tRNAscan-SE Analysis of the Chromobacterium violaceum Genome

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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: Sun Jul 27 15:58:18 PDT 2008

------------------------------------------------------------
Search Mode:                 Bacterial
Searching with:              tRNAscan + EufindtRNA -> Cove
Covariance model:            TRNA2-bact.cm
tRNAscan parameters:         Strict
EufindtRNA parameters:       Relaxed (Int Cutoff= -36)

Reporting HMM/2' structure score breakdown
------------------------------------------------------------

First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read:         1
Seqs w/at least 1 hit:  1
Bases read:             4751080 (x2 for both strands)
Bases in tRNAs:         34510
tRNAs predicted:        304
Av. tRNA length:        113
Script CPU time:        0.85 s
Scan CPU time:          3.78 s
Scan speed:             2513.8 Kbp/sec

First pass search(es) ended: Sun Jul 27 15:58:23 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     304
Cove-confirmed tRNAs:     98
Bases scanned by covels:  38766
% seq scanned by covels:  0.4 %
Script CPU time:          0.80 s
Cove CPU time:            43.95 s
Scan speed:               882.0 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 15:59:12 PDT 2008

Summary
--------
Overall scan speed: 192429.3 bp/sec

tRNAs decoding Standard 20 AA:              98
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                98

tRNAs with introns:     	0

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Isotype / Anticodon Counts:

Ala   : 12	  AGC:         GGC: 3       CGC: 1       TGC: 8     
Gly   : 7	  ACC:         GCC: 5       CCC: 1       TCC: 1     
Pro   : 4	  AGG:         GGG: 1       CGG: 2       TGG: 1     
Thr   : 4	  AGT:         GGT: 2       CGT: 1       TGT: 1     
Val   : 8	  AAC:         GAC: 1       CAC: 2       TAC: 5     
Ser   : 5	  AGA:         GGA: 2       CGA: 1       TGA: 1       ACT:         GCT: 1     
Arg   : 6	  ACG: 3       GCG:         CCG: 1       TCG:         CCT: 1       TCT: 1     
Leu   : 8	  AAG:         GAG: 1       CAG: 4       TAG: 1       CAA: 1       TAA: 1     
Phe   : 2	  AAA:         GAA: 2                               
Asn   : 4	  ATT:         GTT: 4                               
Lys   : 5	                            CTT: 2       TTT: 3     
Asp   : 7	  ATC:         GTC: 7                               
Glu   : 4	                            CTC:         TTC: 4     
His   : 3	  ATG:         GTG: 3                               
Gln   : 2	                            CTG:         TTG: 2     
Ile   : 8	  AAT:         GAT: 8                    TAT:       
Met   : 5	                            CAT: 5                  
Tyr   : 2	  ATA:         GTA: 2                               
Supres: 0	                            CTA:         TTA:       
Cys   : 1	  ACA:         GCA: 1                               
Trp   : 1	                            CCA: 1                  
SelCys: 0	                                         TCA:
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.