gi|256276149|ref|ACXN00000000| Escherichia coli O157:H7 str. FRIK966 , whole .5376914, GC%: 50.24%, length = 5376914 bps

Total : 16 prophage regions have been identified, of which 10 regions are intact, 4 regions are incomplete, 2 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 47.8Kb intact 150 44 1734183-1782036 Enterobacteria phage SfV 49.00% Detail
2 34Kb intact 110 26 1926480-1960561 PHAGE_Entero_2008 51.30% Detail
3 24.2Kb incomplete 30 16 2868996-2893231 Enterobacteria phage mEp460 45.43% Detail
4 10.2Kb incomplete 60 14 3079151-3089415 Stx2-converting phage 1717 48.57% Detail
5 22.6Kb intact 93 34 3544483-3567093 PHAGE_Yersin_413C 54.37% Detail
6 40.1Kb intact 127 48 3537263-3577442 PHAGE_Yersin_413C 52.41% Detail
7 12.9Kb questionable 85 21 3623619-3636523 Enterobacteria phage P4 52.96% Detail
8 62.7Kb intact 150 100 3899453-3962220 Enterobacteria phage HK630 49.01% Detail
9 31.5Kb intact 150 42 4162426-4193934 PHAGE_Entero_2008 49.31% Detail
10 42.5Kb intact 150 43 4322843-4365391 Salmonella phage RE-2010 50.21% Detail
11 5.1Kb questionable 70 4358533-4363638 Enterobacteria phage Mu 50.27% Detail
12 14.4Kb intact 120 19 4368363-4382803 Enterobacteria phage HK106 50.92% Detail
13 102.3Kb intact 150 155 4505852-4608173 Enterobacteria phage Mu 50.50% Detail
14 30.1Kb intact 150 19 4840598-4870791 Enterobacteria phage HK629 51.97% Detail
15 8.5Kb incomplete 20 5104055-5112607 Enterobacteria phage IME10 43.00% Detail
16 21.5Kb incomplete 20 25 5347666-5369205 Escherichia phage TL-2011c 49.21% 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.