Table 5: Detailed evaluation results for PHAST (2011) and PHASTER (2016) run on unannotated genome sequences. Evaluation was made against manual prophage annotations in 54 bacterial genomes from Casjens, S. (2003) Molecular microbiology, 49, 277-300. Prophages predicted by PHASTER that were absent in the evaluation set were manually inspected, and several (marked below with **) were deemed to have good evidence of being true prophages rather than being false positives. =================================================================================== NCBI id: NC_000962 Organism: Mycobacterium tuberculosis H37Rv Gnome size: 4411532 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2970551-2981576 2970065-2980835 2970063-2980833 2970063-2984654 1780643-1788505 FN 1766987-1788115 1766987-1788487 =================================================================================== NCBI id: NC_000913 Organism: Escherichia coli K12 Gnome size: 4639675 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 262552-296320 FN FN FN 2464567-2475651 FN 2465301-2477629 2465301-2477629 2754181-2775804 FN FN FN 564038-584856 563980-585282 564755-586057 564755-586057 1410024-1432281 1409925-1432985 1411899-1434959 1411969-1434812 1196090-1210402 1197865-1215896 1198640-1216671 1198640-1216671 1631063-1650732 1616881-1650732 1627517-1644304 1618855-1653915 2556793-2563354 FN FN FN 2064329-2076158 FN FN FN FALSE POSITIVES 3716547-3722049 =================================================================================== NCBI id: NC_003112 Organism: Neisseria meningitidis MC58 Gnome size: 2272360 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1001560-1005455 998266-1007364 FN FN 1099910-1133980 1099110-1133760 1101164-1133966 1101347-1133966 FALSE POSITIVES 916111-930967 916109-929811 =================================================================================== NCBI id: NC_002947 Organism: Pseudomonas putida KT2440 Gnome size: 6181863 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 4372649-4427414 4375285-4412410 4375283-4412410 4371606-4428763 4417270-4440874 2586633-2625819 2585881-2626121 2586645-2608847 2585879-2626119 3418567-3447235 3401670-3459949 3426049-3447235 3401668-3459947 1738082-1774805 1734865-1780108 1748035-1781069 1734863-1780106 =================================================================================== NCBI id: NC_003902 Organism: Xanthomonas campestris pv. campestris str. ATCC 33913 Gnome size: 5076188 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2435595-2441676 FN 2435792-2454339 2423305-2465700 3523234-3560198 3517532-3560198 3523035-3562020 3517530-3562020 2441850-2447920 FN 2435792-2454339 2423305-2465700 FALSE POSITIVES 1855984-1886789 4258232-4274508 4258232-4274508 5016862-5025976 =================================================================================== NCBI id: NC_002935 Organism: Corynebacterium diphtheriae NCTC 13129 Gnome size: 2488635 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 776521-790960 FN FN FN 2216802-2297805 FN FN FN 1866723-1880855 FN 1863158-1880771 1858843-1893843 154365-190992 151932-190743 151930-190741 154102-190741 =================================================================================== NCBI id: NC_003198 Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18 Gnome size: 4809037 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1888674-1933558 1885617-1927047 1885326-1933598 1885326-1933598 3515470-3548975 3511575-3552602 3504242-3555052 3526926-3550970 1538899-1572919 1538899-1572919 1538899-1572919 1537695-1572919 4473973-4507270 4459146-4507270 4459144-4507514 4462578-4507745 1008747-1052755 1008700-1053062 1008698-1053060 1007350-1053060 4683853-4694545 4683672-4696075 4683670-4696075 4671588-4696873 2760475-2768771 FN FN 2733112-2774301 FALSE POSITIVES 1781177-1787337 1079782-1090874 1781177-1789457 =================================================================================== NCBI id: NC_004337 Organism: Shigella flexneri 2a str. 301 Gnome size: 4607203 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2227585-2235565 2220680-2241353 2220680-2240203 2220679-2240202 238841-251370 236055-252705 236055-252705 235830-252705 899706-918668 899339-921295 