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 8 intact prophage regions have been identified. gi|71732930|ref|AAAM00000000.3| Xylella fastidiosa subsp. sandyi Ann-1 whole genome .5115342, gc%: 51.95% 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 22.1Kb questionable(80) lysis,portal,capsid,head,injection 1-22183 0 21 20 0 95.2% 1 no 4 PHAGE_Xylell_Xfas53 17 80.9% 57.51% 2 37.4Kb intact(120) integrase,protease,tail,plate,capsid,portal 111160-148605 0 32 26 0 81.2% 6 yes 16 PHAGE_Burkho_KS14 6 18.7% 53.71% 3 45.7Kb intact(100) tail,lysin,head,portal,terminase,integrase 466242-511974 1 34 21 2 67.6% 11 yes 17 PHAGE_Pseudo_B3 2 5.8% 57.58% 4 31Kb incomplete(30) integrase 1442361-1473414 1 25 21 0 84% 4 yes 8 PHAGE_Xylell_Xfas53 14 56% 53.01% 5 24.5Kb questionable(90) tail,plate,transposase,integrase 1483856-1508370 0 25 22 0 88% 3 yes 6 PHAGE_Haemop_Aaphi23 11 44% 55.40% 6 28.7Kb intact(120) terminase,portal,head,recombinase,lysin,tail,fiber,integrase,transposase 1690707-1719416 0 30 20 3 76.6% 7 yes 13 PHAGE_Stenot_S1 4 13.3% 59.19% 7 37Kb intact(120) lysin,terminase,portal,head,capsid,tail,plate 2374950-2411949 0 49 40 4 89.7% 5 no 18 PHAGE_Haemop_Aaphi23 16 32.6% 55.78% 8 19.7Kb incomplete(20) integrase 3203727-3223524 1 23 18 0 78.2% 5 yes 11 PHAGE_Xylell_Xfas53 7 30.4% 52.48% 9 26.3Kb intact(150) tail,plate,capsid,portal,terminase,lysin 3496611-3522982 0 32 25 0 78.1% 7 no 13 PHAGE_Vibrio_vB_VpaM_MAR 7 21.8% 56.86% 10 25.7Kb questionable(80) lysin,terminase,portal,head,capsid,tail 3599398-3625158 0 33 25 1 78.7% 7 no 13 PHAGE_Haemop_Aaphi23 10 30.3% 57.18% 11 28.5Kb incomplete(20) tail 3635813-3664394 0 8 6 0 75% 2 yes 6 PHAGE_Microm_12T 1 12.5% 51.30% 12 69.8Kb intact(110) integrase,terminase,tail 3681125-3750990 0 65 30 3 50.7% 32 yes 18 PHAGE_Xylell_Xfas53 11 16.9% 54.70% 13 40.5Kb incomplete(30) integrase 4193764-4234289 0 34 30 1 91.1% 3 yes 14 PHAGE_Xylell_Xfas53 17 50% 53.90% 14 11.3Kb intact(107) integrase 4292795-4304184 1 16 10 0 62.5% 6 yes 4 PHAGE_Stenot_phiSMA9 5 31.2% 45.07% 15 14.3Kb questionable(90) injection,head,capsid,portal,lysin 4307794-4322154 0 16 14 0 87.5% 2 no 4 PHAGE_Xylell_Xfas53 11 68.7% 53.07% 16 26.5Kb questionable(80) integrase,tail,plate,protease 4368450-4394961 0 23 18 0 78.2% 5 yes 13 PHAGE_Burkho_KS14 5 21.7% 54.58% 17 32Kb incomplete(40) coat,integrase 4720398-4752460 0 30 18 1 63.3% 11 yes 14 PHAGE_Xylell_Xfas53 3 10% 49.64% 18 18.1Kb incomplete(30) tail,integrase 4766538-4784643 0 7 5 0 71.4% 2 yes 2 PHAGE_Xylell_Xfas53 4 57.1% 53.11% 19 97.7Kb intact(150) fiber,tail,portal,protease,terminase,lysin,plate,capsid,transposase,integrase 4855997-4953727 6 97 46 6 53.6% 45 yes 30 PHAGE_Stenot_phiSMA9 7 7.2% 51.77% 20 20.3Kb incomplete(60) tail,plate,integrase 4962497-4982839 0 16 11 2 81.2% 3 yes 6 PHAGE_Haemop_Aaphi23 5 31.2% 54.93%