tRNAscan-SE Analysis of the Bacteroides fragilis YCH46 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 14:05:21 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:         2
Seqs w/at least 1 hit:  2
Bases read:             5310990 (x2 for both strands)
Bases in tRNAs:         26679
tRNAs predicted:        243
Av. tRNA length:        109
Script CPU time:        0.91 s
Scan CPU time:          3.65 s
Scan speed:             2910.1 Kbp/sec

First pass search(es) ended: Sun Jul 27 14:05:26 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     243
Cove-confirmed tRNAs:     74
Bases scanned by covels:  30081
% seq scanned by covels:  0.3 %
Script CPU time:          0.59 s
Cove CPU time:            32.50 s
Scan speed:               925.6 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 14:06:01 PDT 2008

Summary
--------
Overall scan speed: 282124.3 bp/sec

tRNAs decoding Standard 20 AA:              72
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      2
                                            -------
Total tRNAs:                                74

tRNAs with introns:     	0

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Isotype / Anticodon Counts:

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