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 13 intact prophage regions have been identified.




gi|257762509|ref|AP010960.1|  Escherichia coli O111:H- str. 11128 DNA, complete genome. .5371077, gc%: 50.62%
                                  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              10.5Kb                   intact(150)                   head,transposase,tail                        608660-619218            0                        16                      15                               1                                100%                             0                                no                               5                                PHAGE_Entero_HK630                         11                               68.7%                            54.68%                        
                                  2              37.1Kb                   intact(150)                   integrase,transposase,head,tail              850423-887549            0                        41                      37                               1                                92.6%                            3                                yes                              13                               PHAGE_Entero_HK629                         16                               39%                              50.59%                        
                                  3              14.5Kb                   incomplete(40)                transposase,protease                         1123381-1137950          0                        25                      18                               4                                88%                              3                                no                               14                               PHAGE_Entero_SfV                           3                                12%                              47.86%                        
                                  4              7.8Kb                    incomplete(30)                transposase                                  1139569-1147425          0                        12                      9                                2                                91.6%                            1                                no                               5                                PHAGE_Entero_4795                          5                                41.6%                            49.42%                        
                                  5              68.4Kb                   intact(120)                   integrase,lysin,terminase,portal,tail,transposase     1183447-1251899          3                        79                      78                               1                                100%                             0                                yes                              16                               PHAGE_Stx2_c_II                            47                               59.4%                            50.10%                        
                                  6              59.5Kb                   intact(150)                   integrase,transposase,lysis,lysin,terminase,head,portal,tail     1435922-1495518          2                        65                      49                               5                                83%                              11                               yes                              16                               PHAGE_Entero_2008                          30                               46.1%                            49.56%                        
                                  7              44.4Kb                   intact(150)                   transposase,lysis,lysin,terminase,portal,protease,tail     1602053-1646484          1                        51                      45                               5                                98%                              1                                yes                              17                               PHAGE_Entero_cdtI                          15                               29.4%                            52.31%                        
                                  8              33.2Kb                   intact(150)                   integrase,transposase,terminase,head,portal,tail     1740090-1773305          0                        37                      33                               2                                94.5%                            2                                yes                              6                                PHAGE_Entero_2008                          26                               70.2%                            53.64%                        
                                  9              35.1Kb                   incomplete(50)                transposase,integrase                        1968267-2003415          2                        33                      21                               4                                75.7%                            8                                yes                              15                               PHAGE_Stx2_c_1717                          5                                15.1%                            48.13%                        
                                  10             52.2Kb                   intact(150)                   tail,transposase,head,portal,terminase,lysin,lysis,integrase     1997785-2050027          0                        44                      37                               3                                90.9%                            4                                yes                              9                                PHAGE_Entero_2008                          29                               65.9%                            50.74%                        
                                  11             24.7Kb                   intact(130)                   capsid,terminase,head,lysin,tail,plate       2199056-2223770          0                        29                      26                               2                                96.5%                            1                                no                               12                               PHAGE_Yersin_413C                          12                               41.3%                            52.70%                        
                                  12             53Kb                     intact(150)                   tail,head,portal,terminase,lysin,protease,integrase     2389426-2442462          3                        68                      62                               2                                94.1%                            4                                yes                              15                               PHAGE_Entero_2008                          31                               45.5%                            52.28%                        
                                  13             51.8Kb                   intact(150)                   tail,head,portal,terminase,transposase,integrase     2536092-2587947          5                        67                      56                               6                                92.5%                            5                                yes                              22                               PHAGE_Entero_HK630                         16                               23.8%                            51.83%                        
                                  14             63.6Kb                   intact(120)                   injection,head,transposase,coat,lysin,integrase     2606597-2670287          2                        70                      69                               1                                100%                             0                                yes                              27                               PHAGE_Entero_Sf6                           20                               28.5%                            48.00%                        
                                  15             38.8Kb                   incomplete(40)                lysis,integrase                              2893240-2932106          0                        20                      14                               3                                85%                              3                                yes                              7                                PHAGE_Stx2_c_1717                          7                                35%                              48.30%                        
                                  16             33.5Kb                   intact(150)                   tail,transposase,terminase,portal,protease     3312379-3345928          1                        39                      34                               1                                89.7%                            4                                no                               9                                PHAGE_Entero_mEp460                        11                               28.2%                            53.56%                        
                                  17             10.4Kb                   incomplete(50)                transposase,tail                             3717302-3727742          0                        12                      5                                0                                41.6%                            7                                no                               4                                PROPHAGE_Escher_MG1655                     2                                16.6%                            42.17%                        
                                  18             15.2Kb                   incomplete(60)                transposase                                  3742782-3758067          0                        20                      6                                2                                40%                              12                               no                               6                                PROPHAGE_Xantho_33913                      1                                5%                               40.76%                        
                                  19             42.6Kb                   intact(150)                   lysis,lysin,terminase,head,portal,tail       4957576-5000205          3                        48                      45                               0                                93.7%                            3                                no                               8                                PHAGE_Entero_2008                          26                               54.1%                            51.81%                        
