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 12 intact prophage regions have been identified.




gi|294489418|ref|CP001969.1|  Escherichia coli IHE3034, complete genome. .5108383, gc%: 50.70%
                                  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              24.4Kb                   incomplete(20)                integrase                                    271118-295549            1                        14                      6                                0                                42.8%                            8                                yes                              6                                PHAGE_Cellul_phiST                         1                                7.1%                             51.05%                        
                                  2              50.8Kb                   intact(150)                   integrase,lysin,lysis,terminase,head,portal,tail     554913-605738            1                        60                      50                               5                                91.6%                            5                                yes                              10                               PHAGE_Entero_mEp460                        23                               38.3%                            50.81%                        
                                  3              10.8Kb                   incomplete(60)                integrase,capsid,head,protease               920418-931237            0                        17                      8                                5                                76.4%                            4                                yes                              6                                PHAGE_Gifsy_1                              2                                11.7%                            48.43%                        
                                  4              33.9Kb                   intact(108)                   transposase,lysis                            964778-998678            0                        39                      35                               3                                97.4%                            1                                yes                              7                                PHAGE_Yersin_413C                          29                               74.3%                            51.40%                        
                                  5              36.3Kb                   intact(127)                   transposase,lysis                            964778-1001166           0                        45                      41                               3                                97.7%                            1                                yes                              8                                PHAGE_Yersin_413C                          34                               75.5%                            51.36%                        
                                  6              50Kb                     intact(150)                   integrase,lysin,lysis,terminase,head,portal,tail     1281903-1331908          0                        56                      48                               5                                94.6%                            3                                yes                              21                               PHAGE_Entero_HK630                         22                               39.2%                            49.84%                        
                                  7              32.5Kb                   intact(150)                   lysis,terminase,head,portal,tail             1444944-1477495          2                        36                      32                               3                                97.2%                            1                                no                               10                               PHAGE_Entero_HK630                         19                               52.7%                            53.59%                        
                                  8              52.6Kb                   intact(150)                   tail,head,capsid,terminase,lysin             2094114-2146778          4                        46                      38                               4                                91.3%                            4                                yes                              18                               PHAGE_Entero_mEp460                        13                               28.2%                            48.80%                        
                                  9              49.9Kb                   intact(120)                   portal,capsid,terminase,head,lysin,tail      2641582-2691550          0                        40                      26                               6                                80%                              8                                yes                              12                               PHAGE_Yersin_413C                          13                               32.5%                            52.16%                        
                                  10             41.5Kb                   intact(100)                   integrase,tail,head,coat,portal,terminase,lysin     2712625-2754131          0                        49                      45                               3                                97.9%                            1                                yes                              21                               PHAGE_Entero_HK620                         18                               36.7%                            46.85%                        
                                  11             54.5Kb                   intact(107)                   lysin,tail,terminase,integrase               2880177-2934745          1                        52                      46                               5                                98%                              1                                yes                              5                                PHAGE_Escher_TL_2011b                      40                               76.9%                            49.11%                        
                                  12             31Kb                     questionable(81)              head,terminase,integrase                     2893768-2924846          1                        37                      33                               3                                97.2%                            1                                yes                              3                                PHAGE_Entero_phiV10                        31                               83.7%                            49.84%                        
                                  13             52.4Kb                   intact(150)                   tail,head,plate,capsid,terminase,integrase     3042227-3094634          0                        52                      46                               5                                98%                              1                                yes                              9                                PHAGE_Salmon_ST64B                         33                               63.4%                            49.97%                        
                                  14             37.2Kb                   intact(139)                   integrase,head                               4921724-4958950          1                        28                      19                               3                                78.5%                            6                                yes                              7                                PHAGE_Entero_P4                            13                               46.4%                            46.55%                        
                                  15             48.5Kb                   intact(150)                   integrase,lysin,terminase,portal,protease,tail     5031567-5080072          3                        54                      49                               4                                98.1%                            1                                yes                              9                                PHAGE_Entero_mEp460                        38                               70.3%                            49.60%                        
