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| tRNAscan-SE Run Options & Statistics |
tRNAscan-SE v.1.23 (April 2002) scan results (on host lowepub.cse.ucsc.edu)
Started: Sun May 18 11:29:39 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: 217790
Seqs w/at least 1 hit: 78419
Bases read: 4045535322 (x2 for both strands)
Bases in tRNAs: 26984686
tRNAs predicted: 308929
Av. tRNA length: 87
Script CPU time: 723.91 s
Scan CPU time: 2187.02 s
Scan speed: 3699.6 Kbp/sec
First pass search(es) ended: Sun May 18 16:26:09 PDT 2008
Cove Stats:
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Candidate tRNAs read: 308929
Cove-confirmed tRNAs: 117579
Bases scanned by covels: 31304962
% seq scanned by covels: 0.4 %
Script CPU time: 683.49 s
Cove CPU time: 27342.85 s
Scan speed: 1144.9 bp/sec
Cove analysis of tRNAs ended: Mon May 19 10:08:58 PDT 2008
Summary
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Overall scan speed: 261531.5 bp/sec
tRNAs decoding Standard 20 AA: 8807
Selenocysteine tRNAs (TCA): 49555
Possible suppressor tRNAs (CTA,TTA): 122
tRNAs with undetermined/unknown isotypes: 89
Predicted pseudogenes: 59006
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Total tRNAs: 117579
tRNAs with introns: 49811
| Ala-AGC: 56 | Ala-GGC: 30 | Ala-CGC: 4 | Ala-TGC: 9 | Gly-ACC: 2 | Gly-GCC: 10 | Gly-CCC: 30 | Gly-TCC: 238 | Pro-GGG: 9 | Pro-CGG: 37 | Pro-TGG: 286 | Thr-GGT: 4 | Thr-CGT: 44 | Thr-TGT: 13 | Val-AAC: 5 | Val-GAC: 11 | Val-CAC: 9 | Val-TAC: 2 | Ser-GGA: 4 | Ser-CGA: 30 | Ser-TGA: 96 | Ser-ACT: 5 | Ser-GCT: 7 | Arg-ACG: 9 | Arg-GCG: 30 | Arg-CCG: 78 | Arg-TCG: 5881 | Arg-CCT: 318 | Arg-TCT: 206 | Leu-AAG: 1 | Leu-GAG: 6 | Leu-CAG: 137 | Leu-TAG: 128 | Leu-CAA: 20 | Leu-TAA: 39 | Phe-AAA: 1 | Phe-GAA: 1 | Asn-ATT: 38 | Asn-GTT: 107 | Lys-CTT: 6441 | Lys-TTT: 261 | Asp-ATC: 3 | Asp-GTC: 5 | Glu-CTC: 386 | Glu-TTC: 101 | His-ATG: 13 | His-GTG: 23 | Gln-CTG: 255 | Gln-TTG: 2704 | Ile-GAT: 1 | Ile-TAT: 10 | Met-CAT: 51 | Tyr-ATA: 3 | Tyr-GTA: 10 | Supres-CTA: 72 | Supres-TTA: 285 | Cys-ACA: 21 | Cys-GCA: 57 | Trp-CCA: 80 | SelCys-TCA: 31088 |
Isotype / Anticodon Counts:
Ala : 32 AGC: 13 GGC: 5 CGC: 5 TGC: 9
Gly : 138 ACC: 1 GCC: 9 CCC: 12 TCC: 116
Pro : 184 AGG: 8 GGG: 2 CGG: 14 TGG: 160
Thr : 46 AGT: 3 GGT: 2 CGT: 18 TGT: 23
Val : 15 AAC: 5 GAC: 3 CAC: 3 TAC: 4
Ser : 68 AGA: 5 GGA: 2 CGA: 15 TGA: 37 ACT: 3 GCT: 6
Arg : 2827 ACG: 13 GCG: 15 CCG: 52 TCG: 2464 CCT: 167 TCT: 116
Leu : 147 AAG: 6 GAG: 3 CAG: 28 TAG: 72 CAA: 9 TAA: 29
Phe : 11 AAA: 2 GAA: 9
Asn : 86 ATT: 23 GTT: 63
Lys : 3079 CTT: 2940 TTT: 139
Asp : 11 ATC: 4 GTC: 7
Glu : 180 CTC: 160 TTC: 20
His : 43 ATG: 12 GTG: 31
Gln : 1779 CTG: 133 TTG: 1646
Ile : 19 AAT: 8 GAT: 1 TAT: 10
Met : 36 CAT: 36
Tyr : 12 ATA: 1 GTA: 11
Supres: 122 CTA: 32 TTA: 90
Cys : 56 ACA: 12 GCA: 44
Trp : 38 CCA: 38
SelCys: 49555 TCA: 49555
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