 4494058 4494128 Asp GTC 0 0 70.49 NC_003424 26 4676632 4676703 Thr AGT 0 0 75.01 NC_003424 27 4758178 4758260 Ala CGC 4758214 4758224 69.67 NC_003424 28 5398948 5399029 Ser AGA 0 0 80.47 NC_003424 29 5194188 5194118 Asp GTC 0 0 70.49 NC_003424 30 5006405 5006333 Arg ACG 0 0 75.46 NC_003424 31 4020308 4020230 Leu AAG 0 0 59.59 NC_003424 32 3766154 3766081 Ile AAT 0 0 66.44 NC_003424 33 3757676 3757605 Glu CTC 0 0 74.15 NC_003424 34 3757252 3757179 Ala AGC 0 0 67.24 NC_003424 35 3744577 3744505 Phe GAA 0 0 69.56 NC_003424 36 3702992 3702910 Val AAC 3702954 3702946 64.30 NC_003424 37 3551997 3551925 Trp CCA 0 0 68.85 NC_003424 38 3163760 3163689 Ala TGC 0 0 68.49 NC_003424 39 3156441 3156370 Thr CGT 0 0 76.00 NC_003424 40 3039929 3039848 Ser AGA 0 0 80.47 NC_003424 41 2836916 2836845 Thr AGT 0 0 76.75 NC_003424 42 2795029 2794932 Leu TAA 2794991 2794976 44.02 NC_003424 43 2676936 2676854 Lys CTT 2676897 2676890 74.69 NC_003424 44 2241412 2241342 Gly GCC 0 0 72.94 NC_003424 45 2206976 2206895 Val AAC 2206938 2206931 63.53 NC_003424 46 1726000 1725926 Lys TTT 0 0 75.86 NC_003424 47 1638524 1638454 Gly GCC 0 0 72.94 NC_003424 48 1595538 1595467 Thr AGT 0 0 75.01 NC_003424 49 1519343 1519250 Leu CAG 1519305 1519296 60.97 NC_003424 50 1477223 1477141 Met CAT 1477185 1477177 54.77 NC_003424 51 1441631 1441560 Pro AGG 0 0 64.72 NC_003424 52 1307182 1307086 Pro CGG 1307145 1307122 57.28 NC_003424 53 1205887 1205816 Ala TGC 0 0 68.49 NC_003424 54 944962 944889 Ala AGC 0 0 67.24 NC_003424 55 728414 728343 Glu TTC 0 0 62.18 NC_003424 56 713371 713299 Val TAC 0 0 76.36 |
Statistics results by 'trnascan'
tRNAscan-SE v.1.23 (April 2002) scan results (on host organism)
Started: Sun Mar 14 00:19:49 MET 2004
------------------------------------------------------------
Sequence file(s) to search: Spombe_972_1.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_1.trna.stat
------------------------------------------------------------
First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read: 1
Seqs w/at least 1 hit: 1
Bases read: 5570797 (x2 for both strands)
Bases in tRNAs: 7049
tRNAs predicted: 78
Av. tRNA length: 90
Script CPU time: 4.97 s
Scan CPU time: 19.09 s
Scan speed: 583.6 Kbp/sec
First pass search(es) ended: Sun Mar 14 00:20:17 MET 2004
Cove Stats:
-----------
Candidate tRNAs read: 78
Cove-confirmed tRNAs: 56
Bases scanned by covels: 8141
% seq scanned by covels: 0.0 %
Script CPU time: 1.07 s
Cove CPU time: 41.65 s
Scan speed: 195.5 bp/sec
Cove analysis of tRNAs ended: Sun Mar 14 00:21:10 MET 2004
Summary
--------
Overall scan speed: 166840.3 bp/sec
tRNAs decoding Standard 20 AA: 56
Selenocysteine tRNAs (TCA): 0
Possible suppressor tRNAs (CTA,TTA): 0
tRNAs with undetermined/unknown isotypes: 0
Predicted pseudogenes: 0
-------
Total tRNAs: 56
tRNAs with introns: 16
| Ala-CGC: 1 | Pro-CGG: 1 | Val-AAC: 2 | Ser-CGA: 1 | Ser-TGA: 1 | Arg-CCG: 1 | Leu-CAG: 1 | Leu-TAG: 1 | Leu-TAA: 1 | Lys-CTT: 3 | Ile-TAT: 1 | Met-CAT: 1 | Tyr-GTA: 1 |
Isotype / Anticodon Counts:
Ala : 6 AGC: 3 GGC: CGC: 1 TGC: 2
Gly : 2 ACC: GCC: 2 CCC: TCC:
Pro : 3 AGG: 1 GGG: CGG: 1 TGG: 1
Thr : 5 AGT: 4 GGT: CGT: 1 TGT:
Val : 4 AAC: 2 GAC: CAC: 1 TAC: 1
Ser : 4 AGA: 2 GGA: CGA: 1 TGA: 1 ACT: GCT:
Arg : 3 ACG: 2 GCG: CCG: 1 TCG: CCT: TCT:
Leu : 4 AAG: 1 GAG: CAG: 1 TAG: 1 CAA: TAA: 1
Phe : 2 AAA: GAA: 2
Asn : 0 ATT: GTT:
Lys : 5 CTT: 3 TTT: 2
Asp : 2 ATC: GTC: 2
Glu : 4 CTC: 2 TTC: 2
His : 0 ATG: GTG:
Gln : 0 CTG: TTG:
Ile : 4 AAT: 3 GAT: TAT: 1
Met : 3 CAT: 3
Tyr : 1 ATA: GTA: 1
Supres: 0 CTA: TTA:
Cys : 3 ACA: GCA: 3
Trp : 1 CCA: 1
SelCys: 0 TCA:
|
CORRESPONDENCE:
Scientific questions: David W. Ussery
Peter Fischer Hallin
