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 9 intact prophage regions have been identified.




gi|345367635|ref|AFDV00000000.1|  Escherichia coli STEC_DG131-3 .0, whole genome .5298033, gc%: 50.64%
                                  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              12.6Kb                   incomplete(30)                virion,transposase                           31839-44510              0                        17                      12                               4                                94.1%                            1                                no                               6                                PHAGE_Entero_SfV                           7                                41.1%                            45.94%                        
                                  2              37.4Kb                   intact(150)                   tail,head,plate,capsid,terminase,lysin,lysis,integrase     758866-796285            0                        56                      42                               10                               92.8%                            4                                yes                              12                               PHAGE_Salmon_ST64B                         28                               50%                              52.45%                        
                                  3              46.9Kb                   intact(150)                   integrase,lysin,lysis,head,capsid,tail,fiber     1125363-1172361          0                        58                      54                               3                                98.2%                            1                                yes                              18                               PHAGE_Entero_lambda                        32                               55.1%                            50.13%                        
                                  4              34.9Kb                   intact(150)                   capsid,tail,lysis,lysin,plate                1526239-1561171          0                        48                      41                               7                                100%                             0                                yes                              3                                PHAGE_Entero_2                             39                               81.2%                            49.90%                        
                                  5              22Kb                     intact(150)                   capsid,tail,lysis,lysin,plate                1539020-1561093          0                        32                      29                               3                                100%                             0                                no                               2                                PHAGE_Entero_2                             28                               87.5%                            53.89%                        
                                  6              29.1Kb                   incomplete(10)                NA                                           1704822-1733989          0                        37                      22                               11                               89.1%                            4                                yes                              13                               PHAGE_Entero_mEp460                        10                               27%                              48.63%                        
                                  7              56.4Kb                   intact(150)                   integrase,tail,protease,portal,terminase,lysin,transposase     2052617-2109029          3                        62                      46                               14                               96.7%                            2                                yes                              19                               PHAGE_Entero_mEp460                        15                               24.1%                            50.58%                        
                                  8              29.9Kb                   intact(150)                   tail,capsid,head,terminase,lysin,lysis       2198425-2228380          0                        39                      31                               7                                97.4%                            1                                no                               16                               PHAGE_Entero_cdtI                          9                                23%                              49.22%                        
                                  9              21.4Kb                   incomplete(20)                integrase                                    2227482-2248975          0                        18                      12                               4                                88.8%                            2                                yes                              9                                PHAGE_Gifsy_2                              4                                22.2%                            44.22%                        
                                  10             44.6Kb                   intact(150)                   protease,tail,terminase,head,portal          2344626-2389255          0                        47                      38                               3                                87.2%                            6                                no                               10                               PHAGE_Entero_4795                          26                               55.3%                            52.56%                        
                                  11             63.1Kb                   intact(100)                   tail,portal,terminase,integrase              2458299-2521405          0                        78                      66                               12                               100%                             0                                yes                              21                               PHAGE_Escher_TL_2011c                      29                               37.1%                            49.57%                        
                                  12             42.8Kb                   intact(110)                   transposase,tail                             3063342-3106209          0                        23                      15                               7                                95.6%                            1                                yes                              9                                PHAGE_Stx2_c_1717                          4                                17.3%                            49.28%                        
                                  13             11.2Kb                   incomplete(40)                integrase,tail                               3107274-3118539          3                        20                      16                               2                                90%                              2                                no                               9                                PHAGE_Entero_mEp460                        6                                30%                              50.32%                        
                                  14             11.2Kb                   incomplete(40)                tail,integrase                               3628114-3639391          0                        12                      9                                2                                91.6%                            1                                yes                              4                                PHAGE_Entero_mEp460                        5                                41.6%                            42.04%                        
