gi|334878367|ref|AFOG00000000| Escherichia coli O104:H4 str. TY-2482 , whole genome shotgun .5291054, GC%: 50.55%, length = 5291054 bps

Total : 16 prophage regions have been identified, of which 4 regions are intact, 10 regions are incomplete, 2 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 7.8Kb incomplete 30 11 290018-297878 Escherichia phage TL-2011c 46.36% Detail
2 13.7Kb incomplete 60 18 487020-500734 PHAGE_Yersin_413C 54.85% Detail
3 38.3Kb incomplete 60 30 568202-606562 Enterobacteria phage mEp460 50.30% Detail
4 36.9Kb incomplete 40 23 2962114-2999032 PHAGE_Entero_Sf6 47.05% Detail
5 9.9Kb incomplete 50 13 3504870-3514823 Stx2-converting phage 1717 52.31% Detail
6 42.2Kb intact 150 53 3834610-3876809 Enterobacteria phage HK630 53.42% Detail
7 12.7Kb incomplete 50 16 4065127-4077843 Escherichia phage P13374 51.61% Detail
8 9.9Kb incomplete 30 11 4094858-4104801 Escherichia phage P13374 53.27% Detail
9 10.2Kb questionable 70 13 4263238-4273516 PHAGE_Yersin_413C 54.31% Detail
10 138.2Kb intact 150 242 4277492-4415780 Escherichia phage P13374 50.03% Detail
11 60.7Kb intact 150 64 4413964-4474747 Escherichia phage P13374 48.52% Detail
12 18.1Kb incomplete 20 22 4519114-4537273 Escherichia phage TL-2011c 42.03% Detail
13 27.2Kb questionable 90 32 4588907-4616200 Escherichia phage TL-2011c 50.10% Detail
14 12Kb incomplete 30 22 4658820-4670893 Enterobacteria phage mEp237 45.54% Detail
15 19.5Kb intact 150 27 4679602-4699193 Enterobacteria phage HK629 53.33% Detail
16 12.5Kb incomplete 10 20 4778962-4791480 Enterobacterial phage mEp234 47.38% 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.