899339-921295 890776-939948 311291-328079 306585-340777 306583-340775 306583-340775 2683559-2698944 FN 2684932-2695524 2680672-2695523 1919854-1942697 1916802-1945128 1916802-1946940 1915149-1950501 2049694-2066397 2032769-2079336 2030315-2079334 2032766-2079333 1175319-1188408 1174944-1188408 1174944-1188408 1174811-1200035 1395280-1421884 1373649-1427197 1387236-1407895 1387236-1425018 1401123-1425759 696659-747734 696659-749966 696659-747734 696659-752084 FALSE POSITIVES 2352233-2367765 492546-495944 260070-271129 2950035-2958559 1081687-1103027 1574398-1588276 3051242-3094081 1574398-1580656 1574398-1583708 3687621-3693861 =================================================================================== NCBI id: NC_002967 Organism: Treponema denticola ATCC 35405 Gnome size: 2843201 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1169950-1202411 1164701-1202621 1175279-1214754 1175279-1214754 =================================================================================== NCBI id: NC_002737 Organism: Streptococcus pyogenes M1 GAS Gnome size: 1852441 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 527569-571887 529593-570496 526682-570494 526682-570494 1773458-1782822 FN FN 1773437-1786762 778642-820599 777508-820962 775802-821679 775802-820960 1192854-1222549 1182570-1222912 1182568-1222912 1182568-1225250 =================================================================================== NCBI id: NC_003030 Organism: Clostridium acetobutylicum ATCC 824 Gnome size: 3940880 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2024020-2074254 2017739-2083829 2013351-2078513 2022678-2069772 1277643-1346789 FN 1274369-1283638 1274369-1314892 =================================================================================== NCBI id: NC_003116 Organism: Neisseria meningitidis Z2491 Gnome size: 2184406 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1768546-1807515 1770842-1807515 1768546-1807515 1768546-1804166 1131796-1138899 FN FN FN 1207416-1236260 1211167-1236054 1218293-1236260 1214074-1236260 =================================================================================== NCBI id: NC_004431 Organism: Escherichia coli CFT073 Gnome size: 5231428 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 1169792-1228729 FN FN FN 909332-942273 907025-945470 908948-945468 908948-945468 3019963-3065315 3007214-3065315 3007212-3065315 3009020-3066948 4923133-4929628 FN FN FN 1397370-1452231 1394721-1452257 1394721-1452255 1394721-1452255 1378215-1388952 1327942-1397351 1324666-1381279 1324634-1387552 1327053-1372820 1327942-1397351 1324666-1381279 1324634-1387552 FALSE POSITIVES 244220-257682 244220-265366 ** =================================================================================== NCBI id: NC_004116 Organism: Streptococcus agalactiae 2603V/R Gnome size: 2160267 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1833318-1867117 1816885-1876443 1816883-1876441 1816883-1876441 558254-599207 550500-617296 550498-617294 550498-617294 FALSE POSITIVES 1944854-1978401 =================================================================================== NCBI id: NC_002745 Organism: Staphylococcus aureus subsp. aureus N315 Gnome size: 2814816 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 2005924-2049520 2005721-2052732 2005721-2052732 2005149-2052732 FALSE POSITIVES 2054348-2076507 2054346-2074317 2054346-2074317 ** 1859152-1881615 =================================================================================== NCBI id: NC_002662 Organism: Lactococcus lactis subsp. lactis Il1403 Gnome size: 2365589 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1036642-1071558 1033815-1077533 1033815-1077531 1033815-1077531 502723-513742 502338-520485 502338-517610 498670-520485 35516-49727 28461-56371 28459-56369 28459-56369 1414112-1456949 1414112-1457046 1414112-1457044 1414112-1457044 2013685-2025635 1997701-2028023 1997699-2028023 1997699-2028023 447236-483244 443687-484066 447143-484064 447143-484064 =================================================================================== NCBI id: NC_002516 Organism: Pseudomonas aeruginosa PAO1 Gnome size: 6264404 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 689236-702529 