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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_003423 1 177153 177224 Gln CTG 0 0 71.48 NC_003423 2 205375 205448 Ala AGC 0 0 67.24 NC_003423 3 245934 246004 Gly TCC 0 0 60.52 NC_003423 4 275619 275690 Gln TTG 0 0 71.12 NC_003423 5 383937 384008 His GTG 0 0 69.87 NC_003423 6 489855 489925 Gly GCC 0 0 72.94 NC_003423 7 578150 578230 Met CAT 578188 578194 55.15 NC_003423 8 636774 636846 Trp CCA 0 0 68.85 NC_003423 9 740189 740260 Glu CTC 0 0 74.15 NC_003423 10 880427 880498 His GTG 0 0 69.87 NC_003423 11 1462331 1462402 Thr TGT 0 0 78.51 NC_003423 12 1556889 1556972 Tyr GTA 1556927 1556936 70.26 NC_003423 13 1558084 1558166 Lys CTT 1558123 1558130 74.83 NC_003423 14 1558464 1558537 Ile AAT 0 0 66.44 NC_003423 15 1560566 1560638 Arg ACG 0 0 75.46 NC_003423 16 1577371 1577444 Ile AAT 0 0 66.44 NC_003423 17 1588237 1588319 Val AAC 1588275 1588283 64.30 NC_003423 18 1588980 1589053 Ala AGC 0 0 67.24 NC_003423 19 1602927 1603010 Tyr GTA 1602965 1602974 70.26 NC_003423 20 1604122 1604204 Lys CTT 1604161 1604168 74.83 NC_003423 21 1604502 1604575 Ile AAT 0 0 66.44 NC_003423 22 1733938 1734010 Trp CCA 0 0 68.85 NC_003423 23 1836299 1836370 Pro AGG 0 0 64.72 NC_003423 24 1991238 1991311 Asn GTT 0 0 86.64 NC_003423 25 2028565 2028635 Gly CCC 0 0 60.35 NC_003423 26 2278370 2278441 Pro AGG 0 0 64.72 NC_003423 27 2898793 2898864 Pro AGG 0 0 64.72 NC_003423 28 3309672 3309766 Ser GCT 3309711 3309721 74.09 NC_003423 29 3773212 3773294 Lys CTT 3773251 3773258 74.69 NC_003423 30 3773636 3773719 Tyr GTA 3773674 3773683 69.62 NC_003423 31 3873121 3873199 Leu AAG 0 0 60.58 NC_003423 32 3898305 3898375 Asp GTC 0 0 70.49 NC_003423 33 3990821 3990894 Asn GTT 0 0 86.64 NC_003423 34 4066717 4066788 Glu CTC 0 0 74.15 NC_003423 35 4169204 4169131 Asn GTT 0 0 81.94 NC_003423 36 3319668 3319597 Pro TGG 0 0 70.03 NC_003423 37 3168295 3168217 Leu AAG 0 0 59.59 NC_003423 38 2749524 2749453 Thr AGT 0 0 75.01 NC_003423 39 2727413 2727335 Leu AAG 0 0 60.58 NC_003423 40 2535526 2535454 Phe GAA 0 0 70.56 NC_003423 41 2393452 2393381 Met CAT 0 0 69.52 NC_003423 42 1784936 1784865 Pro AGG 0 0 64.72 NC_003423 43 1606433 1606361 Arg ACG 0 0 75.46 NC_003423 44 1605978 1605907 Glu TTC 0 0 62.18 NC_003423 45 1605465 1605383 Val AAC 1605427 1605419 64.30 NC_003423 46 1604722 1604649 Ala AGC 0 0 67.24 NC_003423 47 1603823 1603753 Gly GCC 0 0 72.94 NC_003423 48 1603261 1603161 Leu CAA 1603223 1603205 56.07 NC_003423 49 1589200 1589127 Ile AAT 0 0 66.44 NC_003423 50 1578334 1578252 Val AAC 1578296 1578288 64.30 NC_003423 51 1577591 1577518 Ala AGC 0 0 67.24 NC_003423 52 1560795 1560725 Asp GTC 0 0 70.49 NC_003423 53 1559940 1559869 Glu TTC 0 0 62.18 NC_003423 54 1559427 