tRNAscan-SE Analysis of the Escherichia coli K12 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 17:26:10 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:             4639675 (x2 for both strands)
Bases in tRNAs:         28950
tRNAs predicted:        259
Av. tRNA length:        111
Script CPU time:        0.81 s
Scan CPU time:          3.29 s
Scan speed:             2820.5 Kbp/sec

First pass search(es) ended: Sun Jul 27 17:26:14 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     259
Cove-confirmed tRNAs:     88
Bases scanned by covels:  32576
% seq scanned by covels:  0.4 %
Script CPU time:          0.69 s
Cove CPU time:            36.75 s
Scan speed:               886.4 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 17:26:55 PDT 2008

Summary
--------
Overall scan speed: 223383.5 bp/sec

tRNAs decoding Standard 20 AA:              86
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      1
                                            -------
Total tRNAs:                                88

tRNAs with introns:     	0

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Isotype / Anticodon Counts:

Ala   : 5	  AGC:         GGC: 2       CGC:         TGC: 3     
Gly   : 6	  ACC:         GCC: 4       CCC: 1       TCC: 1     
Pro   : 3	  AGG:         GGG: 1       CGG: 1       TGG: 1     
Thr   : 5	  AGT:         GGT: 2       CGT: 2       TGT: 1     
Val   : 7	  AAC:         GAC: 2       CAC:         TAC: 5     
Ser   : 5	  AGA:         GGA: 2       CGA: 1       TGA: 1       ACT:         GCT: 1     
Arg   : 7	  ACG: 4       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   : 6	                            CTT:         TTT: 6     
Asp   : 3	  ATC:         GTC: 3                               
Glu   : 4	                            CTC:         TTC: 4     
His   : 1	  ATG:         GTG: 1                               
Gln   : 4	                            CTG: 2       TTG: 2     
Ile   : 3	  AAT:         GAT: 3                    TAT:       
Met   : 8	                            CAT: 8                  
Tyr   : 3	  ATA:         GTA: 3                               
Supres: 0	                            CTA:         TTA:       
Cys   : 1	  ACA:         GCA: 1                               
Trp   : 1	                            CCA: 1                  
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.