673191-701381 670089-701381 670089-705133 672777-689221 673191-701381 670089-701381 670089-705133 FALSE POSITIVES 780997-796776 780995-796776 780995-796776 ** =================================================================================== NCBI id: NC_005085 Organism: Chromobacterium violaceum ATCC 12472 Gnome size: 4751080 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2303969-2334742 2300705-2344086 2300705-2339162 2285933-2339162 353384-372826 353384-374612 353384-378213 353384-378213 428568-450397 427983-449939 427983-447996 427983-450397 =================================================================================== NCBI id: NC_000964 Organism: Bacillus subtilis subsp. subtilis str. 168 Gnome size: 4214630 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2151284-2285604 2151626-2290857 2151626-2288090 2151626-2288090 2055488-2064044 FN FN FN 2666111-2700582 2653064-2701100 2653062-2701098 2661102-2701754 1320640-1347494 1325096-1348182 1314453-1348182 1314453-1348182 =================================================================================== NCBI id: NC_005362 Organism: Lactobacillus johnsonii NCC 533 Gnome size: 1992676 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 327894-367791 327849-370611 327847-374448 327847-374448 1292553-1330377 1292072-1331686 1287749-1331686 1274090-1331686 =================================================================================== NCBI id: NC_003485 Organism: Streptococcus pyogenes MGAS8232 Gnome size: 1895017 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 293882-332714 283161-348115 277254-332714 277254-332714 1451844-1493373 1443375-1493373 1443373-1493373 1443373-1493373 1041280-1087739 1041280-1088722 1038487-1095615 1038487-1095615 578093-618765 578055-619104 575144-619102 575144-619102 1206360-1241416 1200228-1241780 1200226-1241780 1200226-1244118 =================================================================================== NCBI id: NC_003366 Organism: Clostridium perfringens str. 13 Gnome size: 3031430 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1298199-1327800 1310119-1335464 1310119-1327800 1310119-1327800 =================================================================================== NCBI id: NC_003923 Organism: Staphylococcus aureus subsp. aureus MW2 Gnome size: 2820462 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 2046605-2088749 2036090-2091958 2036088-2091958 2036088-2091958 1529381-1573005 1522195-1584851 1522193-1584849 1522193-1584849 FALSE POSITIVES 836064-854951 836064-853794 826277-860029 ** =================================================================================== NCBI id: NC_005126 Organism: Photorhabdus luminescens subsp. laumondii TTO1 Gnome size: 5688987 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 2552735-2573940 FN FN FN 4190163-4242791 FN FN FN 4340686-4389134 4340329-4385481 4324782-4373679 FN 5175988-5190589 FN FN FN 2088101-2101272 FN FN FN 2800483-2848507 FN FN 2797233-2804653 3774756-3892173 FN FN FN 5201181-5228815 FN 5211071-5239791 FN 4006891-4056690 4007651-4076282 4005528-4094743 3997033-4108102 1267570-1617919 FN FN FN 2331853-2466741 2354852-2390454 2372413-2387799 FN 2955621-2991661 FN FN 2973221-2980853 3409531-3537385 3405940-3468149 3397086-3479941 3397151-3480006 3512834-3535879 3517195-3537385 3512834-3537385 10251-29999 10251-32806 10251-32806 10251-32806 132320-180394 FN FN FN FALSE POSITIVES 490798-502770 3954542-3963528 1785333-1795520 2057383-2065195 1983763-1993171 ** 2035298-2041677 2035298-2041677 ** 5559641-5566514 5559641-5567971 ** =================================================================================== NCBI id: NC_004631 Organism: Salmonella enterica subsp. enterica serovar Typhi Ty2 Gnome size: 4791961 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 4458029-4490856 4446023-4491190 4446021-4491188 4446171-4491331 4671630-4678034 4666561-4678557 4666559-4678557 4654477-4679761 1928058-1972330 1928058-1972330 1927739-1972365 1928058-1973727 2735202-2754628 2734606-2760158 2734604-2760158 2734604-2760158 1314607-1441766 1408218-1441766 1408218-1441766 1394712-1441766 3501128-3538076 3497233-3538262 3489900-3540712 3512586-3536675 FALSE POSITIVES 1193795-1199955 