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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: Mon Jun 8 12:10:22 PDT 2009
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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: 11623
Seqs w/at least 1 hit: 3471
Bases read: 1481241295 (x2 for both strands)
Bases in tRNAs: 9361486
tRNAs predicted: 118257
Av. tRNA length: 79
Script CPU time: 894.56 s
Scan CPU time: 916.99 s
Scan speed: 3230.7 Kbp/sec
First pass search(es) ended: Mon Jun 8 12:46:08 PDT 2009
Cove Stats:
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Candidate tRNAs read: 118257
Cove-confirmed tRNAs: 25194
Bases scanned by covels: 11016972
% seq scanned by covels: 0.4 %
Script CPU time: 322.33 s
Cove CPU time: 8138.06 s
Scan speed: 1353.8 bp/sec
Cove analysis of tRNAs ended: Mon Jun 8 15:49:27 PDT 2009
Summary
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Overall scan speed: 288405.4 bp/sec
tRNAs decoding Standard 20 AA: 15078
Selenocysteine tRNAs (TCA): 111
Possible suppressor tRNAs (CTA,TTA): 19
tRNAs with undetermined/unknown isotypes: 88
Predicted pseudogenes: 9898
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Total tRNAs: 25194
tRNAs with introns: 1155
| Ala-CGC: 1 | Gly-GCC: 7 | Gly-CCC: 5 | Gly-TCC: 2 | Pro-AGG: 9 | Thr-TGT: 1 | Val-AAC: 2 | Val-GAC: 1 | Val-CAC: 107 | Val-TAC: 7 | Ser-TGA: 1 | Ser-GCT: 1 | Arg-TCT: 312 | Leu-AAG: 6 | Leu-GAG: 1 | Leu-CAG: 3 | Leu-TAG: 10 | Leu-CAA: 286 | Leu-TAA: 10 | Phe-AAA: 4 | Asn-GTT: 1 | Lys-TTT: 4 | Asp-GTC: 4 | Glu-CTC: 3 | Glu-TTC: 2 | His-ATG: 4 | His-GTG: 2 | Gln-CTG: 1 | Gln-TTG: 1 | Ile-AAT: 5 | Ile-TAT: 71 | Met-CAT: 4 | Tyr-ATA: 4 | Tyr-GTA: 270 | Cys-GCA: 3 |
Isotype / Anticodon Counts:
Ala : 643 AGC: 99 GGC: 7 CGC: 120 TGC: 417
Gly : 1636 ACC: 15 GCC: 1191 CCC: 379 TCC: 51
Pro : 878 AGG: 348 GGG: 4 CGG: 254 TGG: 272
Thr : 818 AGT: 387 GGT: 13 CGT: 70 TGT: 348
Val : 815 AAC: 236 GAC: 10 CAC: 247 TAC: 322
Ser : 1279 AGA: 391 GGA: 3 CGA: 80 TGA: 225 ACT: 15 GCT: 565
Arg : 889 ACG: 235 GCG: 29 CCG: 62 TCG: 120 CCT: 149 TCT: 294
Leu : 1432 AAG: 312 GAG: 8 CAG: 355 TAG: 356 CAA: 291 TAA: 110
Phe : 262 AAA: 15 GAA: 247
Asn : 1268 ATT: 30 GTT: 1238
Lys : 1872 CTT: 1290 TTT: 582
Asp : 254 ATC: 1 GTC: 253
Glu : 515 CTC: 280 TTC: 235
His : 494 ATG: 19 GTG: 475
Gln : 469 CTG: 345 TTG: 124
Ile : 380 AAT: 281 GAT: 16 TAT: 83
Met : 587 CAT: 587
Tyr : 300 ATA: 6 GTA: 294
Supres: 19 CTA: 9 TTA: 10
Cys : 237 ACA: 11 GCA: 226
Trp : 50 CCA: 50
SelCys: 111 TCA: 111
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