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 3 intact prophage regions have been identified.




gi|188518722|ref|CP000967.1|  Xanthomonas oryzae pv. oryzae PXO99A, complete genome. .5240075, gc%: 63.63%
                                  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              11.6Kb                   incomplete(50)                transposase,tail                             309399-321091            0                        11                      8                                0                                72.7%                            3                                no                               7                                PHAGE_Parame_1                             2                                18.1%                            66.55%                        
                                  2              9.1Kb                    questionable(80)              plate,transposase                            1477498-1486682          0                        7                       6                                0                                85.7%                            1                                no                               4                                PROPHAGE_Xantho_33913                      3                                42.8%                            58.69%                        
                                  3              7.2Kb                    questionable(80)              transposase,envelope                         2027140-2034383          0                        8                       6                                1                                87.5%                            1                                no                               4                                PROPHAGE_Mesorh_MAFF303099                 2                                25%                              60.48%                        
                                  4              12.6Kb                   questionable(90)              tail,transposase,lysin                       2224112-2236785          1                        11                      8                                1                                81.8%                            2                                no                               5                                PROPHAGE_Xantho_33913                      4                                36.3%                            63.32%                        
                                  5              11.8Kb                   questionable(70)              transposase,plate                            2653417-2665315          0                        10                      8                                0                                80%                              2                                no                               7                                PROPHAGE_Xantho_33913                      2                                20%                              60.03%                        
                                  6              11.8Kb                   questionable(70)              transposase,plate                            2865504-2877402          0                        10                      8                                0                                80%                              2                                no                               7                                PROPHAGE_Xantho_33913                      2                                20%                              60.03%                        
                                  7              48.5Kb                   intact(130)                   capsid,terminase,tail,lysin,plate,integrase     3523194-3571728          0                        44                      30                               3                                75%                              11                               yes                              10                               PHAGE_Burkho_KS14                          16                               36.3%                            62.02%                        
                                  8              8Kb                      questionable(70)              transposase                                  3737859-3745860          0                        10                      6                                1                                70%                              3                                no                               4                                PROPHAGE_Brucel_1330                       2                                20%                              62.23%                        
                                  9              5.8Kb                    incomplete(60)                protease,transposase                         4329352-4335220          1                        7                       6                                0                                85.7%                            1                                no                               4                                PROPHAGE_Xantho_33913                      3                                42.8%                            61.48%                        
                                  10             22.4Kb                   intact(150)                   transposase                                  4407677-4430145          0                        29                      21                               0                                72.4%                            8                                no                               3                                PROPHAGE_Xantho_33913                      15                               51.7%                            61.55%                        
                                  11             9.1Kb                    questionable(70)              transposase,tail                             4784804-4793974          0                        11                      8                                1                                81.8%                            2                                no                               6                                PROPHAGE_Xantho_33913                      3                                27.2%                            63.93%                        
                                  12             22.7Kb                   questionable(90)              transposase,tail                             4801493-4824241          0                        13                      10                               1                                84.6%                            2                                yes                              8                                PROPHAGE_Xantho_33913                      3                                23%                              61.58%                        
                                  13             21.3Kb                   intact(130)                   virion,protease,transposase                  5061642-5083038          0                        18                      12                               0                                66.6%                            6                                yes                              7                                PROPHAGE_Xantho_33913                      5                                27.7%                            62.05%                        