1193795-1199955 =================================================================================== NCBI id: NC_003143 Organism: Yersinia pestis CO92 Gnome size: 4653728 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 964013-971311 FN 954442-989832 FN 1392489-1416524 FN FN 1392489-1410182 1233128-1243405 FN FN FN 2554373-2563203 FN FN FN 2363019-2413098 2362962-2404686 2362960-2404684 2362960-2404684 2115626-2122603 FN 2111358-2140547 2111358-2140547 FALSE POSITIVES 1807069-1816414 2965961-2980785 =================================================================================== NCBI id: NC_004668 Organism: Enterococcus faecalis V583 Gnome size: 3218031 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1398097-1443843 1398053-1447105 1398051-1446151 1398051-1447105 2817287-2829554 FN FN FN 2004910-2048146 2021650-2049919 2001579-2020730 2023234-2049919 2023234-2049919 1245337-1259965 1242193-1259965 1245337-1259965 1245337-1259965 2700666-2736808 2697272-2736808 2697272-2736808 2697272-2741423 1923000-1962485 1925423-1948114 1925423-1948114 1925423-1962485 289354-326185 288968-332966 288966-332964 288966-332964 FALSE POSITIVES 2537668-2551243 551891-566251 =================================================================================== NCBI id: NC_003295 Organism: Ralstonia solanacearum GMI1000 Gnome size: 3716413 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2084602-2124346 2080692-2125142 2084443-2125140 2084443-2125140 1003644-1018473 FN FN FN 1781995-1823953 1782598-1838886 1798179-1821238 1797957-1821238 2049204-2056036 FN FN FN 3486521-3505550 FN FN FN 2684129-2695788 FN FN FN 1591303-1598986 FN FN FN 879632-939437 879632-899438 887600-899438 887600-899438 FALSE POSITIVES 3456925-3462472 =================================================================================== NCBI id: NC_003155 Organism: Streptomyces avermitilis MA-4680 Gnome size: 9025608 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 6670511-6721444 6673473-6693625 6678303-6693625 6678303-6695725 =================================================================================== NCBI id: NC_004347 Organism: Shewanella oneidensis MR-1 Gnome size: 4969803 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2788307-2822836 2788307-2822836 2788307-2822836 2788307-2822836 669361-703908 668166-708836 655830-720989 655830-720989 3075409-3126249 3076443-3126351 3076443-3126349 3076443-3126349 FALSE POSITIVES 4434306-4457138 382765-406810 =================================================================================== NCBI id: NC_004741 Organism: Shigella flexneri 2a str. 2457T Gnome size: 4599354 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 238511-254700 235184-256034 235184-256034 234959-256034 1177837-1191596 1177792-1192294 1177790-1192292 1177790-1194524 1614219-1620622 1612770-1624438 1612770-1627925 1612770-1627925 2021895-2044342 2012871-2061855 2006995-2054672 2009447-2054672 313843-327223 309137-339911 309135-339909 309135-339909 1912634-1921793 1872285-1932001 1893682-1923605 1898583-1932798 710297-746123 692891-748184 692891-748184 692891-748241 1901037-1921793 1872285-1932001 1881581-1903815 1881581-1903815 1893682-1923605 1898583-1932798 897790-930670 893482-918345 893482-918345 890253-918345 915755-943797 915753-943795 2678519-2687517 2674260-2688968 2678519-2688968 2674260-2688968 1100131-1105919 FN 1084465-1105919 1084465-1105919 692891-709118 692891-748184 692891-748184 692891-748241 FALSE POSITIVES 2047401-2074125 492349-495747 2058418-2071061 2201408-2220775 2058418-2071061 2201408-2219625 2331690-2347222 2201408-2219625 2586518-2613924 2594187-2620410 4081357-4087597 =================================================================================== NCBI id: NC_004088 Organism: Yersinia pestis KIM Gnome size: 4600755 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2693615-2700576 2676241-2705460 2676239-2705458 2682145-2708206 3389410-3399754 FN FN FN 3595228-3601343 FN 3584471-3619864 FN 2417129-2456467 2415700-2456467 2415700-2456467 2415700-2456467 3237524-3255252 FN FN 3237524-3255252 FALSE POSITIVES 1362250-1377108 =================================================================================== NCBI id: NC_004556 Organism: