GtRNAdb

tRNAscan-SE Analysis of Clostridium botulinum A ATCC 19397

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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 16:08:10 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:             3863450 (x2 for both strands)
Bases in tRNAs:         10771
tRNAs predicted:        120
Av. tRNA length:        89
Script CPU time:        0.63 s
Scan CPU time:          2.10 s
Scan speed:             3679.5 Kbp/sec

First pass search(es) ended: Sun Jul 27 16:08:13 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     120
Cove-confirmed tRNAs:     81
Bases scanned by covels:  12451
% seq scanned by covels:  0.2 %
Script CPU time:          0.30 s
Cove CPU time:            13.91 s
Scan speed:               895.1 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 16:08:42 PDT 2008

Summary
--------
Overall scan speed: 456133.4 bp/sec

tRNAs decoding Standard 20 AA:              80
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                81

tRNAs with introns:     	0

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Isotype / Anticodon Counts:

Ala   : 3	  AGC:         GGC:         CGC:         TGC: 3     
Gly   : 8	  ACC:         GCC: 3       CCC: 1       TCC: 4     
Pro   : 3	  AGG:         GGG:         CGG:         TGG: 3     
Thr   : 5	  AGT:         GGT: 1       CGT:         TGT: 4     
Val   : 5	  AAC:         GAC:         CAC:         TAC: 5     
Ser   : 5	  AGA:         GGA: 1       CGA:         TGA: 2       ACT:         GCT: 2     
Arg   : 6	  ACG: 1       GCG:         CCG:         TCG: 1       CCT: 1       TCT: 3     
Leu   : 6	  AAG:         GAG: 1       CAG:         TAG: 2       CAA: 1       TAA: 2     
Phe   : 2	  AAA:         GAA: 2                               
Asn   : 3	  ATT:         GTT: 3                               
Lys   : 6	                            CTT: 2       TTT: 4     
Asp   : 4	  ATC:         GTC: 4                               
Glu   : 4	                            CTC: 1       TTC: 3     
His   : 2	  ATG:         GTG: 2                               
Gln   : 3	                            CTG: 1       TTG: 2     
Ile   : 2	  AAT:         GAT: 2                    TAT:       
Met   : 8	                            CAT: 8                  
Tyr   : 2	  ATA:         GTA: 2                               
Supres: 0	                            CTA:         TTA:       
Cys   : 2	  ACA:         GCA: 2                               
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.