GtRNAdb

tRNAscan-SE Analysis of Gorilla gorilla gorilla (gorilla) (gorGor3.1 May 2011)

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tRNAscan-SE Run Options & Statistics

tRNAscan-SE v.1.3 (March 2011) scan results (on host aero.cse.ucsc.edu)
Started: Tue Dec 13 11:50:54 PST 2011

------------------------------------------------------------
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:         46823
Seqs w/at least 1 hit:  162
Bases read:             3029553646 (x2 for both strands)
Bases in tRNAs:         3677261
tRNAs predicted:        31097
Av. tRNA length:        118
Script CPU time:        656.84 s
Scan CPU time:          1679.17 s
Scan speed:             3608.4 Kbp/sec

First pass search(es) ended: Tue Dec 13 12:39:03 PST 2011

Cove Stats:
-----------
Candidate tRNAs read:     31097
Cove-confirmed tRNAs:     549
Bases scanned by Cove:  4174768
% seq scanned by Cove:  0.1 %
Script CPU time:          132.72 s
Cove CPU time:            3871.73 s
Scan speed:               1078.3 bp/sec

Cove analysis of tRNAs ended: Tue Dec 13 14:23:27 PST 2011

Summary
--------
Overall scan speed: 955625.8 bp/sec

tRNAs decoding Standard 20 AA:              452
Selenocysteine tRNAs (TCA):                 4
Possible suppressor tRNAs (CTA,TTA):        3
tRNAs with undetermined/unknown isotypes:   3
Predicted pseudogenes:                      87
                                            -------
Total tRNAs:                                549

tRNAs with introns:     	34

| Pro-AGG: 1 | Val-TAC: 1 | Arg-TCT: 5 | Leu-CAA: 6 | Ile-TAT: 5 | Tyr-ATA: 1 | Tyr-GTA: 14 | Cys-ACA: 1 |

Isotype / Anticodon Counts:

Ala   : 35	  AGC: 22      GGC: 2       CGC: 4       TGC: 7     
Gly   : 23	  ACC:         GCC: 11      CCC: 9       TCC: 3     
Pro   : 21	  AGG: 10      GGG:         CGG: 4       TGG: 7     
Thr   : 19	  AGT: 9       GGT:         CGT: 4       TGT: 6     
Val   : 25	  AAC: 7       GAC:         CAC: 11      TAC: 7     
Ser   : 27	  AGA: 10      GGA:         CGA: 5       TGA: 4       ACT:         GCT: 8     
Arg   : 30	  ACG: 7       GCG:         CCG: 5       TCG: 6       CCT: 6       TCT: 6     
Leu   : 33	  AAG: 9       GAG:         CAG: 5       TAG: 4       CAA: 6       TAA: 9     
Phe   : 10	  AAA:         GAA: 10                              
Asn   : 30	  ATT: 1       GTT: 29                              
Lys   : 27	                            CTT: 13      TTT: 14    
Asp   : 17	  ATC:         GTC: 17                              
Glu   : 31	                            CTC: 14      TTC: 17    
His   : 9	  ATG:         GTG: 9                               
Gln   : 23	                            CTG: 16      TTG: 7     
Ile   : 20	  AAT: 12      GAT: 2                    TAT: 6     
Met   : 18	                            CAT: 18                 
Tyr   : 16	  ATA: 1       GTA: 15                              
Supres: 3	                            CTA: 1       TTA: 2     
Cys   : 30	  ACA: 1       GCA: 29                              
Trp   : 8	                            CCA: 8                  
SelCys: 4	                                         TCA: 4     


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.