gi|320668951|ref|AEUC00000000.1| Escherichia coli O157:H7 str. LSU-61 ECOSU61_1, whole genome .5048276, GC%: 50.61%, length = 5048276 bps

Total : 15 prophage regions have been identified, of which 9 regions are intact, 6 regions are incomplete, 0 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 26Kb intact 130 35 372968-399057 PHAGE_Yersin_413C 55.50% Detail
2 21.7Kb intact 150 39 650523-672321 Enterobacteria phage HK630 52.14% Detail
3 20.5Kb incomplete 30 671065-691620 Salmonella phage ST64B 47.35% Detail
4 4.1Kb incomplete 50 703604-707726 Enterobacteria phage cdtI 53.41% Detail
5 51.4Kb intact 150 58 1370792-1422216 PHAGE_Entero_2008 48.93% Detail
6 12.2Kb incomplete 10 20 3346868-3359103 Enterobacteria phage SfV 50.05% Detail
7 17.1Kb intact 150 26 3412097-3429266 Enterobacteria phage HK630 53.53% Detail
8 14.6Kb incomplete 30 15 3457589-3472196 Enterobacteria phage P4 43.00% Detail
9 24.4Kb incomplete 20 25 3799880-3824314 PHAGE_Entero_4795 49.19% Detail
10 21.6Kb intact 150 32 3824400-3846090 Enterobacteria phage HK629 51.51% Detail
11 39.5Kb intact 150 53 4077945-4117507 Enterobacteria phage cdtI 47.95% Detail
12 24.9Kb incomplete 20 21 4653027-4678014 Enterobacteria phage mEp235 48.13% Detail
13 42.3Kb intact 150 52 4677255-4719613 PHAGE_Entero_2008 51.42% Detail
14 22.9Kb intact 150 34 4813330-4836285 Enterobacteria phage HK630 51.45% Detail
15 31.9Kb intact 150 49 5016341-5048254 PHAGE_Entero_2008 50.50% 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.