gi|333011646|ref|AFGX00000000.1| Shigella flexneri K-272 .0, whole genome shotgun .4510648, GC%: 50.95%, length = 4510648 bps

Total : 20 prophage regions have been identified, of which 12 regions are intact, 6 regions are incomplete, 2 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 23.5Kb incomplete 50 141515-165036 PHAGE_Entero_Sf6 52.84% Detail
2 18.4Kb incomplete 50 789258-807657 Enterobacteria phage Mu 49.95% Detail
3 40.6Kb intact 150 33 861214-901845 Prophage Escherichia coli str. K-12 substr. MG1655 50.40% Detail
4 52.1Kb intact 150 62 948679-1000859 Enterobacteria phage mEp460 51.09% Detail
5 14.9Kb intact 110 22 1119202-1134104 PHAGE_Entero_Sf6 49.66% Detail
6 35.5Kb intact 120 28 1186293-1221794 Enterobacteria phage 285P 51.45% Detail
7 19.8Kb intact 120 19 1314075-1333973 PHAGE_Entero_Sf6 51.40% Detail
8 13.7Kb intact 100 21 1466794-1480503 Salmonella phage ST64B 50.61% Detail
9 30.2Kb intact 100 23 1738485-1768755 Prophage Escherichia coli CFT073 49.67% Detail
10 20.8Kb incomplete 60 20 1902290-1923173 PHAGE_Entero_Sf6 49.45% Detail
11 40.9Kb intact 110 20 2143253-2184159 PHAGE_Entero_4795 50.35% Detail
12 7.7Kb incomplete 60 14 2190430-2198138 PHAGE_Entero_Sf6 51.16% Detail
13 52Kb intact 130 35 2242526-2294583 Prophage Escherichia coli CFT073 49.73% Detail
14 6.6Kb questionable 90 11 2291012-2297628 Prophage Escherichia coli CFT073 50.94% Detail
15 36.3Kb intact 150 28 2304506-2340902 Stx2-converting phage 1717 49.92% Detail
16 45.3Kb intact 150 57 2431379-2476751 Enterobacteria phage phiP27 50.89% Detail
17 34.5Kb intact 100 22 2575288-2609821 Prophage Escherichia coli str. K-12 substr. MG1655 51.59% Detail
18 7.1Kb incomplete 30 10 2915319-2922441 Prophage Escherichia coli CFT073 47.48% Detail
19 24.8Kb questionable 70 22 3031862-3056738 Prophage Escherichia coli str. K-12 substr. MG1655 50.26% Detail
20 10Kb incomplete 50 12 3102859-3112921 Enterobacteria phage Mu 51.14% 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.