gi|315629557|ref|ADEJ00000000| Clostridium difficile 6534 , whole genome shotgun sequence. .4344228, GC%: 28.95%, length = 4344228 bps

Total : 15 prophage regions have been identified, of which 1 regions are intact, 11 regions are incomplete, 3 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 13.7Kb incomplete 40 20 43372-57141 Clostridium phage phiC2 28.35% Detail
2 11.5Kb incomplete 30 20 259087-270643 PHAGE_Clostr_CD119 29.89% Detail
3 29.2Kb incomplete 20 21 957539-986774 PHAGE_Ectoca_1 30.79% Detail
4 26.3Kb questionable 80 25 1006342-1032663 Clostridium phage phiMMP04 27.68% Detail
5 39Kb intact 140 65 1984734-2023822 Clostridium phage phiMMP02 29.87% Detail
6 13.1Kb incomplete 40 19 3466013-3479160 PHAGE_Clostr_st 24.45% Detail
7 11.2Kb incomplete 30 20 3505478-3516745 Enterococcus phage phiEF24C 26.30% Detail
8 20.2Kb incomplete 50 16 3518362-3538628 Clostridium phage phiMMP04 26.72% Detail
9 15.9Kb incomplete 40 13 3548776-3564754 PHAGE_Clostr_CD119 27.80% Detail
10 22.3Kb incomplete 30 10 3563366-3585753 Clostridium phage phiCD6356 26.85% Detail
11 26.8Kb questionable 80 44 4073401-4100245 Clostridium phage phiC2 31.51% Detail
12 24.1Kb incomplete 60 31 4135586-4159735 Clostridium phage phiMMP04 34.19% Detail
13 10.7Kb incomplete 20 20 4205790-4216549 Clostridium phage phiC2 26.58% Detail
14 10.8Kb incomplete 60 16 4233876-4244744 Clostridium phage phiC2 29.22% Detail
15 50.8Kb questionable 80 68 4258052-4308865 Clostridium phage phiC2 29.19% 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.