tRNAscan-SE Analysis of the Escherichia coli O157H7 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 17:32:25 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:  2
Bases read:             5594477 (x2 for both strands)
Bases in tRNAs:         32715
tRNAs predicted:        296
Av. tRNA length:        110
Script CPU time:        0.97 s
Scan CPU time:          3.91 s
Scan speed:             2861.6 Kbp/sec

First pass search(es) ended: Sun Jul 27 17:32:31 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     296
Cove-confirmed tRNAs:     103
Bases scanned by covels:  36859
% seq scanned by covels:  0.3 %
Script CPU time:          0.79 s
Cove CPU time:            41.00 s
Scan speed:               899.0 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 17:33:15 PDT 2008

Summary
--------
Overall scan speed: 239746.2 bp/sec

tRNAs decoding Standard 20 AA:              101
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      1
                                            -------
Total tRNAs:                                103

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   : 4	  AGG:         GGG: 1       CGG: 1       TGG: 2     
Thr   : 4	  AGT:         GGT: 2       CGT: 1       TGT: 1     
Val   : 7	  AAC:         GAC: 2       CAC:         TAC: 5     
Ser   : 5	  AGA:         GGA: 2       CGA: 1       TGA: 1       ACT:         GCT: 1     
Arg   : 17	  ACG: 4       GCG:         CCG: 1       TCG: 3       CCT: 1       TCT: 8     
Leu   : 7	  AAG:         GAG: 1       CAG: 3       TAG: 1       CAA: 1       TAA: 1     
Phe   : 2	  AAA:         GAA: 2                               
Asn   : 4	  ATT:         GTT: 4                               
Lys   : 5	                            CTT:         TTT: 5     
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   : 15	                            CAT: 15                 
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.