tRNAscan-SE Run Options & Statistics

	
tRNAscan-SE v.2.0 (Sept 2015) scan results (on host zam.soe.ucsc.edu)
Started: Fri Sep 25 00:22:31 PDT 2015

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Search Mode:                 Eukaryotic
Searching with:              Infernal First Pass->Infernal
Perform isotype specific model scan
Covariance model:            infernal-1.1/TRNAinf-euk.cm
Infernal first pass cutoff score: 0
Isotype specific

Reporting HMM/2' structure score breakdown
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First-pass (tRNAscan/EufindtRNA) Stats:
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Sequences read:         66
Seqs w/at least 1 hit:  46
Bases read:             2730871774 (x2 for both strands)
Bases in tRNAs:         6785801
tRNAs predicted:        99114
Av. tRNA length:        68
Script CPU time:        2801.84 s
Scan CPU time:          4476.54 s
Scan speed:             1220.1 Kbp/sec

First pass search(es) ended: Fri Sep 25 01:41:10 PDT 2015

Infernal Stats:
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Candidate tRNAs read:     99114
Infernal-confirmed tRNAs:     11398
Bases scanned by Infernal:  8768081
% seq scanned by Infernal:  0.2 %
Script CPU time:          491.58 s
Infernal CPU time:            48319.28 s
Scan speed:               181.5 bp/sec

Infernal analysis of tRNAs ended: Sat Sep 26 06:58:21 PDT 2015

Overall scan speed: 97376.0 bp/sec

tRNAs decoding Standard 20 AA:              2334
Selenocysteine tRNAs (TCA):                 3
Possible suppressor tRNAs (CTA,TTA):        4
tRNAs with undetermined/unknown isotypes:   179
Predicted pseudogenes:                      8878
                                            -------
Total tRNAs:                                11398

tRNAs with introns:     	98

| Ala-AGC: 8 | Ala-GGC: 2 | Ala-CGC: 1 | Ala-TGC: 2 | Gly-CCC: 1 | Pro-GGG: 1 | Pro-TGG: 1 | Thr-AGT: 1 | Val-AAC: 3 | Val-CAC: 1 | Ser-AGA: 21 | Ser-GGA: 1 | Ser-CGA: 1 | Ser-TGA: 2 | Ser-ACT: 1 | Ser-GCT: 2 | Arg-TCT: 5 | Leu-AAG: 1 | Leu-GAG: 1 | Leu-CAG: 2 | Leu-CAA: 5 | Phe-GAA: 1 | Asn-GTT: 3 | Lys-CTT: 1 | Lys-TTT: 1 | His-ATG: 1 | His-GTG: 1 | Gln-CTG: 3 | Ile-TAT: 4 | Met-CAT: 1 | Tyr-ATA: 1 | Tyr-GTA: 13 | Supres-TTA: 2 | Cys-GCA: 3 |

Isotype / Anticodon Counts:

Ala   : 189	  AGC: 117     GGC: 25      CGC: 14      TGC: 33    
Gly   : 64	  ACC: 11      GCC: 36      CCC: 7       TCC: 10    
Pro   : 27	  AGG: 12      GGG: 1       CGG: 3       TGG: 11    
Thr   : 62	  AGT: 30      GGT: 16      CGT: 6       TGT: 10    
Val   : 56	  AAC: 28      GAC: 2       CAC: 19      TAC: 7     
Ser   : 1247	  AGA: 24      GGA: 5       CGA: 8       TGA: 8       ACT: 66      GCT: 1136  
Arg   : 60	  ACG: 6       GCG: 1       CCG: 3       TCG: 5       CCT: 23      TCT: 22    
Leu   : 76	  AAG: 5       GAG: 2       CAG: 12      TAG: 5       CAA: 44      TAA: 8     
Phe   : 8	  AAA:         GAA: 8                               
Asn   : 210	  ATT: 16      GTT: 194                             
Lys   : 59	                            CTT: 39      TTT: 20    
Asp   : 25	  ATC: 5       GTC: 20                              
Glu   : 29	                            CTC: 21      TTC: 8     
His   : 14	  ATG: 1       GTG: 13                              
Gln   : 22	                            CTG: 14      TTG: 8     
Ile   : 60	  AAT: 18      GAT: 33                   TAT: 9     
Met   : 21	                            CAT: 21                 
Tyr   : 18	  ATA: 1       GTA: 17                              
Supres: 4	                            CTA: 2       TTA: 2     
Cys   : 77	  ACA: 3       GCA: 74                              
Trp   : 10	                            CCA: 10                 
SelCys: 3	                                         TCA: 3