GtRNAdb

tRNAscan-SE Analysis of Silicibacter TM1040

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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 May 18 13:53:35 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:         3
Seqs w/at least 1 hit:  3
Bases read:             4153699 (x2 for both strands)
Bases in tRNAs:         39304
tRNAs predicted:        335
Av. tRNA length:        117
Script CPU time:        0.59 s
Scan CPU time:          3.37 s
Scan speed:             2465.1 Kbp/sec

First pass search(es) ended: Sun May 18 13:53:39 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     335
Cove-confirmed tRNAs:     62
Bases scanned by covels:  43994
% seq scanned by covels:  0.5 %
Script CPU time:          0.71 s
Cove CPU time:            47.63 s
Scan speed:               923.7 bp/sec

Cove analysis of tRNAs ended: Sun May 18 13:54:46 PDT 2008

Summary
--------
Overall scan speed: 158841.3 bp/sec

tRNAs decoding Standard 20 AA:              61
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      1
                                            -------
Total tRNAs:                                62

tRNAs with introns:     	0

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Isotype / Anticodon Counts:

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