gi|296498250|ref|ADTX00000000.1| Escherichia coli MS 153-1 .1, whole genome .5087744, GC%: 50.48%, length = 5087744 bps

Total : 14 prophage regions have been identified, of which 5 regions are intact, 5 regions are incomplete, 4 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 16.3Kb questionable 70 26 10517-26831 PHAGE_Entero_2008 52.19% Detail
2 13.2Kb intact 120 20 48959-62233 Enterobacteria phage HK629 51.44% Detail
3 15.6Kb questionable 70 26 363979-379641 Enterobacteria phage N15 52.31% Detail
4 16.9Kb incomplete 10 30 1975391-1992357 PHAGE_Stx2_c_I 50.27% Detail
5 41.9Kb incomplete 50 42 2265878-2307794 Stx2-converting phage 1717 49.73% Detail
6 25.1Kb intact 150 37 2311133-2336291 Enterobacteria phage mEp460 49.56% Detail
7 6.7Kb incomplete 60 10 2678667-2685385 Stx2-converting phage 1717 52.08% Detail
8 32.6Kb questionable 70 19 2993934-3026591 Prophage Escherichia coli O157:H7 str. Sakai 48.07% Detail
9 12.5Kb incomplete 40 27 3380329-3392835 PHAGE_Gifsy_1 48.80% Detail
10 48.5Kb intact 100 25 3396951-3445461 PHAGE_Entero_4795 47.82% Detail
11 8.6Kb incomplete 50 16 3686770-3695425 Enterobacteria phage mEp460 46.45% Detail
12 36.9Kb questionable 80 10 3779168-3816077 PHAGE_Entero_Sf6 49.58% Detail
13 22.2Kb intact 150 36 3811975-3834195 Enterobacteria phage HK629 49.35% Detail
14 31.4Kb intact 150 33 4362857-4394343 PHAGE_Entero_2008 47.99% Detail
Legend:
REGION: the number assigned to the region
REGION_LENGTH: the length of the sequence of that region (in bp)
COMPLETENESS: a prediction of whether the region contains a intact or incomplete prophage based on the above criteria
SCORE: the score of the region based on the above criteria
#CDS: the number of coding sequnce
REGION_POSITION: the start and end positions of the region on the bacterial chromosome
PHAGE: the phage with the highest number of proteins most similar to those in the region
GC_PERCENTAGE: the percentage of gc nucleotides of the region
DETAIL: detail info of the region


txt file for download


Criteria for scoring prophage regions (as intact, questionable, or incomplete):
Method 1:
1. If the number of certain phage organism in this table is more than or equal to 100% of the total number of CDS of the region,
    the region is marked with total score 150. If less than 100%, method 2 and 3 will be used.

Method 2:
1. If the number of certain phage organism in this table is more than 50% of the total number of CDS of the region, that phage
    organism is considered as the major potential phage for that region; the percentage of the total number
    of that phage organism in this table in the total number of proteins of the region is calculated and
    then multipled by 100; the percentage of the length of that phage organism in this table in the length
    of the region is calculated and then multipled by 50 (phage head's encapsulation capability is considered).

Method 3:
1. If any of the specific phage-related keywords (such as 'capsid', 'head', 'integrase', 'plate', 'tail', 'fiber',
    'coat', 'transposase', 'portal', 'terminase', 'protease' or 'lysin') are present, the score will be increased
    by 10 for each keyword found.
2. If the size of the region is greater than 30 Kb, the score will be increased by 10.
3. If there are at least 40 proteins in the region, the score will be increased by 10.
4. If all of the phage-related proteins and hypothetical proteins constitute more than 70% of
    the total number of proteins in the region, the score will be increased by 10.

Compared the total score of method 2 with the total score of method 3, the bigger one is chosen as the total score of the region.
If the region's total score is less than 70, it is marked as incomplete; if between 70 to 90, it is marked as questionable; if greater than 90, it is marked as intact.