Gene/fragment and flanking sequence:

Gene: tmRNA
3980874 acgagttgtt agactgaagt gctcgctgac ttccgtcggc gggtcctact cGGGGCTGAT
3980814 CGGTTTCGAC TTCGTGCGTC GAGATAGGGG AAGCGTGTCG GTGCAGGCTG GAGACCACCG
3980754 TAAGCGTCGC AGCAACCAAT TAAGCGCCGA TTCCAATCAG CGCGACTACG CCCTCGCTGC
3980694 CTAAGTAGCG CCGGCTAGTC TGTCGGCCCG GGTTATGCTC CCAGACCCGG ATGCCGGCAT
3980634 CATCTATGGG AGCTCACCGT CCTCGCCGGT CGCGGGTGAG GTCGGAACAT CAAACAGCGA
3980574 CTGGGATCGT CATCTCGGCT TGTTCGCGTG ACCGGGAGAT CCAAGTAGAG ACATAGCGGA
3980514 CTGCACACGG AGAAGCCCTA ACAACACGAC GGAGGACCCG GGTTCAATTC CCGGCAGCTC
3980454 CACAAaggcg ccccacctgt tatcgcaggt ggggcgcctt tttgcgtgca gcggtc

tmRNA Fragment
3976705 gcgactagag gccacaggac tgctgctcga catctacgag gttctagcac aGGTTCAATT
3976645 CCCGaCAGCT CCACgagaag gcgccccacc tgttcaggtg gggcgctttc gtcgtctcta
3976585 cgggc

Gene (GREEN CAPS): 3980450..3980823
Displaced gene fragment (GREEN, mismatches lowercase): 3976632..3976654
Match (underlined) extends 3-prime beyond tmRNA: 0 bp
Index point: nt 364
Mismatches: 13
Damage within repeat (Red): none
Supplemental Island Information
Island Length: 3798 bp
Mononucleotide (difference to replicon): 1.35
Dinucleotide bias (between genome and island): 0.15
Minimum distance between integrase and endpoint: 2.07
Density of hypothetical proteins (fold over replicon): 0.23
Housekeeping index: -11.48

Potential integrases in NC_018581
11546231155798
15178201519148
24901292491307
33295463329914
33298803330785
38029873803340
39796503980435Integrase in the opposite orientation as tmRNA

Potential fragments for tmRNA
39766323976654


Genes: 3
LeftRightStrandAnnotation
39771393977984+ID=404216084; acc=YP_006670279.1; Name=hypothetical protein KTR9_3488;
39786483979580-ID=404216085; acc=YP_006670280.1; Name=hypothetical protein KTR9_3489;
39798243980435+ID=404216086; acc=YP_006670281.1; Name=Integrase;

Sequence:     

