gi|342360612|ref|AE005674.2| Shigella flexneri 2a str. 301, complete genome. .4607202, GC%: 50.89%, length = 4607202 bps

Total : 13 prophage regions have been identified, of which 8 regions are intact, 2 regions are incomplete, 3 regions are questionable.
REGIONREGION_LENGTHCOMPLETENESSSCORE#CDSREGION_POSITIONPOSSIBLE PHAGEGC_PERCENTAGEDETAIL
1 16.8Kb intact 140 20 235830-252705 PHAGE_Entero_IME10_NC_019501, ...... 51.43% Detail
2 42.3Kb intact 150 31 304245-346620 PHAGE_Shigel_SfII_NC_021857, ...... 47.86% Detail
3 55.5Kb intact 150 64 696659-752195 PHAGE_Gifsy_1_NC_010392, ...... 52.28% Detail
4 20Kb intact 150 28 898668-918668 PHAGE_Pectob_ZF40_NC_019522, ...... 49.69% Detail
5 14.4Kb questionable 90 16 1174910-1189400 PHAGE_Shigel_SfIV_NC_022749, ...... 50.67% Detail
6 20.6Kb intact 120 28 1387236-1407895 PHAGE_Stx2_converting_I_NC_003525, ...... 50.22% Detail
7 17Kb questionable 90 20 1409936-1426965 PHAGE_Entero_BP_4795_NC_004813, ...... 48.68% Detail
8 31.7Kb intact 150 33 1915149-1946939 PHAGE_Entero_mEp460_NC_019716, ...... 52.59% Detail
9 55.4Kb intact 150 45 2030314-2085766 PHAGE_Shigel_SfIV_NC_022749, ...... 48.22% Detail
10 11.3Kb questionable 80 12 2229978-2241352 PHAGE_Entero_P1_NC_005856, ...... 52.42% Detail
11 10.5Kb intact 100 13 2684931-2695523 PHAGE_Aeromo_vB_AsaM_56_NC_019527, ...... 49.77% Detail
12 8.1Kb incomplete 40 4115337-4123496 PHAGE_Ectoca_siliculosus_virus_1_NC_002687, ...... 52.32% Detail
13 14.6Kb incomplete 60 16 4505106-4519772 PHAGE_Cronob_vB_CsaM_GAP32_NC_019401, ...... 52.91% Detail
Legend:
REGION: the number assigned to the region
REGION_LENGTH: the length of the sequence of that region (in bp)
COMPLETENESS: a prediction of whether the region contains a intact or incomplete prophage based on the above criteria
SCORE: the score of the region based on the above criteria
#CDS: the number of coding sequnce
REGION_POSITION: the start and end positions of the region on the bacterial chromosome
PHAGE: the phage with the highest number of proteins most similar to those in the region
GC_PERCENTAGE: the percentage of gc nucleotides of the region
DETAIL: detail info of the region


txt file for download


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.