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tRNAscan-SE Analysis of Takifugu rubripes (fr2 Oct 2004)

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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 10:48:36 PDT 2008

------------------------------------------------------------
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
------------------------------------------------------------

First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read:         2
Seqs w/at least 1 hit:  2
Bases read:             400525790 (x2 for both strands)
Bases in tRNAs:         295589
tRNAs predicted:        2882
Av. tRNA length:        102
Script CPU time:        77.96 s
Scan CPU time:          254.54 s
Scan speed:             3147.1 Kbp/sec

First pass search(es) ended: Sun May 18 10:54:42 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     2882
Cove-confirmed tRNAs:     722
Bases scanned by covels:  335937
% seq scanned by covels:  0.0 %
Script CPU time:          8.84 s
Cove CPU time:            326.54 s
Scan speed:               1028.8 bp/sec

Cove analysis of tRNAs ended: Sun May 18 11:04:01 PDT 2008

Summary
--------
Overall scan speed: 1199394.5 bp/sec

tRNAs decoding Standard 20 AA:              588
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   10
Predicted pseudogenes:                      123
                                            -------
Total tRNAs:                                722

tRNAs with introns:     	43

| Val-CAC: 1 | Arg-GCG: 1 | Arg-TCT: 12 | Leu-CAA: 9 | His-ATG: 1 | Ile-TAT: 5 | Tyr-GTA: 14 |

Isotype / Anticodon Counts:

Ala   : 27	  AGC: 13      GGC:         CGC: 6       TGC: 8     
Gly   : 34	  ACC:         GCC: 18      CCC: 4       TCC: 12    
Pro   : 23	  AGG: 10      GGG:         CGG: 6       TGG: 7     
Thr   : 32	  AGT: 18      GGT:         CGT: 6       TGT: 8     
Val   : 48	  AAC: 15      GAC:         CAC: 24      TAC: 9     
Ser   : 38	  AGA: 11      GGA:         CGA: 3       TGA: 8       ACT:         GCT: 16    
Arg   : 50	  ACG: 16      GCG: 1       CCG: 3       TCG: 7       CCT: 10      TCT: 13    
Leu   : 52	  AAG: 11      GAG:         CAG: 21      TAG: 4       CAA: 9       TAA: 7     
Phe   : 20	  AAA:         GAA: 20                              
Asn   : 24	  ATT:         GTT: 24                              
Lys   : 38	                            CTT: 18      TTT: 20    
Asp   : 25	  ATC: 1       GTC: 24                              
Glu   : 35	                            CTC: 20      TTC: 15    
His   : 22	  ATG: 2       GTG: 20                              
Gln   : 22	                            CTG: 13      TTG: 9     
Ile   : 18	  AAT: 12      GAT:                      TAT: 6     
Met   : 35	                            CAT: 35                 
Tyr   : 15	  ATA: 1       GTA: 14                              
Supres: 0	                            CTA:         TTA:       
Cys   : 12	  ACA:         GCA: 12                              
Trp   : 18	                            CCA: 18                 
SelCys: 1	                                         TCA: 1     


The Genomic tRNA Database is curated by Todd Lowe and Patricia Chan. Please email lowe@soe.ucsc.edu with any questions and comments. To submit corrections, please use our Bug and Request Tracking System.