gi|159530897|ref|ABHQ00000000.1| Escherichia coli O157:H7 str. EC4076 , whole .5705645, GC%: 50.56%, length = 5705645 bps

Total : 18 prophage regions have been identified, of which 10 regions are intact, 3 regions are incomplete, 5 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 20.5Kb questionable 70 23 227841-248349 Stx2-converting phage 1717 42.37% Detail
2 38.5Kb intact 150 40 910315-948905 Enterobacteria phage cdtI 49.40% Detail
3 81.1Kb intact 140 86 1826051-1907245 PHAGE_Stx2_c_II 47.63% Detail
4 29Kb incomplete 50 20 2015907-2044998 Enterobacteria phage mEp460 47.56% Detail
5 34Kb intact 150 38 2505365-2539439 Enterobacteria phage HK630 53.48% Detail
6 52.2Kb intact 150 68 3045428-3097687 PHAGE_Entero_2008 51.73% Detail
7 20.5Kb incomplete 40 20 3721786-3742337 Stx2-converting phage 1717 48.07% Detail
8 24Kb questionable 86 31 3823324-3847402 PHAGE_Yersin_413C 53.41% Detail
9 35.7Kb intact 120 46 3823195-3858963 PHAGE_Yersin_413C 50.66% Detail
10 10.9Kb incomplete 20 16 3882032-3893009 Enterobacteria phage N15 49.22% Detail
11 49.6Kb intact 150 47 3898627-3948269 Enterobacteria phage lambda 50.25% Detail
12 26.9Kb questionable 70 14 3991326-4018313 Enterobacteria phage HK97 46.86% Detail
13 72.1Kb intact 150 56 4831215-4903346 PHAGE_Entero_2008 50.50% Detail
14 66.4Kb intact 150 51 4934444-5000879 PHAGE_Entero_4795 50.91% Detail
15 31.9Kb intact 150 38 5002215-5034177 Enterobacteria phage cdtI 54.27% Detail
16 19.3Kb questionable 90 25 5346545-5365863 Stx2-converting phage 1717 53.41% Detail
17 47.8Kb intact 150 58 5428274-5476125 PHAGE_Entero_2008 53.31% Detail
18 46.7Kb questionable 80 19 5543947-5590681 Enterobacteria phage HK629 51.63% 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.