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|256276149|ref|ACXN00000000| Escherichia coli O157:H7 str. FRIK966 , whole .5376914, gc%: 50.24% 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 47.8Kb intact(150) integrase,lysis,terminase,portal,capsid,tail,transposase 1734183-1782036 0 44 39 4 97.7% 1 yes 9 PHAGE_Entero_SfV 29 65.9% 49.00% 2 34Kb intact(110) tail,portal,head,terminase,lysin 1926480-1960561 0 26 21 4 96.1% 1 yes 7 PHAGE_Entero_2008 14 53.8% 51.30% 3 24.2Kb incomplete(30) transposase,integrase 2868996-2893231 0 16 14 1 93.7% 1 yes 7 PHAGE_Entero_mEp460 8 50% 45.43% 4 10.2Kb incomplete(60) transposase,tail 3079151-3089415 0 14 8 4 85.7% 2 no 4 PHAGE_Stx2_c_1717 5 35.7% 48.57% 5 22.6Kb intact(93) tail,lysis 3544483-3567093 0 34 30 4 100% 0 no 5 PHAGE_Yersin_413C 25 73.5% 54.37% 6 40.1Kb intact(127) tail,lysis 3537263-3577442 0 48 40 6 95.8% 2 yes 6 PHAGE_Yersin_413C 34 70.8% 52.41% 7 12.9Kb questionable(85) head 3623619-3636523 0 21 17 4 100% 0 no 5 PHAGE_Entero_P4 10 47.6% 52.96% 8 62.7Kb intact(150) transposase,lysin,integrase,tail,head,portal,terminase 3899453-3962220 2 100 67 26 93% 7 yes 23 PHAGE_Entero_HK630 24 24% 49.01% 9 31.5Kb intact(150) integrase,tail,terminase,lysin 4162426-4193934 0 42 24 15 92.8% 3 yes 12 PHAGE_Entero_2008 13 30.9% 49.31% 10 42.5Kb intact(150) plate,tail,integrase,capsid,terminase,head,lysin 4322843-4365391 0 43 29 12 95.3% 2 yes 17 PHAGE_Salmon_RE_2010 11 25.5% 50.21% 11 5.1Kb questionable(70) virion,transposase 4358533-4363638 0 9 8 0 88.8% 1 no 5 PHAGE_Entero_Mu 4 44.4% 50.27% 12 14.4Kb intact(120) tail,protease 4368363-4382803 0 19 17 1 94.7% 1 no 12 PHAGE_Entero_HK106 4 21% 50.92% 13 102.3Kb intact(150) tail,head,portal,terminase,lysin,transposase,virion,protease,plate,envelope,lysis,recombinase,integrase 4505852-4608173 0 155 133 15 95.4% 7 yes 38 PHAGE_Entero_Mu 37 23.8% 50.50% 14 30.1Kb intact(150) transposase,tail,head,integrase 4840598-4870791 0 19 17 0 89.4% 2 yes 4 PHAGE_Entero_HK629 11 57.8% 51.97% 15 8.5Kb incomplete(20) integrase 5104055-5112607 0 6 6 0 100% 0 yes 5 PHAGE_Entero_IME10 2 33.3% 43.00% 16 21.5Kb incomplete(20) integrase 5347666-5369205 2 25 15 7 88% 3 yes 13 PHAGE_Escher_TL_2011c 3 12% 49.21%