tRNAscan-SE Analysis of the Bacillus licheniformis ATCC 14580 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 13:55:16 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:             4222334 (x2 for both strands)
Bases in tRNAs:         20765
tRNAs predicted:        194
Av. tRNA length:        107
Script CPU time:        0.71 s
Scan CPU time:          3.02 s
Scan speed:             2796.2 Kbp/sec

First pass search(es) ended: Sun Jul 27 13:55:20 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     194
Cove-confirmed tRNAs:     72
Bases scanned by covels:  23481
% seq scanned by covels:  0.3 %
Script CPU time:          0.47 s
Cove CPU time:            25.57 s
Scan speed:               918.3 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 13:55:48 PDT 2008

Summary
--------
Overall scan speed: 283663.7 bp/sec

tRNAs decoding Standard 20 AA:              71
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   1
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                72

tRNAs with introns:     	0

|

Isotype / Anticodon Counts:

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