Replicon Annotation Table

Stenotrophomonas_maltophilia_K279a - IS_012560

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IS Name ISStma11

- Name of the reference IS - Must respect the ISfinder nomenclature standarts.
ORF Name Smlt2413 - Predicted ORF Name. Automatic generated in protein annotation steps.
Previous Annotation - Previous orf annotation (for comparison purpose)
IS Structure - [ C ] complete, [ P ] partials, [ SIR ] solo IRs [ ND ] Not determined.
Complete and broken IS ? - Occurrence of complete and disrupted IS (Y for yes, N for no and ND not determined [solo IRs]
Number of ORFs - Number of Open Reading frames in the detected IS(s).
False Positive Prediction? - Set YES for false positive IS transposase prediction.
IS ORF(s) List - ID of each ORF composed by this ISs (Partial ISs with no ORFs please put `not_found`)
% of DNA Similarity - % of DNA Similarity against the reference IS sequence.
% of Similarity AAs (ISfinder First hit) - % of Protein Similarity against the first hit in ISfinder Database.
% of AAs Similarity (Replicon First hit) - % of Protein Similarity against the first hit in this replicon.
Identified IS Family ISL3 - IS family detected by the automatic annotation.
ORF Left End - ORF Left postion in the replicon.
ORF Right End - ORF Right postion in the replicon.
ORF Size (bp) - ORF size in base pairs (included stop codon).
ORF Size (aa) - ORF size in aminoacids.
Strand - ORF Orientation.
Type - [ T ] for transposase, [ P ] for passenger genes, [ A ] for accessory gene or [ ND ] for not determined.
IS Left End - IS Left coordinate in the replicon.
IS Right End - IS Right coordinate in the replicon.
IS Length (bp) - IS Length in base pairs (included Inverted Repeats, and excluding the Direct Repeats).
DR Size (bp) - Direct Repeats Size in base pairs. [Some IS(s) doesn't have DRs]
IR Size (bp) - Inverted Repeats Size in base pairs. [example 22/30, 22 matches in 30 nucleotides]
IS Coordinates Present (for partials) Only for Partials - Coordinates of the partials IS. [example 100366 (218) - 101333 (1185)] )
Length of Partial (bp) Only for Partials - Partials IS size in base pairs.
General Comments - General Comments: Feel free to put all observations regarding the annotation.
The automatic annotation process could generate automatic comments between brackets
ORF protein sequence - Fasta protein sequence of this open reading frame.
[Not present in solo IRs and in some cases of partial ISs].
IS fasta sequence - IS Fasta sequence (with IRs and without DRs)
IS Left End - Left end of the element. [For IR identification - Some ISs do not have IRs ]
IS Right End - Right inverted end of the element [For IR identification - Some ISs don not have IRs ].
Insertion Site - Insertion site with the presence or absence of DRs [Only show in complete ISs].
(Please respect the example: ATCGATCG ( ATCG ) ATCGATCG ).