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 14 intact prophage regions have been identified.




gi|254590536|ref|CP001368.1|  Escherichia coli O157:H7 str. TW14359, complete genome. .5528136, gc%: 50.51%
                                  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              13.8Kb                   intact(110)                   integrase,transposase,tail                   302573-316461            0                        18                      17                               0                                94.4%                            1                                yes                              12                               PHAGE_Entero_HK106                         4                                22.2%                            46.79%                        
                                  2              26.3Kb                   intact(150)                   lysin,terminase,portal,protease,tail         906979-933321            0                        27                      25                               1                                96.2%                            1                                no                               5                                PHAGE_Entero_cdtI                          21                               77.7%                            52.01%                        
                                  3              47.6Kb                   intact(150)                   envelope,transposase,lysin,portal,head,tail     1167539-1215181          2                        56                      42                               11                               94.6%                            3                                no                               20                               PHAGE_Entero_HK630                         11                               19.6%                            51.65%                        
                                  4              50.5Kb                   intact(150)                   integrase,lysin,terminase,head,portal,tail     1482524-1533046          0                        57                      45                               9                                94.7%                            3                                yes                              20                               PHAGE_Entero_2008                          22                               38.5%                            49.26%                        
                                  5              46.5Kb                   intact(150)                   integrase,recombinase,lysis,envelope,head,capsid,tail     1546959-1593488          0                        42                      39                               0                                92.8%                            3                                yes                              14                               PHAGE_Entero_lambda                        25                               59.5%                            51.04%                        
                                  6              6.6Kb                    questionable(70)              tail,transposase,protease                    1593526-1600172          0                        8                       5                                1                                75%                              2                                no                               3                                PHAGE_Stx2_c_1717                          3                                37.5%                            46.58%                        
                                  7              50.1Kb                   intact(150)                   lysin,terminase,portal,head,tail,integrase     1689811-1739996          2                        39                      36                               2                                97.4%                            1                                yes                              13                               PHAGE_Entero_HK630                         15                               38.4%                            50.29%                        
                                  8              45.4Kb                   intact(150)                   integrase,lysis,terminase,portal,protease,tail,transposase     1736123-1781546          1                        58                      45                               12                               98.2%                            1                                yes                              24                               PHAGE_Entero_cdtI                          14                               24.1%                            52.48%                        
                                  9              93.1Kb                   intact(150)                   tail,head,portal,lysis,integrase,transposase,terminase,lysin     2068687-2161822          5                        114                     98                               8                                92.9%                            8                                yes                              28                               PHAGE_Entero_2008                          56                               49.1%                            52.30%                        
                                  10             15Kb                     intact(100)                   transposase,tail                             2504677-2519677          0                        17                      14                               0                                82.3%                            3                                no                               6                                PHAGE_Entero_PsP3                          5                                29.4%                            52.75%                        
                                  11             53.4Kb                   intact(150)                   tail,head,portal,terminase,transposase       2574599-2628094          5                        48                      40                               7                                97.9%                            1                                yes                              21                               PHAGE_Entero_HK630                         13                               27%                              51.51%                        
                                  12             62.5Kb                   intact(150)                   tail,head,portal,terminase,lysis,transposase,integrase     2656374-2718900          3                        73                      71                               2                                100%                             0                                yes                              9                                PHAGE_Stx2_c_1717                          61                               83.5%                            50.77%                        
                                  13             35.7Kb                   intact(131)                   tail,lysis                                   2806423-2842191          0                        48                      42                               2                                91.6%                            4                                yes                              8                                PHAGE_Yersin_413C                          34                               70.8%                            50.66%                        
                                  14             69.7Kb                   intact(150)                   tail,head,portal,terminase,lysin,recombinase,transposase,integrase     2875085-2944833          3                        67                      60                               2                                92.5%                            5                                yes                              21                               PHAGE_Entero_2008                          18                               26.8%                            51.20%                        
                                  15             76.1Kb                   intact(140)                   tail,transposase,portal,terminase,lysin,integrase,injection     3187249-3263362          4                        83                      78                               1                                95.1%                            4                                yes                              14                               PHAGE_Stx2_c_II                            37                               44.5%                            48.42%                        
                                  16             23.9Kb                   questionable(90)              transposase,lysin,integrase                  3535218-3559150          0                        30                      20                               3                                76.6%                            7                                yes                              10                               PHAGE_Stx2_c_1717                          11                               36.6%                            41.74%                        
                                  17             20.5Kb                   questionable(90)              integrase,transposase,tail                   4639945-4660486          0                        17                      9                                5                                82.3%                            3                                yes                              6                                PHAGE_Stx2_c_1717                          4                                23.5%                            45.82%                        
                                  18             21.7Kb                   incomplete(50)                tail,integrase                               5131436-5153196          1                        20                      18                               0                                90%                              2                                yes                              7                                PHAGE_Entero_mEp460                        10                               50%                              47.52%                        