Xylella fastidiosa Temecula1 Gnome size: 2519802 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2005731-2020421 2004606-2022616 2005890-2022616 FN 1847752-1855582 FN FN FN 1161143-1217907 1161143-1180387 1161143-1180387 1161143-1180387 1170407-1224505 1194458-1217907 1180582-1226126 1117952-1142627 1128432-1143339 1132387-1143339 1117952-1143372 454017-467611 450846-469025 446956-480065 450825-469025 1288547-1392763 1288547-1331541 1288023-1331541 1288547-1331541 1362504-1398130 1362502-1398128 1372023-1401198 1550281-1556188 FN FN FN FALSE POSITIVES 942607-968324 =================================================================================== NCBI id: NC_003997 Organism: Bacillus anthracis str. Ames Gnome size: 5227293 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 447387-484339 442051-487498 442049-487496 442049-487496 3745958-3791042 3743583-3795491 3743581-3795489 3743581-3795489 3456916-3505685 3452696-3517428 3452694-3517426 3453806-3485787 3488693-3522745 4842149-4858240 4845037-4858240 4845035-4859679 4845035-4859679 =================================================================================== NCBI id: NC_004578 Organism: Pseudomonas syringae pv. tomato str. DC3000 Gnome size: 6397126 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 4515380-4530373 4505490-4530373 4505488-4530373 4505488-4530373 4528890-4566113 625118-647483 FN 623546-651202 623546-651202 2252628-2264999 FN 2253004-2271122 2253004-2271122 3824683-3865352 3825217-3859789 3825215-3859787 3824685-3865355 4543843-4563495 4531874-4564742 4531872-4566113 4528890-4566113 FALSE POSITIVES 4442166-4460297 4442166-4460297 4442166-4460297 ** =================================================================================== NCBI id: NC_004567 Organism: Lactobacillus plantarum WCFS1 Gnome size: 3308274 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 590128-633804 589964-631772 589608-631770 589962-631770 2161732-2203820 2156168-2225486 2157270-2197761 2163796-2218520 2188411-2232769 2998563-3007280 FN FN FN 2204171-2218342 2156168-2225486 2188411-2232769 2163796-2218520 FALSE POSITIVES 1083489-1105634 =================================================================================== NCBI id: NC_002488 Organism: Xylella fastidiosa 9a5c Gnome size: 2679306 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 489619-530138 486958-528483 486956-528481 486956-528481 2008224-2022372 2005406-2022394 2006087-2024354 2006087-2024354 649115-690375 647699-697035 647699-697033 647699-697033 2361812-2404268 2358989-2416179 2361812-2388777 2349016-2412964 2177071-2183135 2176140-2198391 2170954-2199787 FN 1514347-1541075 1500396-1549341 1514344-1557570 1500394-1549339 1585980-1631056 1585875-1640907 1585873-1640907 1574065-1646561 FALSE POSITIVES 1776441-1788720 =================================================================================== NCBI id: NC_002678 Organism: Mesorhizobium loti MAFF303099 Gnome size: 7036071 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 6975631-7011591 6975487-7020725 6975231-7011108 6975485-7020723 313639-359457 313234-360978 321147-347654 321147-347654 6587513-6595756 FN 6592538-6608727 6592538-6615456 FALSE POSITIVES 4868226-4896693 4803034-4831740 4865354-4893831 4868224-4896691 =================================================================================== NCBI id: NC_003210 Organism: Listeria monocytogenes EGD-e Gnome size: 2944528 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2361897-2400243 2360908-2403235 2360908-2403235 2360714-2403235 120654-131380 120654-136290 120654-131380 116972-131380 FALSE POSITIVES 166687-174556 =================================================================================== NCBI id: NC_002695 Organism: Escherichia coli O157:H7 str. Sakai Gnome size: 5498450 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2158314-2203914 2156899-2247603 2153413-2254887 2153413-2254351 300072-310238 300054-324555 291210-317713 285544-328827 1161297-1210641 1161098-1210748 1159810-1178581 1159810-1210746 1180157-1209126 5041093-5079469 5041093-5082381 5042064-5079469 5042064-5079469 1245217-1308182 1245905-1316399 1245903-1316397 1245903-1316397 1921472-1970014 1921443-1972369 1921441-1972367 