gi|343142142|ref|AFWO00000000| Escherichia coli O104:H4 str. GOS1, whole genome shotgun sequence. .5311118, GC%: 50.60%, length = 5311118 bps

Total : 12 prophage regions have been identified, of which 5 regions are intact, 5 regions are incomplete, 2 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 40.8Kb incomplete 50 24 216612-257497 PHAGE_Entero_Sf6 46.37% Detail
2 74.9Kb intact 130 61 808685-883610 Escherichia phage P13374 50.21% Detail
3 10Kb intact 100 11 1180730-1190751 Enterobacteria phage HK630 55.36% Detail
4 15.1Kb incomplete 50 17 1652015-1667169 Stx2-converting phage 86 49.00% Detail
5 49Kb intact 120 59 1913792-1962844 PHAGE_Stx2_c_II 50.01% Detail
6 45Kb intact 120 64 2090803-2135871 Enterobacteria phage mEp460 50.36% Detail
7 23.7Kb questionable 80 20 2482403-2506113 Escherichia phage P13374 52.73% Detail
8 51.9Kb intact 150 64 2537480-2589415 Enterobacteria phage lambda 51.41% Detail
9 21.5Kb incomplete 30 23 3387424-3408951 Enterobacteria phage mEp460 48.90% Detail
10 24.4Kb questionable 80 24 4802328-4826807 PHAGE_Yersin_413C 49.55% Detail
11 18.1Kb incomplete 10 16 4900587-4918721 Escherichia phage TL-2011c 51.15% Detail
12 5.8Kb incomplete 30 5260022-5265886 Enterobacteria phage phiP27 52.86% 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.