gi|326348094|ref|AERP00000000.1| Escherichia coli O157:H7 str. 1044 , whole genome .5487708, GC%: 50.43%, length = 5487708 bps

Total : 23 prophage regions have been identified, of which 9 regions are intact, 10 regions are incomplete, 4 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 45.1Kb intact 150 52 635-45748 Enterobacteria phage Mu 55.59% Detail
2 52.6Kb intact 150 59 74762-127435 PHAGE_Entero_2008 52.94% Detail
3 35.6Kb intact 150 39 217187-252795 Enterobacteria phage HK630 52.89% Detail
4 37.9Kb incomplete 60 46 288867-326777 PHAGE_Stx2_c_II 48.66% Detail
5 25.9Kb intact 150 27 428434-454397 PHAGE_Entero_2008 55.55% Detail
6 10.4Kb questionable 70 12 771953-782421 PHAGE_Entero_4795 54.52% Detail
7 41.4Kb intact 110 42 1542660-1584101 PHAGE_Stx1_converting 51.19% Detail
8 32.9Kb incomplete 30 28 1974675-2007659 Enterobacteria phage mEp460 49.17% Detail
9 80.4Kb intact 150 112 1996703-2077182 PHAGE_Entero_2008 50.13% Detail
10 8.5Kb incomplete 20 2323866-2332418 Enterobacteria phage IME10 43.00% Detail
11 47.2Kb intact 100 43 2491595-2538880 PHAGE_Gifsy_2 45.56% Detail
12 19.2Kb intact 150 24 2657872-2677138 Enterobacteria phage lambda 54.41% Detail
13 30.7Kb intact 150 48 2799059-2829812 PHAGE_Entero_2008 52.68% Detail
14 21.1Kb questionable 80 28 3167886-3189006 Enterobacteria phage PsP3 50.11% Detail
15 30.7Kb incomplete 40 33 3988733-4019501 Enterobacteria phage mEp460 50.48% Detail
16 25.9Kb incomplete 20 30 4031428-4057399 Enterobacteria phage mEp460 49.16% Detail
17 12.8Kb incomplete 60 16 4146200-4159066 PHAGE_Entero_2008 44.40% Detail
18 15.2Kb questionable 70 20 4172259-4187487 Salmonella phage ST64B 51.18% Detail
19 28.6Kb incomplete 50 20 4179253-4207863 Enterobacteria phage lambda 48.75% Detail
20 30.5Kb incomplete 30 36 4601991-4632495 PHAGE_Stx1_converting 51.20% Detail
21 6.4Kb incomplete 40 11 4819495-4825993 PHAGE_Entero_2008 49.70% Detail
22 11.2Kb incomplete 30 22 4965469-4976765 PHAGE_Entero_2008 49.28% Detail
23 25.8Kb questionable 90 21 5075289-5101106 Stx2-converting phage 1717 44.26% 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.