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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_003421 1 71400 71471 His GTG 0 0 69.87 NC_003421 2 140967 141038 Glu CTC 0 0 74.15 NC_003421 3 578847 578919 Arg TCT 0 0 73.59 NC_003421 4 817425 817498 Ile AAT 0 0 63.37 NC_003421 5 847701 847782 Ser AGA 0 0 80.47 NC_003421 6 925852 925924 Arg ACG 0 0 75.46 NC_003421 7 947262 947335 Asn GTT 0 0 86.64 NC_003421 8 1066628 1066709 Ser AGA 0 0 80.47 NC_003421 9 1068029 1068099 Asp GTC 0 0 70.49 NC_003421 10 1069166 1069244 Leu AAG 0 0 60.58 NC_003421 11 1071093 1071175 Lys CTT 1071132 1071139 74.69 NC_003421 12 1093137 1093207 Asp GTC 0 0 70.49 NC_003421 13 1093634 1093716 Val AAC 1093672 1093680 64.30 NC_003421 14 1106708 1106808 Leu CAA 1106746 1106764 56.07 NC_003421 15 1109739 1109810 Thr AGT 0 0 75.01 NC_003421 16 1110226 1110298 Arg ACG 0 0 75.46 NC_003421 17 1257092 1257186 Ser GCT 1257131 1257141 74.09 NC_003421 18 1478933 1479015 Lys CTT 1478972 1478979 74.69 NC_003421 19 1693612 1693708 Ser TGA 1693649 1693663 78.22 NC_003421 20 1693716 1693787 Met CAT 0 0 69.52 NC_003421 21 1705798 1705871 Asn GTT 0 0 86.64 NC_003421 22 1792852 1792923 Pro AGG 0 0 64.72 NC_003421 23 1848542 1848613 His GTG 0 0 69.87 NC_003421 24 1867034 1867105 Gln TTG 0 0 69.22 NC_003421 25 2041255 2041325 Gly TCC 0 0 64.15 NC_003421 26 2075983 2076077 Ser GCT 2076022 2076032 74.09 NC_003421 27 2143381 2143311 Asp GTC 0 0 70.49 NC_003421 28 2078965 2078894 Gln TTG 0 0 69.22 NC_003421 29 1779976 1779895 Ser AGA 0 0 80.47 NC_003421 30 1365060 1364989 Thr TGT 0 0 79.00 NC_003421 31 1210718 1210646 Val TAC 0 0 76.36 NC_003421 32 1146163 1146091 Phe GAA 0 0 69.56 NC_003421 33 1143517 1143435 Lys CTT 1143478 1143471 74.69 NC_003421 34 1110456 1110386 Asp GTC 0 0 70.49 NC_003421 35 1109959 1109877 Val AAC 1109921 1109913 64.30 NC_003421 36 1101469 1101398 Glu CTC 0 0 74.15 NC_003421 37 1098270 1098199 Glu CTC 0 0 74.15 NC_003421 38 1096885 1096785 Leu CAA 1096847 1096829 56.07 NC_003421 39 1093854 1093783 Thr AGT 0 0 75.01 NC_003421 40 1093367 1093295 Arg ACG 0 0 75.46 NC_003421 41 1068254 1068182 Arg ACG 0 0 75.46 NC_003421 42 1067164 1067092 Arg TCG 0 0 62.90 NC_003421 43 1065860 1065778 Val AAC 1065822 1065814 64.30 NC_003421 44 1065117 1065044 Ala AGC 0 0 67.24 NC_003421 45 820637 820567 Gly GCC 0 0 72.94 NC_003421 46 473280 473199 Ser AGA 0 0 80.47 NC_003421 47 331300 331228 Phe GAA 0 0 69.56 NC_003421 48 113786 113716 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 00:25:58 MET 2004
------------------------------------------------------------
Sequence file(s) to search: Spombe_972_3.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_3.trna.stat
------------------------------------------------------------
First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read: 1
Seqs w/at least 1 hit: 1
Bases read: 2456786 (x2 for both strands)
Bases in tRNAs: 4861
tRNAs predicted: 60
Av. tRNA length: 81
Script CPU time: 2.14 s
Scan CPU time: 8.46 s
Scan speed: 580.8 Kbp/sec
First pass search(es) ended: Sun Mar 14 00:26:10 MET 2004
Cove Stats:
-----------
Candidate tRNAs read: 60
Cove-confirmed tRNAs: 48
Bases scanned by covels: 5701
% seq scanned by covels: 0.1 %
Script CPU time: 0.86 s
Cove CPU time: 27.58 s
Scan speed: 206.7 bp/sec
Cove analysis of tRNAs ended: Sun Mar 14 00:26:45 MET 2004
Summary
--------
Overall scan speed: 125859.9 bp/sec
tRNAs decoding Standard 20 AA: 48
Selenocysteine tRNAs (TCA): 0
Possible suppressor tRNAs (CTA,TTA): 0
tRNAs with undetermined/unknown isotypes: 0
Predicted pseudogenes: 0
-------
Total tRNAs: 48
tRNAs with introns: 11
| Val-AAC: 3 | Ser-TGA: 1 | Ser-GCT: 2 | Leu-CAA: 2 | Lys-CTT: 3 |
Isotype / Anticodon Counts:
Ala : 1 AGC: 1 GGC: CGC: TGC:
Gly : 3 ACC: GCC: 2 CCC: TCC: 1
Pro : 1 AGG: 1 GGG: CGG: TGG:
Thr : 3 AGT: 2 GGT: CGT: TGT: 1
Val : 4 AAC: 3 GAC: CAC: TAC: 1
Ser : 7 AGA: 4 GGA: CGA: TGA: 1 ACT: GCT: 2
Arg : 6 ACG: 4 GCG: CCG: TCG: 1 CCT: TCT: 1
Leu : 3 AAG: 1 GAG: CAG: TAG: CAA: 2 TAA:
Phe : 2 AAA: GAA: 2
Asn : 2 ATT: GTT: 2
Lys : 3 CTT: 3 TTT:
Asp : 4 ATC: GTC: 4
Glu : 3 CTC: 3 TTC:
His : 2 ATG: GTG: 2
Gln : 2 CTG: TTG: 2
Ile : 1 AAT: 1 GAT: TAT:
Met : 1 CAT: 1
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
