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 10 intact prophage regions have been identified.




gi|349736152|ref|CP003034.1|  Escherichia coli O7:K1 str. CE10, complete genome. .5313531, gc%: 50.56%
                                  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              32.2Kb                   intact(150)                   transposase,lysin,lysis,head,capsid,tail     568489-600732            0                        41                      35                               2                                90.2%                            4                                no                               11                               PHAGE_Entero_lambda                        23                               56%                              52.10%                        
                                  2              16.2Kb                   incomplete(40)                integrase,transposase                        824561-840854            0                        15                      15                               0                                100%                             0                                yes                              8                                PHAGE_Entero_HK620                         7                                46.6%                            44.54%                        
                                  3              60.9Kb                   intact(150)                   integrase,lysin,terminase,portal,capsid,head,tail     1083871-1144835          0                        61                      53                               6                                96.7%                            2                                yes                              25                               PHAGE_Entero_HK97                          15                               24.5%                            49.80%                        
                                  4              14.2Kb                   questionable(70)              integrase,capsid,head,terminase              1260413-1274669          0                        19                      11                               8                                100%                             0                                yes                              8                                PHAGE_Salmon_ST64B                         3                                15.7%                            51.57%                        
                                  5              55.4Kb                   questionable(90)              integrase,transposase,terminase,tail         1267134-1322606          0                        55                      44                               8                                94.5%                            3                                yes                              14                               PHAGE_Burkho_BcepMu                        27                               49%                              52.26%                        
                                  6              62.2Kb                   intact(120)                   integrase,transposase,terminase,tail,fiber     1280287-1342547          0                        76                      57                               16                               96%                              3                                yes                              20                               PHAGE_Burkho_BcepMu                        33                               43.4%                            51.19%                        
                                  7              48Kb                     intact(150)                   transposase,head,capsid,tail,fiber           1453157-1501210          2                        53                      38                               14                               98.1%                            1                                yes                              12                               PHAGE_Entero_lambda                        20                               37.7%                            51.82%                        
                                  8              42.8Kb                   intact(150)                   tail,plate,lysin,lysis,capsid,transposase     1751814-1794644          0                        37                      35                               2                                100%                             0                                yes                              6                                PHAGE_Entero_2                             29                               78.3%                            51.37%                        
                                  9              52.1Kb                   intact(150)                   transposase,tail,head,capsid                 1810335-1862517          0                        61                      48                               7                                90.1%                            6                                no                               18                               PHAGE_Entero_lambda                        21                               34.4%                            50.29%                        
                                  10             46Kb                     intact(120)                   tail,head,portal,terminase,lysin,integrase     2475612-2521614          2                        55                      46                               4                                90.9%                            5                                yes                              11                               PHAGE_Entero_2008                          26                               47.2%                            51.10%                        
                                  11             44.7Kb                   intact(120)                   transposase,lysis,lysin,tail,head,terminase,integrase     2938839-2983553          1                        50                      45                               4                                98%                              1                                yes                              6                                PHAGE_Entero_phiV10                        38                               76%                              49.24%                        
                                  12             43.8Kb                   questionable(90)              head,terminase,integrase                     2939670-2983553          1                        39                      37                               1                                97.4%                            1                                yes                              4                                PHAGE_Entero_phiV10                        33                               84.6%                            49.19%                        
                                  13             12.5Kb                   intact(100)                   tail,head,plate,transposase                  3120485-3132999          0                        13                      11                               2                                100%                             0                                no                               4                                PHAGE_Salmon_ST64B                         7                                53.8%                            50.12%                        
                                  14             19.5Kb                   incomplete(40)                tail,transposase                             4816201-4835719          0                        26                      22                               4                                100%                             0                                no                               6                                PHAGE_Burkho_BcepMu                        17                               65.3%                            48.76%                        
                                  15             49.3Kb                   intact(150)                   integrase,lysis,lysin,terminase,portal,protease,tail     5237358-5286739          0                        59                      54                               4                                98.3%                            1                                yes                              13                               PHAGE_Entero_cdtI                          38                               64.4%                            49.76%                        