1921441-1972367 2896151-2943747 2888774-2947429 2888774-2947429 2888774-2946279 3480256-3505039 3479659-3500191 3479657-3500189 3452715-3498417 310806-324405 300054-324555 291210-317713 285544-328827 892240-929292 891110-929696 891108-929694 891108-929694 1594751-1609184 1586046-1621990 1586046-1621988 1586046-1623575 1541626-1589842 1541512-1591832 1538645-1591830 1538645-1591830 1586046-1621990 1586046-1621988 1586046-1623575 3193144-3200085 3192962-3201514 3191900-3201512 3190520-3204375 2593128-2612026 2592961-2614081 2592106-2616977 2592106-2616977 2667460-2713016 2668009-2712038 2668007-2712036 2668007-2712036 1618212-1665394 1586046-1621990 1586046-1621988 1586046-1623575 1609998-1656531 1615552-1666524 1615552-1666524 1756865-1804219 1770296-1823989 1757549-1814804 1757549-1814804 2211826-2254161 2156899-2247603 2153413-2254887 2153413-2254351 FALSE POSITIVES 1437802-1446999 =================================================================================== NCBI id: NC_004307 Organism: Bifidobacterium longum NCC2705 Gnome size: 2256640 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1298692-1312867 1288884-1312690 1288882-1312690 1288882-1312867 =================================================================================== NCBI id: NC_004310 Organism: Brucella suis 1330 Gnome size: 2107794 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 578085-584879 578497-592232 578497-592232 578473-593729 =================================================================================== NCBI id: NC_003212 Organism: Listeria innocua Clip11262 Gnome size: 3011208 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 78505-114250 74218-115503 74218-115501 74218-115501 155931-166661 151526-171570 151526-166661 149752-166661 2407382-2445891 2405898-2462230 2406426-2446744 2406426-2446744 1246563-1294235 1245851-1297056 1245851-1297054 1240803-1297008 2591482-2625807 2580954-2629862 2580952-2629860 2580952-2629860 1713958-1762089 1710191-1767458 1710189-1767456 1710189-1767456 =================================================================================== NCBI id: NC_003197 Organism: Salmonella typhimurium LT2 Gnome size: 4857432 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 2728976-2776816 2729000-2776892 2731822-2776890 2715700-2780003 962612-1006517 961043-1003236 961043-1006517 961043-1002017 2042050-2059909 FN FN FN 2844427-2879233 2844267-2879414 2844265-2879414 2834592-2882784 2330961-2345217 2327474-2344711 2330961-2345217 2330961-2345217 4417918-4438335 4417918-4438335 4417918-4438335 4417918-4438335 1098228-1143714 1098181-1144022 1098179-1144020 1096831-1144020 FALSE POSITIVES 1957835-1973856 1957835-1971770 1957835-1971770 ** =================================================================================== NCBI id: NC_004557 Organism: Clostridium tetani E88 Gnome size: 2799251 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1138054-1181003 1137606-1171268 1137606-1185305 1137606-1188667 1663821-1696302 1651670-1710164 1657696-1693071 1657696-1693071 2242455-2281387 2243717-2282092 2232193-2282092 2237704-2282092 =================================================================================== NCBI id: NC_000907 Organism: Haemophilus influenzae Rd KW20 Gnome size: 1830138 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 1559962-1594275 1558774-1597183 1558774-1597183 1558774-1597183 1499076-1513073 1495051-1513250 1495049-1513250 1495049-1513073 FALSE POSITIVES 1636791-1643216 1636791-1643216 ** =================================================================================== NCBI id: NC_002570 Organism: Bacillus halodurans C-125 Gnome size: 4202352 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 10970-22161 FN FN 10970-22161 1381009-1384348 FN FN FN 1028696-1039160 1025611-1043075 1025611-1043075 1025611-1043075 3617919-3652122 3625321-3655581 3606875-3658248 3606875-3658248 FALSE POSITIVES 3783921-3800789 =================================================================================== NCBI id: NC_004070 Organism: Streptococcus pyogenes MGAS315 Gnome size: 1900521 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1313282-1351250 1313282-1354214 1313282-1354212 1313194-1351386 749213-788176 742916-788642 