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.
   


Totally 7 intact prophage regions have been identified.




gi|383403426|ref|CP002967.1|  Escherichia coli W, complete genome. .4897452, gc%: 50.85%
                                  REGION         REGION_LENGTH            COMPLETENESS(score)           SPECIFIC_KEYWORD                             REGION_POSITION          TRNA_NUM                 TOTAL_PROTEIN_NUM       PHAGE_HIT_PROTEIN_NUM            HYPOTHETICAL_PROTEIN_NUM         PHAGE+HYPO_PROTEIN_PERCENTAGE    BACTERIAL_PROTEIN_NUM            ATT_SITE_SHOWUP                  PHAGE_SPECIES_NUM                MOST_COMMON_PHAGE_NAME                     MOST_COMMON_PHAGE_NUM            MOST_COMMON_PHAGE_PERCENTAGE     GC_PERCENTAGE                 
                                 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
                                  1              39.6Kb                   intact(150)                   tail,plate,head,protease,virion,portal,transposase     292365-332044            0                        57                      57                               0                                100%                             0                                no                               4                                PHAGE_Entero_Mu                            54                               94.7%                            52.25%                        
                                  2              36.5Kb                   intact(150)                   capsid,tail,lysis,lysin,plate,transposase     957085-993658            0                        49                      44                               5                                100%                             0                                yes                              6                                PHAGE_Entero_2                             38                               77.5%                            50.27%                        
                                  3              25Kb                     incomplete(20)                integrase                                    1487132-1512191          0                        21                      14                               6                                95.2%                            1                                yes                              10                               PHAGE_Gifsy_2                              5                                23.8%                            47.23%                        
                                  4              9.2Kb                    incomplete(40)                lysin,terminase                              1512615-1521884          2                        14                      11                               3                                100%                             0                                no                               8                                PHAGE_Entero_phiP27                        3                                21.4%                            48.89%                        
                                  5              44.8Kb                   intact(150)                   recombinase,tail,head,portal,terminase,envelope,lysin,integrase     1740203-1785057          0                        49                      39                               6                                91.8%                            4                                yes                              14                               PHAGE_Entero_HK629                         22                               44.8%                            50.96%                        
                                  6              21.7Kb                   intact(93)                    tail,lysis                                   2303355-2325077          0                        30                      30                               0                                100%                             0                                no                               6                                PHAGE_Yersin_413C                          25                               83.3%                            55.27%                        
                                  7              34.8Kb                   intact(131)                   tail,lysis                                   2303227-2338042          0                        45                      41                               2                                95.5%                            2                                yes                              7                                PHAGE_Yersin_413C                          35                               77.7%                            51.27%                        
                                  8              44Kb                     intact(120)                   integrase,tail,injection,head,coat,portal,terminase     2614678-2658768          0                        62                      58                               2                                96.7%                            2                                yes                              26                               PHAGE_Entero_IME10                         15                               24.1%                            47.40%                        
                                  9              39.5Kb                   intact(146)                   tail,lysis                                   4323668-4363170          0                        51                      45                               3                                94.1%                            3                                yes                              6                                PHAGE_Yersin_413C                          39                               76.4%                            51.79%                        