>Gordonia sp. KTR9|3980552-3976554|100bp flanks
ggtgaccgccgcggacgcgcgccggggaaacgggaatgaactctgcgcaacgagttgttagactgaagtgctcgctgacttccgtcggcgggtcctactcGGGGCTGATCGGTTTCGACTTCGTGCGTCGAGATAGGGGAAGCGTGTCGGTGCAGGCTGGAGACCACCGTAAGCGTCGCAGCAACCAATTAAGCGCCGATTCCAATCAGCGCGACTACGCCCTCGCTGCCTAAGTAGCGCCGGCTAGTCTGTCGGCCCGGGTTATGCTCCCAGACCCGGATGCCGGCATCATCTATGGGAGCTCACCGTCCTCGCCGGTCGCGGGTGAGGTCGGAACATCAAACAGCGACTGGGATCGTCATCTCGGCTTGTTCGCGTGACCGGGAGATCCAAGTAGAGACATAGCGGACTGCACACGGAGAAGCCCTAACAACACGACGGAGGACCCGGGTTCAATTCCCGGCAGCTCCACAAAGGCGCCCCACCTGTTATCGCAGGTGGGGCGCCTTTTTGCGTGCAGCGGTCGGTGGCAGAAATTGCGTTGGACACATTCTGGACACGGCCCGTTTCGTCGGCGTGTCGCAGTGCCGCTCCCATGCGGTCGGCGATGTCGCCGAGGTCGTCGTCGAACAGGTGTGGCCGTACAGGTCGAGCGTCATGGTCGCGGCCTTGTGGCCGAGCTGACGCTGAACCGTCTTCATGTGCGCCCCGGAGCGGATTATCAGGGATGCGGCCGTGTGTCGGAGGCCGTGCGCGGGGGACGCGGGGAACGATGGATCGGCGGCGTGTAGTCGTTCGACGGCCTTGGTGAACCAGTGCGTTGTCATGGGTGGTCGTATCGGTGTGCCATCGGGTCGGGACCAGAGCAGTTCGTCACGACCGCGCTGGTCCGTGATGGGGGCCAACAGCTCGGCTACTTCGGTTGGGATCGCAATGGTGCGCGTCTCGCAACCAGAAGGTGGTGCTGGTCCAGGCCAGTTCGGGCTGTCTGTGTTGCGCCCGTCCGGCTTTGTCGAGATAGCCACCGCTGGCTGAAACAGAATAGGCGCCGAAGGGCCCGCACCAACTATGGGCCCAGTTGGGCAGGCGCCTTTTGCCATAGGCCGAGTCAACCTTCCGTTCGTGTCGGGCGAGGACTGGCCAGAGGAAGGACCCAAACGGGGTGAGTCATAGTAGGTCGAAGACGGTTGCATGGACAACTGGAAATCTCGGCGATCTGCAGCGCGGCAGTTGTGGCCACAGAACGACTGGCCGCTTGGGTTACGTACGACCTATACCTGTTCCTGCCTTCATCCCCGAATTTCCCGCACTCCGCAGTCGTCAACAGGTGCTACCGTGACCCTGTGGCAAAAGACCTTAAGGTTTTCATCAGCTGGTCGGGCGATCCTTCCAAAGATATTGCACTGATATGGCATGAATTGGTTAATCAGCTCTTCGACACCGTAACTCCGTTTGTTTCCGATACTGACATAGAAGCTGGAGCGCGCGGTTTGGACGATATCAAGAATGAGTTGGACGGAACCAGCTTCGCGATTGTAGTTGTCACTCGCGCGAATCAGAGTGCGCCTTGGCTGAACTTTGAAGCGGGCGCAATATCTAGACAAATGGGCTCCGATTATGATTTGCGTGTAGCACCGTGCCTTGTAGACTTCGAGAAAGCCACCGAACTTACTAGTCCGCTAAAACAGTTTCAAGCGAACCTCCTAAATGAAGAGGGGATCACCAAGATACTGGCGTCAATAGCTAGGGCGGCAGACGTCGAATGGAACACAAAGGCTGGGATAGTCGCAGCTGTATTGCCATCATTCTTGGAACGTTTCCTAGCCATCAGGGATACTGCTCCGCCACCGGAGGTTCCAAAGCGGTCGCCGGACGCGATGGTCGAGGAAGTGCTCGAACTCGTGAGGGAACTCCACCGCGAGAGCATGGGAACGACCGCACGAGCAGAGGCGGAACGGTCTAATTCTCAAAAGAGCTCGACAATAGCGATAGACGATCCGGTCGCGATAGCAGCTCTAGTCGCCCGCGGAATTATCACCGAAGTCGCTGGAAAATCGTCCAGTGCTCAGGGTCTAGACTACAAAGTCAGGACCTACGATGGTGGAATAATAATTGCTGAGTTGCTTGGGTTCCCTGAAAGTATGAGAGCTGAAGTTGTCGAAAAGATGACTGACTCAGGATTGTTTCTGTCAGTCAGAGAGGTTGGAAAAGGTGGTTCGCTAGTTCGGATTGCTGGGCAGCTCAAACTCAGAAGGGACGCAATAGTTGGACCGTAGGACGCGCTGCGCCCGTACTGCGCCGCGATGCCCTCCACCTCTAGCTCACCATCAACCATGAGCCGATAGACCCTCTCGGCCACGACGACAGGCCAGCGGTCGACGGCCGGCGAAGTCATGGCACTATTGGTCGCGATCCTGAACCATGTGACAAGGCGAGGAGGCGAAACGAGATTCGGGGCCAGCTCGTATCACCGAGCGCGACTCAGATGAAACACTACGAGCAAACCAAGTTTCCTGGAGAGCGCTAGGTCGAAGTGTATGTAGTGAAGGACGGCTGCGTTGTACATAGACACCGCGTATGCAGTTCCTGTTGGGGCCGGTAGTTGATCCAATAACCCGCGCCCTGCCGTGCTGGGTATCCGCCTGTTGCTGGCCGAACCTGTTTGAGCATTGTTTCAATGTACGCACAAGCTGTTCGATCAGCACGTCGTCATTATTACCGCCCGTCGCCGATTGGGGGTGATGCTCGGTGTACCACCGTAACCGCGGGCGTACTCGTCCGTTCCTTATATCGCTTAGGCGTAGTCAACTCGACGGAGGCTTCTTCAGGTTTTCCTGACCAACGTCCGCGGTAAGAGATCTCGCCCGGCCTCGGCCGCAGTAAGAGCCGCTGACCAGCGAGCGGACTCTGAGAGTTGGTGTTCGGGATGTGACTAGACCTTAGTTAGATGGCTTATTCAACCACTGAAATAATCGCGCGATCTTCCCTTGGGGGCGTGGTTCCCCGTGGACTACCTGAGTCTCATTCGCGAAACAGTTGATCAAAGGGTTCGGGTGGTGGAAGAACTGGGATCGATTATTGTCTGGAATTCCCGTTCTCCGCCATTCGTAGCGCACGCCGATAGATCCGACATAGCAGGCGAACACGCAACCATCCACACGTGAGTAGTCGGGCTTCAAGAACACTGCACCCGGGCTTATCGTCAAACCTTTACGGGCGGGAGAATCATGGATTGAGTCCGTGGTGACGAGGGCCATGTGGGCGTCTATCATGTCGTCTGCTCCATTCAAGAAATCGCGAACCGACTGAGGGACTTCGATGCCCGTGCGGACCATCTGGCAGCCAAAATGCTTGGCGTAATATCGAGCGAGGTTTAATACCGTTGGCTGCCAGCCCATTCCATAAACGTCGGCGAATCCGATTCCTGGTAGGTGGCGCGCGTAAGGGTGAGTCACGAGATAGTCGGAGAATGTGTCGTAAGCAAGGTCGAACGGTTGCGACCGCGCGTTATTGCACCGGTCGCACATCGATTTGGGAAACTTCACTACTCCGTATCGGTCCCGTTTGACTCCAGACTTACCGCGGATCTCTCTCCGCTGCCCAGTGTCGTCGCCCCACAAGAGCGTATCCCCGCTCATGAGTCGAACGAGGTCTGACGCTTTGTATTTGTGCTCTCCCGTCGTCGCTGGACGGGAGCGGCACCACCAGCAAACGCCGTCGAAGTCAACGAGAAGGTGCGCTACATCGTCGCGTGACAGGAAACTCCTATCCTCCGCCGTACTCACAAGACCCCCTAGCTCGGTACACGATGCAAACAATAGTCGACCACCTCGTGGATAGGTTTGCGTCGATGTAGGCGGCGCAACTGTACTAGAGCAAAAGCCCACTGGTGATGCTGTGCGGTAGAGATGTCGACTCGAGGAGGTGTCGGGCAATAGAGCAGTTGGAGCAATATCGCGGTCTCTGTGACTCTTGTGGGACCTGAGCGCCGCCTAGGTAATGTTGACTCGAAGCCACACGCTATCTGAGCGCAGCGTAGTCACACACTATCGGTGTAGACCATGGGTACACGGCTGCTGTTTACTCCACGCCCCCGTCGGTACATAGCTGATCGTGTGTGCAAATGCACGTGCGTCGGCGCCCAGCCACGGGGCAGTCTTGGCCATCTTCGGGGCGCGCTGACCCCGTTTGAGCACCACTCAATCTGACTGACTCACTGCGACTAGAGGCCACAGGACTGCTGCTCGACATCTACGAGGTTCTAGCACAGGTTCAATTCCCGACAGCTCCACgagaaggcgccccacctgttcaggtggggcgctttcgtcgtctctacgggcaggtcggctacccggtgctcagcgcgtcgagggtcgcactctcgcgatg