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 6 intact prophage regions have been identified.




gi|296493068|ref|ADTJ00000000.1|  Escherichia coli MS 198-1 .1, whole genome .5236490, gc%: 50.67%
                                  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              11.9Kb                   questionable(80)              lysin,lysis,terminase,transposase            147663-159590            0                        22                      18                               1                                86.3%                            3                                no                               10                               PHAGE_Entero_HK629                         6                                27.2%                            43.91%                        
                                  2              32.5Kb                   intact(150)                   tail,head,portal,terminase                   242468-274988            0                        52                      40                               3                                82.6%                            9                                no                               16                               PHAGE_Entero_HK630                         17                               32.6%                            53.23%                        
                                  3              15.2Kb                   incomplete(10)                NA                                           419564-434763            0                        27                      18                               0                                66.6%                            9                                no                               17                               PHAGE_Stx2_c_I                             2                                7.4%                             48.75%                        
                                  4              20.2Kb                   incomplete(60)                transposase,tail,integrase                   635487-655705            0                        7                       6                                0                                85.7%                            1                                yes                              5                                PHAGE_Erwini_ENT90                         2                                28.5%                            52.28%                        
                                  5              14Kb                     questionable(80)              tail                                         740591-754622            0                        18                      16                               1                                94.4%                            1                                no                               11                               PHAGE_Entero_PsP3                          6                                33.3%                            53.33%                        
                                  6              11.6Kb                   incomplete(60)                integrase,transposase,tail                   1183107-1194777          0                        19                      19                               0                                100%                             0                                no                               7                                PHAGE_Yersin_413C                          12                               63.1%                            54.99%                        
                                  7              62.2Kb                   intact(110)                   tail,protease,transposase,recombinase        1211645-1273918          0                        74                      30                               2                                43.2%                            42                               yes                              12                               PHAGE_Yersin_413C                          13                               17.5%                            49.24%                        
                                  8              29.5Kb                   questionable(90)              injection,head,capsid,portal,tail            1449369-1478950          0                        47                      41                               4                                95.7%                            2                                no                               19                               PHAGE_Entero_IME10                         7                                14.8%                            47.64%                        
                                  9              16.2Kb                   incomplete(30)                tail,lysin                                   2168555-2184799          2                        26                      20                               2                                84.6%                            4                                no                               12                               PHAGE_Entero_epsilon15                     4                                15.3%                            49.54%                        
                                  10             45.5Kb                   intact(95)                    integrase,terminase,head                     2333506-2379057          1                        47                      44                               2                                97.8%                            1                                yes                              9                                PHAGE_Entero_phiV10                        36                               76.5%                            50.50%                        
                                  11             52.3Kb                   intact(103)                   integrase,terminase,head,tail,transposase     2333506-2385845          1                        58                      50                               5                                94.8%                            3                                yes                              12                               PHAGE_Entero_phiV10                        39                               67.2%                            49.96%                        
                                  12             22.5Kb                   incomplete(40)                tail                                         2553407-2575953          0                        28                      18                               1                                67.8%                            9                                no                               12                               PHAGE_Yersin_413C                          5                                17.8%                            49.99%                        
                                  13             8.5Kb                    incomplete(50)                transposase                                  2810627-2819200          0                        17                      8                                5                                76.4%                            4                                no                               7                                PHAGE_Yersin_413C                          2                                11.7%                            48.94%                        
                                  14             20.1Kb                   intact(150)                   tail,protease,portal,terminase,envelope,lysin     3349625-3369812          0                        30                      24                               1                                83.3%                            5                                no                               6                                PHAGE_Entero_mEp460                        18                               60%                              49.55%                        
                                  15             17.7Kb                   incomplete(40)                tail,recombinase                             3812236-3829984          0                        10                      6                                0                                60%                              4                                yes                              4                                PHAGE_Entero_4795                          3                                30%                              54.01%                        
                                  16             38.6Kb                   incomplete(60)                integrase,tail                               4841943-4880547          0                        30                      21                               1                                73.3%                            8                                yes                              15                               PHAGE_Entero_IME10                         3                                10%                              47.75%                        
                                  17             25.9Kb                   incomplete(40)                transposase,head                             4995441-5021377          0                        16                      10                               1                                68.7%                            5                                yes                              6                                PHAGE_Cronob_vB_CsaM_GAP32                 3                                18.7%                            52.65%                        
                                  18             45Kb                     intact(130)                   protease,portal,capsid,terminase,head,lysin,tail,plate     5180133-5225171          0                        50                      26                               7                                66%                              17                               yes                              14                               PHAGE_Yersin_413C                          10                               20%                              52.71%                        
