gi|323175365|ref|ADUP00000000.1| Escherichia coli LT-68 gecLT68.assembly.10, whole genome shotgun .5189427, GC%: 50.85%, length = 5189427 bps

Total : 25 prophage regions have been identified, of which 14 regions are intact, 6 regions are incomplete, 5 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 7.2Kb intact 100 12 5574-12834 Stx2-converting phage 1717 54.69% Detail
2 13.9Kb intact 100 18 17243-31205 Enterobacteria phage P1 49.15% Detail
3 59.5Kb intact 150 68 92138-151727 Pectobacterium phage ZF40 49.24% Detail
4 19.7Kb incomplete 40 10 268194-287927 PHAGE_Yersin_413C 46.59% Detail
5 40.7Kb incomplete 50 44 509001-549735 PHAGE_Gifsy_2 49.39% Detail
6 13.1Kb intact 120 17 564052-577223 Enterobacteria phage phiP27 53.65% Detail
7 56Kb intact 150 92 674051-730140 Enterobacteria phage mEp460 48.68% Detail
8 44Kb questionable 70 29 2208327-2252400 PHAGE_Entero_Sf6 49.49% Detail
9 43.8Kb intact 120 62 2295911-2339741 Burkholderia phage BcepNY3 50.97% Detail
10 57.9Kb intact 150 64 2392911-2450833 Salmonella phage ST64B 49.57% Detail
11 45.8Kb questionable 80 33 2610508-2656396 Enterobacteria phage mEp460 49.79% Detail
12 18.4Kb incomplete 60 24 2848777-2867212 Enterobacteria phage PsP3 52.66% Detail
13 26Kb intact 150 35 2919988-2946017 Enterobacteria phage 285P 53.27% Detail
14 35.2Kb intact 150 45 2919231-2954448 Enterobacteria phage 285P 51.80% Detail
15 55Kb intact 150 66 3028302-3083400 Enterobacteria phage mEp460 52.13% Detail
16 24.2Kb questionable 80 23 3138662-3162953 PHAGE_Gifsy_1 49.61% Detail
17 28.5Kb intact 140 42 3305023-3333579 Enterobacteria phage P2 52.23% Detail
18 25.9Kb incomplete 40 3716624-3742541 Enterobacteria phage mEp460 49.87% Detail
19 30.8Kb questionable 70 18 3998162-4029024 PHAGE_Bacter_2 49.49% Detail
20 10.8Kb questionable 70 16 4088107-4098932 Enterobacteria phage Mu 49.63% Detail
21 24.6Kb incomplete 60 38 4212071-4236694 Burkholderia phage BcepMu 53.49% Detail
22 53.1Kb intact 150 62 4522044-4575143 Stx2-converting phage 86 50.03% Detail
23 12.8Kb incomplete 60 18 4820858-4833680 Enterobacteria phage PsP3 52.48% Detail
24 42Kb intact 150 44 4964176-5006241 Enterobacteria phage HK629 49.96% Detail
25 43.8Kb intact 150 57 5145547-5189427 PHAGE_Yersin_413C 52.46% 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.