gi|295901270|ref|ADVA00000000| Escherichia coli O157:H7 str. EC4191 , whole genome .5201104, GC%: 50.22%, length = 5201104 bps

Total : 20 prophage regions have been identified, of which 5 regions are intact, 13 regions are incomplete, 2 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 30.8Kb intact 97 38 64074-94949 PHAGE_Yersin_413C 49.11% Detail
2 34Kb intact 150 45 488115-522114 Enterobacteria phage mEp460 50.34% Detail
3 23.2Kb incomplete 20 11 754487-777777 PHAGE_Entero_Sf6 48.87% Detail
4 26.4Kb incomplete 40 23 1095617-1122081 Rhodothermus phage RM378 48.07% Detail
5 57.4Kb intact 150 44 1227593-1285052 Enterobacteria phage mEp460 50.43% Detail
6 14.1Kb incomplete 30 21 1316704-1330893 Stx2-converting phage 1717 47.96% Detail
7 15.6Kb incomplete 50 21 1453538-1469232 Escherichia phage TL-2011c 51.25% Detail
8 26.9Kb incomplete 30 12 1468587-1495492 Salmonella phage vB_SosS_Oslo 48.49% Detail
9 7.9Kb incomplete 50 11 1756663-1764653 Stx2-converting phage 1717 49.07% Detail
10 28.4Kb incomplete 10 1768598-1797003 Enterobacteria phage N15 49.55% Detail
11 13.6Kb incomplete 50 20 2053077-2066748 Enterobacteria phage PsP3 52.02% Detail
12 30.7Kb incomplete 30 15 2167214-2197917 Escherichia phage TL-2011c 50.92% Detail
13 16Kb questionable 70 25 3019258-3035269 PHAGE_Entero_2008 47.62% Detail
14 24.5Kb incomplete 60 25 3449167-3473668 Stx2-converting phage 1717 45.85% Detail
15 24.7Kb incomplete 30 12 3611242-3635953 PHAGE_Yersin_413C 52.46% Detail
16 24.6Kb incomplete 40 16 3912974-3937668 Stx2-converting phage 86 47.48% Detail
17 56.3Kb intact 150 69 4045888-4102242 Enterobacteria phage HK630 49.18% Detail
18 49Kb intact 150 55 4258563-4307657 Enterobacteria phage HK630 50.39% Detail
19 30.9Kb incomplete 60 25 4505235-4536212 PHAGE_Entero_2008 52.36% Detail
20 16.2Kb questionable 70 13 4990651-5006857 PHAGE_Stx2_c_II 43.97% 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.