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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 11:28:47 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: 11900
Seqs w/at least 1 hit: 6798
Bases read: 2917974530 (x2 for both strands)
Bases in tRNAs: 39928688
tRNAs predicted: 519290
Av. tRNA length: 76
Script CPU time: 11382.19 s
Scan CPU time: 1905.44 s
Scan speed: 3062.8 Kbp/sec
First pass search(es) ended: Sun May 18 15:35:48 PDT 2008
Cove Stats:
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Candidate tRNAs read: 519290
Cove-confirmed tRNAs: 225600
Bases scanned by covels: 47198375
% seq scanned by covels: 0.8 %
Script CPU time: 1558.43 s
Cove CPU time: 39305.41 s
Scan speed: 1200.8 bp/sec
Cove analysis of tRNAs ended: Mon May 19 19:56:37 PDT 2008
Summary
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Overall scan speed: 107770.8 bp/sec
tRNAs decoding Standard 20 AA: 31873
Selenocysteine tRNAs (TCA): 3155
Possible suppressor tRNAs (CTA,TTA): 242
tRNAs with undetermined/unknown isotypes: 1140
Predicted pseudogenes: 189190
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Total tRNAs: 225600
tRNAs with introns: 4276
| Ala-AGC: 6 | Ala-GGC: 32 | Ala-CGC: 2 | Ala-TGC: 29 | Gly-ACC: 122 | Gly-GCC: 1826 | Gly-CCC: 74 | Gly-TCC: 102 | Pro-GGG: 4 | Pro-CGG: 1 | Pro-TGG: 1 | Thr-AGT: 6 | Thr-GGT: 8 | Thr-CGT: 2 | Thr-TGT: 5 | Val-AAC: 3 | Val-GAC: 48 | Val-CAC: 4 | Val-TAC: 8 | Ser-AGA: 8 | Ser-GGA: 13 | Ser-CGA: 2 | Ser-TGA: 3 | Ser-ACT: 22 | Ser-GCT: 148 | Arg-ACG: 8 | Arg-GCG: 34 | Arg-CCG: 1 | Arg-TCG: 7 | Arg-CCT: 12 | Arg-TCT: 15 | Leu-AAG: 6 | Leu-GAG: 5 | Leu-CAG: 8 | Leu-TAG: 2 | Leu-CAA: 9 | Leu-TAA: 4 | Phe-AAA: 7 | Phe-GAA: 46 | Asn-ATT: 7 | Asn-GTT: 16 | Lys-CTT: 3 | Lys-TTT: 8 | Asp-ATC: 14 | Asp-GTC: 174 | Glu-CTC: 11 | Glu-TTC: 47 | His-ATG: 6 | His-GTG: 49 | Gln-CTG: 7 | Gln-TTG: 11 | Ile-AAT: 3 | Ile-GAT: 8 | Ile-TAT: 6 | Met-CAT: 2 | Tyr-ATA: 15 | Tyr-GTA: 94 | Supres-CTA: 6 | Supres-TTA: 9 | Cys-ACA: 136 | Cys-GCA: 918 | Trp-CCA: 55 | SelCys-TCA: 28 |
Isotype / Anticodon Counts:
Ala : 334 AGC: 61 GGC: 53 CGC: 41 TGC: 179
Gly : 8377 ACC: 209 GCC: 2632 CCC: 3429 TCC: 2107
Pro : 37 AGG: 14 GGG: 3 CGG: 7 TGG: 13
Thr : 55 AGT: 25 GGT: 3 CGT: 11 TGT: 16
Val : 258 AAC: 39 GAC: 55 CAC: 99 TAC: 65
Ser : 637 AGA: 41 GGA: 213 CGA: 22 TGA: 29 ACT: 39 GCT: 293
Arg : 931 ACG: 51 GCG: 234 CCG: 57 TCG: 26 CCT: 307 TCT: 256
Leu : 174 AAG: 17 GAG: 25 CAG: 18 TAG: 14 CAA: 64 TAA: 36
Phe : 413 AAA: 47 GAA: 366
Asn : 81 ATT: 13 GTT: 68
Lys : 358 CTT: 111 TTT: 247
Asp : 360 ATC: 37 GTC: 323
Glu : 2493 CTC: 618 TTC: 1875
His : 237 ATG: 36 GTG: 201
Gln : 173 CTG: 104 TTG: 69
Ile : 68 AAT: 28 GAT: 18 TAT: 22
Met : 46 CAT: 46
Tyr : 967 ATA: 179 GTA: 788
Supres: 242 CTA: 162 TTA: 80
Cys : 14125 ACA: 1931 GCA: 12194
Trp : 1749 CCA: 1749
SelCys: 3155 TCA: 3155
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