tRNA/fragment and flanking sequence:

tRNA
2983208 agccgtgcac acgggttcga ttcccgtctc cacctccagg ttcaaccccc aGCGCGATTA
2983268 GCTCAGCGGG AGAGCGCTTC CCTGACACGG AAGAGGTCAC TGGTTCAATC CCAGTATCGC
2983328 GCACCAgtgt tcgagcaggt caggcctggt ttttaccggg ccttcgccgt ttccgcg

tDNA Fragment
2992879 tcagaggctt tctgtacagg tcagacagta tcccaccggc ccactagtga aACTGGTTCA
2992939 ATCCCAGTAT CGCGCACCAc gattgacctg cggtttcatc cacaaaatct gggctgcgtg
2992999 aactaaatgt

tRNA gene (GREEN CAPS): 2983259..2983333
Displaced gene fragment (GREEN, mismatches lowercase): 2992930..2992957
Match (underlined) extends 3-prime beyond tDNA: 0 bp
Index point: nt 65
Mismatches: 0
Damage within repeat (Red): none
Junction: T-stem junction site
Supplemental Island Information
Island Length: 9624 bp
Mononucleotide (difference to replicon): 1.31
Dinucleotide bias (between genome and island): 0.05
Minimum distance between integrase and endpoint: 2.35
Density of hypothetical proteins (fold over replicon): 0.26
Housekeeping index: -17.42

Potential integrases in NC_009565
11805451181012
11808561181143
25926312593185
29916502992825Integrase in the opposite orientation as tDNA
42118064212090

Potential fragments for tRNA-Val(GAC)
743697743685
13713651371348
17025371702519
26572742657262
29929572992930


Genes: 13
LeftRightStrandAnnotation
29834402983871+ID=148823838; acc=YP_001288592.1; Name=hypothetical protein TBFG_12663;
29838682984866+ID=148823839; acc=YP_001288593.1; Name=integrase;
29848802985344+ID=148823840; acc=YP_001288594.1; Name=hypothetical protein TBFG_12665;
29857542987193-ID=148823841; acc=YP_001288595.1; Name=phiRv2 prophage protein;
29872012987734-ID=148823842; acc=YP_001288596.1; Name=phiRv2 prophage protease;
29878872988378-ID=148823843; acc=YP_001288597.1; Name=phiRv2 prophage protein;
29885452988868-ID=148823844; acc=YP_001288598.1; Name=phiRv2 prophage protein;
29889482989193-ID=148823845; acc=YP_001288599.1; Name=phiRv2 prophage protein;
29891902990617-ID=148823846; acc=YP_001288600.1; Name=phiRv2 prophage protein;
