GtRNAdb

tRNAscan-SE Analysis of Loxodonta africana (elephant) (Broad/July 2009)

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tRNAscan-SE Run Options & Statistics

tRNAscan-SE v.1.3 (March 2011) scan results (on host isla)
Started: Tue Dec 13 14:16:56 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:         2353
Seqs w/at least 1 hit:  1319
Bases read:             3196760833 (x2 for both strands)
Bases in tRNAs:         49181590
tRNAs predicted:        635192
Av. tRNA length:        77
Script CPU time:        6403.97 s
Scan CPU time:          1778.51 s
Scan speed:             3594.9 Kbp/sec

First pass search(es) ended: Tue Dec 13 16:36:41 PST 2011

Cove Stats:
-----------
Candidate tRNAs read:     635192
Cove-confirmed tRNAs:     80599
Bases scanned by Cove:  59344607
% seq scanned by Cove:  0.9 %
Script CPU time:          2715.49 s
Cove CPU time:            35811.27 s
Scan speed:               1657.1 bp/sec

Cove analysis of tRNAs ended: Thu Dec 15 22:00:44 PST 2011

Summary
--------
Overall scan speed: 136879.2 bp/sec

tRNAs decoding Standard 20 AA:              20532
Selenocysteine tRNAs (TCA):                 256
Possible suppressor tRNAs (CTA,TTA):        26
tRNAs with undetermined/unknown isotypes:   387
Predicted pseudogenes:                      59398
                                            -------
Total tRNAs:                                80599

tRNAs with introns:     	269

| Ala-CGC: 1 | Ala-TGC: 1 | Gly-ACC: 2 | Gly-GCC: 2 | Gly-CCC: 5 | Gly-TCC: 46 | Pro-AGG: 1 | Pro-GGG: 2 | Pro-CGG: 1 | Thr-TGT: 1 | Ser-AGA: 1 | Ser-CGA: 1 | Ser-GCT: 33 | Arg-GCG: 1 | Arg-CCG: 2 | Arg-CCT: 10 | Arg-TCT: 47 | Leu-AAG: 1 | Leu-TAG: 1 | Leu-CAA: 27 | Leu-TAA: 14 | Phe-AAA: 4 | Phe-GAA: 1 | Asn-GTT: 1 | Lys-TTT: 9 | Glu-CTC: 4 | Glu-TTC: 4 | His-GTG: 1 | Gln-TTG: 2 | Ile-TAT: 5 | Tyr-ATA: 5 | Tyr-GTA: 22 | Supres-CTA: 2 | Supres-TTA: 2 | Cys-ACA: 1 | Cys-GCA: 4 | Trp-CCA: 1 | SelCys-TCA: 1 |

Isotype / Anticodon Counts:

Ala   : 263	  AGC: 80      GGC: 6       CGC: 25      TGC: 152   
Gly   : 4577	  ACC: 55      GCC: 414     CCC: 334     TCC: 3774  
Pro   : 46	  AGG: 18      GGG: 3       CGG: 4       TGG: 21    
Thr   : 234	  AGT: 34      GGT: 153     CGT: 17      TGT: 30    
Val   : 234	  AAC: 59      GAC: 10      CAC: 56      TAC: 109   
Ser   : 11306	  AGA: 32      GGA: 7       CGA: 119     TGA: 38      ACT: 663     GCT: 10447 
Arg   : 972	  ACG: 23      GCG: 55      CCG: 7       TCG: 46      CCT: 184     TCT: 657   
Leu   : 289	  AAG: 32      GAG: 5       CAG: 23      TAG: 19      CAA: 184     TAA: 26    
Phe   : 53	  AAA: 5       GAA: 48                              
Asn   : 916	  ATT: 94      GTT: 822                             
Lys   : 235	                            CTT: 90      TTT: 145   
Asp   : 87	  ATC: 12      GTC: 75                              
Glu   : 550	                            CTC: 64      TTC: 486   
His   : 91	  ATG: 9       GTG: 82                              
Gln   : 99	                            CTG: 53      TTG: 46    
Ile   : 226	  AAT: 71      GAT: 133                  TAT: 22    
Met   : 72	                            CAT: 72                 
Tyr   : 41	  ATA: 9       GTA: 32                              
Supres: 26	                            CTA: 16      TTA: 10    
Cys   : 203	  ACA: 28      GCA: 175                             
Trp   : 38	                            CCA: 38                 
SelCys: 256	                                         TCA: 256   


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.