tRNAscan-SE Analysis of the Bifidobacterium longum Genome

[Main Overview] [Secondary Structures]	[Analysis Notes]
[tRNAs by Isotype] [tRNAs by Locus]	[Run Options/Stats]
[tRNA Alignments][FASTA Seqs]	[Genome DB] [Genome Seq]

[BLAST] [Download] [Bugs/Requests] [Citation] [Legend]

[GtRNAdb Home] [tRNAscan-SE Server] [Lowe Lab] [Other Links]

tRNAscan-SE Run Options & Statistics


tRNAscan-SE v.1.23 (April 2002) scan results (on host lowedev.cse.ucsc.edu)
Started: Sun Jul 27 14:17:59 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:             2260266 (x2 for both strands)
Bases in tRNAs:         22127
tRNAs predicted:        186
Av. tRNA length:        118
Script CPU time:        0.38 s
Scan CPU time:          1.82 s
Scan speed:             2483.8 Kbp/sec

First pass search(es) ended: Sun Jul 27 14:18:01 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     186
Cove-confirmed tRNAs:     57
Bases scanned by covels:  24731
% seq scanned by covels:  0.5 %
Script CPU time:          0.44 s
Cove CPU time:            28.60 s
Scan speed:               864.7 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 14:18:32 PDT 2008

Summary
--------
Overall scan speed: 144703.3 bp/sec

tRNAs decoding Standard 20 AA:              56
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      1
                                            -------
Total tRNAs:                                57

tRNAs with introns:     	0

|

Isotype / Anticodon Counts:

Ala   : 4	  AGC:         GGC: 2       CGC: 1       TGC: 1     
Gly   : 5	  ACC:         GCC: 3       CCC: 1       TCC: 1     
Pro   : 3	  AGG:         GGG: 1       CGG: 1       TGG: 1     
Thr   : 4	  AGT:         GGT: 1       CGT: 2       TGT: 1     
Val   : 5	  AAC:         GAC: 2       CAC: 2       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   : 5	  AAG:         GAG: 1       CAG: 1       TAG: 1       CAA: 1       TAA: 1     
Phe   : 1	  AAA:         GAA: 1                               
Asn   : 3	  ATT:         GTT: 3                               
Lys   : 2	                            CTT: 1       TTT: 1     
Asp   : 2	  ATC:         GTC: 2                               
Glu   : 2	                            CTC: 1       TTC: 1     
His   : 1	  ATG:         GTG: 1                               
Gln   : 2	                            CTG: 1       TTG: 1     
Ile   : 1	  AAT:         GAT: 1                    TAT:       
Met   : 3	                            CAT: 3                  
Tyr   : 1	  ATA:         GTA: 1                               
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.