29906192991011-ID=148823847; acc=YP_001288601.1; Name=phiRv2 prophage protein;
29910082991268-ID=148823848; acc=YP_001288602.1; Name=phiRv2 prophage protein;
29912852991647-ID=148823849; acc=YP_001288603.1; Name=phiRv2 prophage protein;
29916502992777-ID=148823850; acc=YP_001288604.1; Name=phiRv2 prophage integrase;

Sequence:     

>Mycobacterium tuberculosis F11|2983224-2993048|100bp flanks
atcaaatcccagcggtggagtggccgagtggtgaggcaacggcctgcaaagccgtgcacacgggttcgattcccgtctccacctccaggttcaacccccaGCGCGATTAGCTCAGCGGGAGAGCGCTTCCCTGACACGGAAGAGGTCACTGGTTCAATCCCAGTATCGCGCACCAGTGTTCGAGCAGGTCAGGCCTGGTTTTTACCGGGCCTTCGCCGTTTCCGCGCAATAAACGCGCAATAGTGCCGCCGCTGGGTGCGCCCCACGGAGGAGTTTGCTAAATGACCACCACGCCCCGACAACCCCTGTTCTGCGCCCACGCCGACACCAACGGCGACCCGGGCCGCTGCGCCTGCGGCCAGCAGCTCGCCGACGTCGGCCCGGCCACCCCGCCACCGCCCTGGTGCGAACCGGGCACCGAACCCATCTGGGAGCAGCTCACCGAACGATACGGCGGCGTCACAATCTGCCAGTGGACACGATATTTTCCGGCCGGCGACCCGGTGGCTGCCGACGTGTGGATCGCCGCCGACGATCGTGTCGTTGACGGCCGGGTGCTGCGCACCCAACCGGCGATTCACTACACGGAACCGCCCGTGTTGGGGATCGGCCCGGCGGCGGCCCGCCGGCTGGCCGCTGAGCTGCTCAACGCCGCCGACACCCTCGACGACGGCCGCCGGCAGCTAGACGACCTCGGCGAACACCGGCGGTGAACACCGCGACCCGGGTCCGGCTGGCCCGCAAACGCGCCGACCGGCTCAATCTGAAACTAATCAAGAACGGCCACCACTTCAGGTTGCGTGACGCCGACGAGATCACGCTGGCGGTCGGGCACCTAGGGGTGGTGGAAGCCTTCCTGGCGGCGGCCAAGTCGCAAAACAAGCCGCCCGGTCCGCCGCCGAGCCTCCACGCCCCGCCATCCTGGCGGCGCGACATCGACGACTACCTGCTCAACCTGAACGCCGCCGGTCAACGCCCAGCGACGATCCGGCTACGCAAGACGGTGCTGTGCGCAGCCGCCCACGGCCTCGGCCGCCCACCCGCCGACGTCACCGCCGAACACCTCCTGGACTGGCTAGGCAAACAGCAGCACCTCTCCCCAGAGGGCCGCAAAACCTATCGCAGCACGTTGCGGGGCTTCTTCGTGTGGGCCTACGAAATGGACCGGGTGCGCGACTATGTCGCAGACTCCCTGCCTAAGGTGCGCTGCCCGAAACAGCCGCCCCGCCCGGCCGGCGACGACGTCTGGCAAGCGGCGCTGGCCAAGGCCGACCGTCGAATCGAGCTGATGATCCGCCTAGCCGGTGAGGCCGGGCTGCGACGCGCCGAAGCCGCCCAGGCGCACACCGGCGACTTGATGGACGGCGGGCTTCTCCTCGTTCACGGCAAAGGTGGTAAACGCCGTATTGTGCCGATCAGCGACTACTTGGCCGCGCTCATCCGCGACACCCCGCACGGCTACCTGTTCCCCAACGGCACCGGCGGCCACCTCACCGCCGAACACGTGGGAAAACTCGTCTCCCGGGCATTACCCGGTGACGCGACCATGCACACCCTGCGGCACCGATACGCCACCCGCGCCTACCGCGGCTCCCACAACTTGCGAGCTGTACAACAACTTCTCGGTCACGCCTCGATCGTGACAACAGAACGCTACACAGCGCTGTGCGACGACGAGGTGCGCGCCGCAGCAGCAGCCGCATGGTGAGTCGCCCTGGCGTTTGCTGCAGCCGATCGGCGTCACCCCCGACAGGCGGCTCGTATTCGGCCAGCGGCGGCTCGAGGCTGCACGGCTGCTCGGATGGGAGCGCATCCCGGTGCACGTGTGCCACACGATCGCCGACGTGGTCGACCGGGCCAAAGCCGAACGCTCCGAAAACACGCTTCGCAAGGATTTCACCCCCTCGGAGCTGCTCGCCGCTGGTCGCCGGATCGCCGAGCTGGAACGGCCGAAAGCCAAACAGCGGCAACGCGAAGGCGGCGACCATGGCCGCCAGGCTCGATATTCTGGCTTAGGCTCCATGGAGCCTAAGCCAGAATCAGAGCGCGATGCCCACAAAGCCGACACTGCCATCAGCGAAGCCCTCGGCATCTCCCGCGGCCACTACCAGCGGCTCAAACGAATCGACAACGCAACCCGCAGCGAAGCTGGCTACCGGGATGGTTTAAACGGTTGGAGCGGCTGACCGCCGGTGCCCGGGATGGGCCCCGGCGGCAACTTGTCCAACGGGCGACGCTCACGTCCACGCTTGCGCAGCTCATCTTCGGCGGCCTTGCGTGCCTGCTCAGCCTGGCGGCGCCAAGCCTCATAGCGACGCCGAATCTCCCTCTCAATCGCGCGCTGCACACCCATCCGGAACTGATCCTGGACACGCTGCTGCTGCCGAACCCAACGCTCAAGCTCACGCCGGTAGTCGTTGACTGATCTCGCCACCCAAAATCACCCCTCTTGACCCTCTTGGTTCTCTTTTTGGCGGCGTGGGCGACCCGGCACCCCTAAGTCTCCGGGCCGTGCGGGCCGCTGGGAGCCGAAAGGTTGCTAAAGTTCTCCCTTTTTGCCCGCACGACCCGAAAAGGGCCGCCCACGCCTGGCACCTACGCGGTGGTCTGCACCTTCAGCACGCGGAACGCATTGTCCACCAGCACATCAGAACCGACTCGGAACCAGCAGAAGAATCCGCGCTGTCCGGTCGGTCGGCGGTTGCCGCCGAACACGTGCGGCACCAGCTCCACCGTCGACCCGACCCGGTCGGTGATGATGAACTGCTTCCAGTCGCCAAGCACCAGCGGGTAATTGGTGGCGGTCACCGCCGCGTCCACGGTGTCCATGTTCGACACCTCCCAGATGTGTTTCCCGGCCAGCATCGGCGGGCTGGCGTGCAGCGATGGGAATTTCAGCGCCCCATTCGCGGTTTCCGCCTGGCGCAGCACGTTGATGGTGGACAAGTTCGCCGCGAACGCGCTGTTGGATTGAAAGCGCGGCGGCAACGCCGACTGCAGCGCGTAAACGTCGGCGGCTACAACGGCTTCCGTCCCCGCGCCGGTGACGGTGTAGTCCGCGGTGCCGGTCAGTGCGGAGACGAATCCGGTGGGCTCGCCGTTGCCGGAGCCGCTGACGAACGCCGCCGCCTGCAGCTGCTCAACCGAATCCGCTAGGACGCGGCCCACCTCTGCGACGAATCCGGCGGCGTCACCCTCAATCTCGAGACTGAACGGAATCCAGCAGGAGCCACGGTAGCTCGGCACCGCCGGCTGGGCCAGCGTTGGCGAATCGTCGGACACCTCCTGGGCTTCGGAGTACCAATGAGCCTCGGCGCCTTCGGAGGTCACGCCCCGCCAAACCTCGGAGGTCGTTTGCACCACCCTCGCCACCTGCCGGATCGGATTCGTTGAACCATCACCCGACAGCAGAATCGCCGGATCCAGCGCCGCCGGGATCAAAAACCCGCCGGCGGTGTCCACCAAGCCCATTGCTCGCTGCTCGGCGGCCACCGCGGCCGCCTCACGCCACGCGGCCGCTTCCCGGTCGGTCCAGGTCGTGTGCCCCGCAACAGGGTTCGAAACCCTCTTGACGAACGCCCCCAGGTAGTCGCGGTTGCCGGTGGCCGCCAGCCAGCGCTGCGCCCACGACGTCGACTGCGGCGGCCCGGTGCGGCACAAGGTTTCCGCGGCTTCCGCCGCCCGCGACGACATCAGGCCATCGCGCACACAAACGTCCAGTGTGCGAAACGCGGTGTCGCGCAACGAGTTGCCCGGCGGCGCGTCGCCGTCGTCGCCGCCGGTGGGAGCACCGGGCACCACCCTCAGCTCACCGGCCCGGCAGCGGCGCAGCGCCTCCTCGGCTTCGCGGCCGCGGCGGCGCTGCTCCGCCCGCAGTTCCTCGGCGTGGCGTGTCAGCGCCTGAAAACGTTGCGCCACATCACCGGTCAGGTCGCCCTCGACGGAGTCGAGGAGCTGTTTTGCCGCGGAACGGGTTTCGTCGAGGCTGAGCTGTTTGATGTCGCCATCGTCAGCGAAATGTTGTTCATTAGTCATGAGAGAGTTACCAATCCATCAGGGCTAACCTGGCTTCGGCTAGCGAACGGGAAACGACTGCAAGCGATTCCGCGCGCACACCGGCGATCTGCGCGCCCAGATAGGCCGGAACGCCGGTCAAGGAGACCTCCAACAGCGCCGCCTCGACCCGCACGATCACATCCCCTTCCCGGCGGTCCCGGATCGGCCGGAAACCCACCGAAAACGCGTCCACCACACCAGCTTTCACATTCGCCAGGGCCTCGTCGCCGTCCGGGGTGTTCGCAAGCTCGAACGCCCCGAACAAGCCGTGAGGCTCCTCACGCAGCTCGACGGCCCGGCCAACCGGGTAGCGGGTTCGAGCGTCGTGGGAGACCAGCAGCTTCACCTTGTGGCCGCGCTCAGCGATGGAGCGCCGAAAAGCGCCAGGAGCGAACATTTCCCGGAACTCGCCGTCGAGGTCGCGGACGGTGGTCACCTCGCCATAAGGCACGATGACGCCGTACACGGTGCGGCCCTCACCAGGCCGCAGCTCGGCCGTGCGGAAAAGGATGCTACTCAAAATTCGGCCACCGCCTAGCAGACGCAAGAAACGCGCGGAATCGCTTGTGGCGCATGGCGGCCGCTATCCGGGTTCCAGCCGCCCCGCGGCGACTGCCCGGCGTCGGCGGATGCCGAGATGCCAAACTCGATTGTATCACACACAAAAGGTCATCACCGGTCTGGGGCGAACGGGTTGAACTCGTCGTCGTCGGGGTCCCCCGCCGCCGCCAGCACAGCAGCCAAATTCGCCTCAGCGCTTGGCGTGCACCCCAATTCGCGCGCGAGCACCAAAACGTCCCTCGTCGCGGCCCGGGCCGCGGCCACGGCAGGATGCACCGTCACCCGTCGGCTGCGGGCGTTCGTCGCGATGAAACCCTGTTCACGGTAGGCTGTTACAGCCTGCATGAGCTGATCCCAGGCGACGCAGAAGGAGGTCAGCACCCCAAGGTCGGACTCCTTCAGCAGGTTTAATGCCGCAAGCTCGGGAACGACGCGCCCCCACATGTCTTTAGCGCCTGGCGGCAACCAATCCGGGCATTCCGGCGCAACACGCTCGAACGCCGCCGGTGGTGTAACCCGCCGGCCGCCAGAATCACGGCCCGGCGAGCGGCCGCCGAGGAGTTTCAACTGCGCCGGCGCCGGCGCGGGACCACGCCTACCCATTTTCAACACCACCCTCCTCTTTCCGGGTTTCGGGTCGCGAATGCCATGATGCCAAAAAACGCCCCATAAAACTTGAGCGCGCACACGCTCTCCCACCGTGGCGGTGTCCGGTCGGGCGGTTTCTGGCGATGGCAACCCACCCCCCCTACCTGCGGGTTTCGGGTTTTCACTGTTTGCTGTCGGGTTCGTCGGGGAAGTGATACGGATGCCAGCCGAGCTTCATCCCCGCCTCAAGCCGGCGCTGCTCATCGTCGAGATGCATCGACAACAGCGCCAGTTCGGCTGTGTCGTCGTCGATTTCGTGTGATGTCGCCACCATCTCGGCGTACGCTCGGCGGATAGCCTCGAGGTCGCGCTGCCGTTGGGCGCGGCGCTGCTCGGCGGACGGAACGTCGGCCGGCCAACCATGTTGCCGCCCAACGCGATTCCGACGCGGGGCGTTGAGCCCTGCGGCGATGGCTGGCTGGCGTTTAGTGCGCTTGTGGGTCAATGATGGGCTCCTTTCTCCCTGGAAAATGATGTGATCGACGGTGTTCCGGGTGTCCGACAGTCGGGTTCTCTCGGCGGGCTCACGGCGGATCACCCCGGTCGACGGCCGCCGCCGCGGCGGCCGTCGCGGCGAACAAAACGGCCGCGACGCCGTGCGACTCCGCCACAGCGCGGACCAACGCTCGCGCAAGCTCGACGGCCGCGGTCCGCCATGCGCCCGCGGCGTCGCCGGCCAGCGCGGCGGCCGAAGCCTCGACTGGCGGGCCGCCGACAAGCTCGTCCGCGGCGGCCAGCAACGTCCGAGCAGCCAACGCGTGGCCGCTCATCGGGCGCCGTCCCGAGCGCTAGCCGCCGCTCGACCTCGGCAGGGCCGGCATTTGCCGGCGGCCTTGGCCTCAGTACTGAGGAGCTTGTTGGGGCATCCCGGCCCGGAGCACAGCGGCGCGTCGCCGTTGGGGTGCCCGTTGGGCGCCGGCGGCTCGTACGGCAAGTCGCCCGCCTCCGGGAGATCGGTTGCATCGGTTGCGCCGGTTGCATCACCGGGATCGCCAACCGGCGGTGAAACCGCGGAAACCGCGGAAACCGATAAATCTCGTTCCTCGGGGGTTTCGTCGTCGGCAGAGAGATACCGGGACCACGCATCCTCGAACTGGGTCCGCGAATACCCTTTGTAGGGTGGTTCGCCACCACTGTGCTGGAACTTCGGCCCGATGCCGTATCTGCCGAGCCGGGTCGCGAGGCCGCGCGCGTCGAGCGGGTCGCCGCGGCGGATGGAGCCCCACGGTCCCTCCTCCATCCGGTTCAGTCCGGTCAGGATGTCGCTGGTGCGCATCCGGTCCCGGTCGCTGAAGACTCGACGGATATCCCGCAGCAGCAGCACGCCTATGCTGGGCTTGGCTCCTCGATTTGCGGTTGCATCCGTTTCTGCGGTTGCACGGGCGGTTTTGGGCCAGTGCCCGCCCGCGGTGTCAGCAACCGCAACCAGGGACTCCCAGACGTCGGCGCGCCGGTCGGTCACCCCGTCCGGCATCGCCGGCCAACCGCTTTCCAGCGGGTTAATGGCGGCCGCCCAGTTCGCCAACCGGTCGTGCAGCTTCTCGGCCTCGGGGCCGTTGACGCGGGGGCGCCACGGCTCCACGGGTTCGGTTGGTGCCCTCCTGCGCATCCTCACCACGATCGACCGAGACATGATGGTGTCGGGCAGGTCGTCGAGGCCGGCCAAGGCGACCGCACAGTACGCTGGCAGTTCCTCGGTCTCAACGATCTTGCCGCGGATGACGCAGCGGCCCGCGACGGCTCCCTTGCGGTGGCCGGCGTTGATCACGCCGCGAATTTCCTCGTGTTCTTTAGCTTTCGGGCCAAACAGGGTGTCACACTCGTCGTACAGGACGGTCGGCCGCCCGACCGGATCGGCCACCCGACGGAACAGGTAGGCCGGTGTGCAGTTGATGGCATGCACCGGCCGGGGCACTAGCGGTTCCGTGACTTCGAGTGCGCGGCTCTTGCCAGAGCCGGGTTCCGGTGACAAAAAAGCGATTCGGGGCGTTGAGTCCCACGCCTCCATAAACCAGCAATGCGCAATCCAGAGGGTGTGCGCGATCAGTTCATGGTCGCTTGGATAGACTACGAACCGCCGCAAGAATGCCCTAATGTCGTCGAGCAATTCGGCGCCGACCGGCGGCATCGGCTGGCCGTCCTCGTCACACCAGATCGGGTCGGGATAGTCACGGCCGTAGGGGATGTCAGCCATCTCAGACCACCACCCGCCGAATGTAGGCGTCACGCCGACGCTGGATCTCCCGAGAGACCGCCGGCCAGTCGGCGGCGGCGGATACGTCACGTGATGCCTCGGCCGACGCGGCCTGGCACGTCTCCACCCGGAGTGCCCAATGCCGAGCAGCGTCGCAGATCGCGGCCCATTTGACCGGGTCGGTGTCGTCGAGGTCGCACCACGCCGGGGTGCCGGCCATCGGCCATTCCACGGCGGCGGCCAGGGTCGGTGCGACATACTCGTGCACCGACCACCACGACACGGCGCGGGACGCGGTAGGATCGGTGCTAGACGGTGTGGCGACTGTCGCGGGTGCCCGGTCCTCTGTGGCCGGGCATCGTCGCGTCGGCGGCGACCCGCCGACGGCGGTCATGCGGCACCACCGAACGGGTGCATGGCGCCGTCGACCTCATCGCGGCGCAGACGGACGAGGCGGGTGCCGGAGCGGTATCCGCGTAGGCGGCCGTCGGCGATCATCTGGCGGACCGTGCGGTCGGTGACCGCTAGATATTCGGCGGCCTCACTGATCGTGATGTACCGCCGTGACAACGGGGGAGCGTCTGCCATGCCGGGCCTTTCGGTCTCGTGAGAGACCGTCCACCCGAGACTCGGCGACGGGAACGCGCACATGCGCGCACCGGAAAATTTACCCGCCTAGCTGGCTCAAGCGCAAGCATAATGCGCTGAACGGAATTACGTGTCGCGCCTCTGCTATTGATGGATCGTCAGCGTCGGGGATGGTCGACGTTCTCAGCTCGTGAAGCTTCGCCCCGAAACCGTCGAGGATCGCCGCGGCGGTCATCTCGGATATCGGCGCATACTTTCGGCATGCCCGGCATTCGAGTTTCCACTCGATATGGCGGCCCCACTGTGTTTCGGTGAAGCGGGTGTTCGACCGCATCTGTATGTGCCCGCCGGCGGGTCGTTCGTCGTCGATCCAGGCGATGATGAGCGCTCCCGGTTCGTCGTCGCAGTTGCACATAACTACGTACTTAACCGCATCGGCCATCATCACATCTCCTGGTTCTCGGCCAGTTTGCTTAACAGTGCGGCGATTTCGCGGTCCCGGCCCTTGGCGGCGTGCTGGTAGCGGAGTGCGGCGCCGGCTGTGCTGTGTCCTAGCCGCTGCATCAGTTCGGCCAGTGTGGCGCCGGTGGATGCAGCCAACACGGCGCCGGAGTGTCGAAGGTCGTGCACCCGTAAGTCTGGTCGGCCGGCGGCTTTTCGGGCCTTGTAGAACATGCGGTACAGCGCCGAGGGTGCTAGGTGACGGTTGGGGTCGTTGACCGATGGGAACAGCAGGGACTCCCGGCCGGGGTTGACGTGTTTGTGAAGGTGGTCTTCGATGGCGGGTATCAGATGTGGCGGGATACTTATGTCGCGCACTCCCGCATCGCTTTTCGGTGTCGTCACCTTGAAGCCTTCGCCCACCCGAACGACAGCCCGCCGCACCCGCGCAACCTCGCCGTGCAGGTCGATGTCTTTGCGGCGTAATTCGGTCAGCTCGCCGTAGCGCATGGCCAGCCATGCCGCCATCAGCACGAACGCCTGGTAGGGGTCGGGCATGGCTTTGGTGATGGTTTCCAGCTCGTCGAGGGTGGCGGGCCTGATCTTGTGGACGCGGCGGGCGGTGGACGCGCCTGAGATGCGGCAGGGGTTGGAGTCGATCAGGTCGTCGGCCAAGGCGGTCTGCATGATTGCGCGCAGCAAGCTGTAGGAGTGTGCCCGCATGGTCGGTGTGCCCACGGCGGTGGTGGCGTACCAGCGGCGCACGGCGGCCGGGGTGATGTCGCGTAGGTCGGTGTCAGCGAAGGTGGCCAGGATGTGGTTGTCCAGCAGTTTGCGATAGTGGGCGCGGGTGCGGTCCTTGATTCCACGCTGCTTCAGCCATCCTTCGGCGTACTCACCGAATGGGGCTCCGGGGCGGTCTTCCTGACCCGATGCCGGGGACCATAGTTGTCGGTCGATTTCGCGGCGGCGGTCGGTGAGCCATGCTTCGGCGTCGATCTTGGCGTTGAAGGTTTTGGGGGCGATGTACACGCGGCCGTCGGGGCCGGTGTAGCTGGCTTGCCAGCGGCCGGAGTTGAACTGTCGGATGCGACCGAATTTGCGTCTCTGACGCTTGCCGGTTTGCGTCACTGTCGTCCCCTGTCCCGCGCAATAAACGCGCAATAAGAGACTACATCAGATGCCGCTTGCTTCCGCACGCTTCCGGGGGTACTGTTGTCTATGTCGCCTGGTCAGAGGCTTTCTGTACAGGTCAGACAGTATCCCACCGGCCCACTAGTGAAACTGGTTCAATCCCAGTATCGCGCACCAcgattgacctgcggtttcatccacaaaatctgggctgcgtgaactaaatgtgaactgactcggtgcaaccaccgaaaggttcctctgttccgtgcccacg