1559345 Val AAC 1559389 1559381 64.30 NC_003423 55 1558684 1558611 Ala AGC 0 0 67.24 NC_003423 56 1557785 1557715 Gly GCC 0 0 72.94 NC_003423 57 1557223 1557123 Leu CAA 1557185 1557167 56.07 NC_003423 58 1556533 1556453 Met CAT 1556495 1556489 55.15 NC_003423 59 1556447 1556374 Asn GTT 0 0 86.64 NC_003423 60 1360919 1360822 Leu TAA 1360881 1360866 42.88 NC_003423 61 1080692 1080591 Arg CCT 1080656 1080627 57.05 NC_003423 62 664533 664452 Ser AGA 0 0 80.47 NC_003423 63 522398 522324 Lys TTT 0 0 77.52 NC_003423 64 246423 246351 Arg TCT 0 0 69.29 NC_003423 65 205158 205088 Gly TCC 0 0 64.75 NC_003423 66 178618 178547 Gln CTG 0 0 71.48 NC_003423 67 177678 177607 Gln TTG 0 0 71.12 NC_003423 68 100763 100693 Gly GCC 0 0 72.94 |
Statistics results by 'trnascan'
tRNAscan-SE v.1.23 (April 2002) scan results (on host organism)
Started: Sun Mar 14 00:23:08 MET 2004
------------------------------------------------------------
Sequence file(s) to search: Spombe_972_2.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_2.trna.stat
------------------------------------------------------------
First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read: 1
Seqs w/at least 1 hit: 1
Bases read: 4468099 (x2 for both strands)
Bases in tRNAs: 7308
tRNAs predicted: 83
Av. tRNA length: 88
Script CPU time: 3.99 s
Scan CPU time: 15.43 s
Scan speed: 579.1 Kbp/sec
First pass search(es) ended: Sun Mar 14 00:23:30 MET 2004
Cove Stats:
-----------
Candidate tRNAs read: 83
Cove-confirmed tRNAs: 68
Bases scanned by covels: 8470
% seq scanned by covels: 0.0 %
Script CPU time: 1.21 s
Cove CPU time: 44.02 s
Scan speed: 192.4 bp/sec
Cove analysis of tRNAs ended: Sun Mar 14 00:24:26 MET 2004
Summary
--------
Overall scan speed: 138224.3 bp/sec
tRNAs decoding Standard 20 AA: 68
Selenocysteine tRNAs (TCA): 0
Possible suppressor tRNAs (CTA,TTA): 0
tRNAs with undetermined/unknown isotypes: 0
Predicted pseudogenes: 0
-------
Total tRNAs: 68
tRNAs with introns: 17
| Val-AAC: 4 | Ser-GCT: 1 | Arg-CCT: 1 | Leu-CAA: 2 | Leu-TAA: 1 | Lys-CTT: 3 | Met-CAT: 2 | Tyr-GTA: 3 |
Isotype / Anticodon Counts:
Ala : 5 AGC: 5 GGC: CGC: TGC:
Gly : 7 ACC: GCC: 4 CCC: 1 TCC: 2
Pro : 5 AGG: 4 GGG: CGG: TGG: 1
Thr : 2 AGT: 1 GGT: CGT: TGT: 1
Val : 4 AAC: 4 GAC: CAC: TAC:
Ser : 2 AGA: 1 GGA: CGA: TGA: ACT: GCT: 1
Arg : 4 ACG: 2 GCG: CCG: TCG: CCT: 1 TCT: 1
Leu : 6 AAG: 3 GAG: CAG: TAG: CAA: 2 TAA: 1
Phe : 1 AAA: GAA: 1
Asn : 4 ATT: GTT: 4
Lys : 4 CTT: 3 TTT: 1
Asp : 2 ATC: GTC: 2
Glu : 4 CTC: 2 TTC: 2
His : 2 ATG: GTG: 2
Gln : 4 CTG: 2 TTG: 2
Ile : 4 AAT: 4 GAT: TAT:
Met : 3 CAT: 3
Tyr : 3 ATA: GTA: 3
Supres: 0 CTA: TTA:
Cys : 0 ACA: GCA:
Trp : 2 CCA: 2
SelCys: 0 TCA:
|
CORRESPONDENCE:
Scientific questions: David W. Ussery
Peter Fischer Hallin
