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| tRNAscan-SE Run Options & Statistics |
tRNAscan-SE v.1.23 (April 2002) scan results (on host lowedev.cse.ucsc.edu)
Started: Sun May 18 15:33:40 PDT 2008
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Search Mode: Eukaryotic
Searching with: tRNAscan + EufindtRNA -> Cove
Covariance model: TRNA2-euk.cm
tRNAscan parameters: Strict
EufindtRNA parameters: Relaxed (Int Cutoff= -32.1)
Reporting HMM/2' structure score breakdown
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First-pass (tRNAscan/EufindtRNA) Stats:
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Sequences read: 41
Seqs w/at least 1 hit: 41
Bases read: 2531673953 (x2 for both strands)
Bases in tRNAs: 46095714
tRNAs predicted: 547372
Av. tRNA length: 84
Script CPU time: 11319.95 s
Scan CPU time: 1658.87 s
Scan speed: 3052.3 Kbp/sec
First pass search(es) ended: Sun May 18 19:12:34 PDT 2008
Cove Stats:
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Candidate tRNAs read: 547372
Cove-confirmed tRNAs: 88181
Bases scanned by covels: 53758922
% seq scanned by covels: 1.1 %
Script CPU time: 1576.72 s
Cove CPU time: 38752.41 s
Scan speed: 1387.2 bp/sec
Cove analysis of tRNAs ended: Mon May 19 18:22:18 PDT 2008
Summary
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Overall scan speed: 94983.0 bp/sec
tRNAs decoding Standard 20 AA: 5164
Selenocysteine tRNAs (TCA): 11785
Possible suppressor tRNAs (CTA,TTA): 61
tRNAs with undetermined/unknown isotypes: 90
Predicted pseudogenes: 71081
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Total tRNAs: 88181
tRNAs with introns: 16487
| Ala-AGC: 10 | Ala-GGC: 7 | Ala-CGC: 2 | Ala-TGC: 12 | Gly-ACC: 3 | Gly-GCC: 63 | Gly-CCC: 6 | Gly-TCC: 285 | Pro-AGG: 75 | Pro-GGG: 111 | Pro-CGG: 34 | Pro-TGG: 290 | Thr-AGT: 1 | Thr-GGT: 8 | Thr-CGT: 14 | Thr-TGT: 9 | Val-GAC: 5 | Val-CAC: 9 | Val-TAC: 4 | Ser-AGA: 16 | Ser-GGA: 9 | Ser-CGA: 8 | Ser-TGA: 53 | Ser-ACT: 4 | Ser-GCT: 5 | Arg-ACG: 6 | Arg-GCG: 14 | Arg-CCG: 32 | Arg-TCG: 1598 | Arg-CCT: 100 | Arg-TCT: 225 | Leu-AAG: 5 | Leu-GAG: 11 | Leu-CAG: 419 | Leu-TAG: 131 | Leu-CAA: 41 | Leu-TAA: 21 | Phe-AAA: 1 | Phe-GAA: 4 | Asn-ATT: 17 | Asn-GTT: 37 | Lys-CTT: 2001 | Lys-TTT: 237 | Asp-ATC: 3 | Asp-GTC: 13 | Glu-CTC: 54 | Glu-TTC: 150 | His-ATG: 18 | His-GTG: 38 | Gln-CTG: 174 | Gln-TTG: 6220 | Ile-GAT: 1 | Ile-TAT: 11 | Met-CAT: 34 | Tyr-GTA: 12 | Supres-CTA: 44 | Supres-TTA: 325 | Cys-ACA: 9 | Cys-GCA: 36 | Trp-CCA: 71 | SelCys-TCA: 3331 |
Isotype / Anticodon Counts:
Ala : 40 AGC: 16 GGC: 6 CGC: 6 TGC: 12
Gly : 56 ACC: GCC: 16 CCC: 16 TCC: 24
Pro : 60 AGG: 13 GGG: 11 CGG: 9 TGG: 27
Thr : 43 AGT: 8 GGT: 3 CGT: 14 TGT: 18
Val : 27 AAC: 7 GAC: 3 CAC: 10 TAC: 7
Ser : 63 AGA: 11 GGA: CGA: 14 TGA: 20 ACT: 5 GCT: 13
Arg : 345 ACG: 8 GCG: 7 CCG: 8 TCG: 117 CCT: 171 TCT: 34
Leu : 71 AAG: 4 GAG: 4 CAG: 31 TAG: 13 CAA: 12 TAA: 7
Phe : 10 AAA: GAA: 10
Asn : 84 ATT: 27 GTT: 57
Lys : 2879 CTT: 2706 TTT: 173
Asp : 24 ATC: 4 GTC: 20
Glu : 144 CTC: 122 TTC: 22
His : 616 ATG: 58 GTG: 558
Gln : 578 CTG: 172 TTG: 406
Ile : 16 AAT: 10 GAT: TAT: 6
Met : 42 CAT: 42
Tyr : 28 ATA: 4 GTA: 24
Supres: 61 CTA: 35 TTA: 26
Cys : 26 ACA: GCA: 26
Trp : 12 CCA: 12
SelCys: 11785 TCA: 11785
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