742914-788640 742914-793050 1137743-1171867 1131000-1172231 1130998-1172231 1130998-1174569 1410725-1450458 1410544-1452968 1410542-1452968 1398706-1455520 977738-1018193 977437-1019176 974608-1026068 974608-1026068 1230304-1271815 1227589-1283430 1227589-1283428 1227589-1283428 =================================================================================== NCBI id: NC_004722 Organism: Bacillus cereus ATCC 14579 Gnome size: 5411809 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1805567-1866036 1803337-1866036 1803335-1866036 1803335-1866036 2531805-2565093 2520846-2580417 2520823-2579367 2520823-2579367 2355784-2369311 FN FN FN 3660466-3668825 3657003-3668825 3655937-3668825 3657054-3681623 FALSE POSITIVES 5089874-5096462 =================================================================================== NCBI id: NC_002978 Organism: Wolbachia endosymbiont of Drosophila melanogaster Gnome size: 1267782 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 567453-582561 548107-572145 548107-573485 548107-573485 572259-584372 245829-275225 236216-278994 236214-278992 235113-279194 551654-558625 548107-572145 548107-573485 548107-573485 623343-634537 626322-642427 626320-642425 626320-642425 FALSE POSITIVES 437078-443628 =================================================================================== NCBI id: NC_002655 Organism: Escherichia coli O157:H7 EDL933 Gnome size: 5528445 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1879335-1897622 1862359-1931572 1862359-1935058 1849488-1947048 3551577-3565707 3549508-3567481 3549506-3567479 3522564-3565707 2966382-3015014 2961049-3018696 2961049-3018696 2959005-3017546 2668339-2688870 2668172-2689292 2667317-2692188 2667317-2692188 2285976-2330172 2272363-2331832 2272753-2330172 2275684-2342415 300073-310251 300055-324556 291211-317714 285545-328828 1897625-1908911 1862359-1931572 1862359-1935058 1849488-1947048 1702185-1725748 1693971-1748316 1699525-1757930 1699525-1757930 310756-323112 300055-324556 291211-317714 285545-328828 1250521-1295458 1250321-1295565 1249033-1295563 1249033-1295563 1330857-1391923 1330722-1400171 1330720-1400169 1330720-1400169 1678706-1693737 1678682-1693909 1683407-1692862 1655548-1696145 1849488-1879269 1862359-1931572 1862359-1935058 1849488-1947048 1909139-1930250 1862359-1931572 1862359-1935058 1849488-1947048 892845-930943 892759-931347 892757-931345 892757-931345 1730065-1756006 1693971-1748316 1699525-1757930 1699525-1757930 1626722-1673485 1626608-1675808 1623741-1675806 1623741-1675806 1655548-1696145 2743223-2788348 2743226-2788403 2743224-2788401 2743224-2788401 2118738-2165694 2107529-2165694 2107527-2165694 2116354-2148177 3263064-3270404 3262918-3271470 3261856-3271468 3260476-3274334 FALSE POSITIVES 1125968-1135165 1521574-1530771 =================================================================================== NCBI id: NC_004606 Organism: Streptococcus pyogenes SSI-1 Gnome size: 1894275 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1107957-1147543 1098748-1161350 1098746-1161348 1098746-1161348 725017-759141 724653-759313 724653-759311 722315-759311 446427-486160 443902-486333 443902-486331 443902-486331 625070-666334 624977-669296 623853-669296 623853-669296 545636-583603 545489-583680 545487-583678 545487-583678 878690-919064 877707-924830 877707-924828 877707-924828 =================================================================================== NCBI id: NC_002758 Organism: Staphylococcus aureus subsp. aureus Mu50 Gnome size: 2878529 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 917507-962565 917452-961932 910703-961979 911668-978880 2083515-2126110 2084317-2129322 2082980-2129322 2084317-2129322 2124924-2152937 2124922-2150747 2124922-2150747 FALSE POSITIVES 865041-882822 854223-895164 ** 1936945-1959408 =================================================================================== NCBI id: NC_003919 Organism: Xanthomonas axonopodis pv. citri str. 306 Gnome size: 5175554 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 3105263-3115868 3081511-3127794 3081509-3127792 3081509-3127792 1211424-1228677 FN 1209301-1229038 1209301-1229038 ===================================================================================