Table 4: Detailed evaluation results for PHAST (2011) and PHASTER (2016) run on GenBank annotated genomes. 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 2970065-2983874 2970063-2983874 2970063-2984654 1780643-1788505 1766989-1788505 1766987-1788505 1766987-1788505 =================================================================================== NCBI id: NC_000913 Organism: Escherichia coli K12 Gnome size: 4639675 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 262552-296320 262124-296432 262898-297206 262898-297719 2464567-2475651 2464378-2475651 2465301-2477629 2465301-2477629 2754181-2775804 2753821-2780748 2754896-2777782 2746434-2777782 564038-584856 563980-585282 564755-586057 564755-586057 1410024-1432281 1404587-1432838 1395952-1435051 1395952-1435051 1196090-1210402 1191881-1218961 1196867-1216671 1196867-1216671 1631063-1650732 1631063-1662537 1619557-1656744 1619557-1656744 2556793-2563354 FN FN 2558575-2567625 2064329-2076158 FN FN 2068952-2082547 FALSE POSITIVES 3716547-3722049 4505466-4540762 4491197-4548442 4491197-4548442 ** =================================================================================== NCBI id: NC_003112 Organism: Neisseria meningitidis MC58 Gnome size: 2272360 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1001560-1005455 998362-1007364 FN FN 1099910-1133980 1101164-1133760 1101164-1133760 1101164-1133760 =================================================================================== NCBI id: NC_002947 Organism: Pseudomonas putida KT2440 Gnome size: 6181863 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 4372649-4427414 4375285-4412410 4375283-4415646 4371606-4427497 4405478-4435736 2586633-2625819 2586633-2625819 FN 2586633-2625819 3418567-3447235 3411568-3447570 3411566-3447568 3411566-3447568 1738082-1774805 1748226-1781071 1734863-1780106 1748226-1781069 =================================================================================== NCBI id: NC_003902 Organism: Xanthomonas campestris pv. campestris str. ATCC 33913 Gnome size: 5076188 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2435595-2441676 2423307-2465702 2423305-2465700 2423305-2465700 3523234-3560198 3517532-3560198 3523035-3562020 3517530-3562020 2441850-2447920 2423307-2465702 2423305-2465700 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 1863158-1880855 1858843-1880989 154365-190992 151932-190743 151930-190741 151930-190741 =================================================================================== NCBI id: NC_003198 Organism: Salmonella enterica subsp. enterica serovar Typhi str. CT18 Gnome size: 4809037 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1888674-1933558 1879228-1939495 1879226-1937407 1879226-1937407 3515470-3548975 3511575-3552602 3504242-3555052 3504242-3555052 1538899-1572919 1538899-1572919 1538899-1572919 1528904-1575847 4473973-4507270 4462430-4507604 4462428-4507602 4462428-4507602 1008747-1052755 1008700-1053062 1008698-1053060 1005402-1057040 4683853-4694545 4683672-4695076 4683670-4695074 4683670-4695074 2760475-2768771 FN FN 2733112-2774301 =================================================================================== NCBI id: NC_004337 Organism: Shigella flexneri 2a str. 301 Gnome size: 4607203 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2227585-2235565 FN 2229979-2240203 2229979-2240203 238841-251370 235830-252705 235830-252705 235830-252705 899706-918668 898668-918668 898668-918668 895439-918668 311291-328079 306585-340777 306583-340775 306583-340775 2683559-2698944 2680811-2695524 2684932-2695524 2684932-2695524 1919854-1942697 1915150-1945164 1915150-1946940 1915150-1950502 2049694-2066397 2032769-2079336 2030315-2079334 2032767-2079334 1175319-1188408 1174912-1189402 1174910-1189400 1174811-1200035 1395280-1421884 1387236-1426965 1387236-1407895 1387236-1407895 1409936-1425018 1409936-1425018 696659-747734 696659-752084 696659-752084 696659-752084 FALSE POSITIVES 1081687-1103027 260070-274057 =================================================================================== 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 1773439-1786764 1773437-1786762 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 2013351-2078513 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 1768546-1807515 1131796-1138899 1129591-1138899 1129591-1138899 FN 1207416-1236260 1214074-1225850 FN 1214074-1236054 =================================================================================== 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 3007212-3065718 3009020-3066948 4923133-4929628 FN FN FN 1397370-1452231 1394721-1452257 1394721-1452255 1394721-1452255 1378215-1388952 1377875-1389094 1377873-1389092 1377873-1389092 1327053-1372820 1327916-1375035 1327914-1375035 1327914-1375035 FALSE POSITIVES 4955800-4971387 236993-283987 ** 4961854-4967870 ** =================================================================================== 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 554829-600594 554829-601907 554829-600594 FALSE POSITIVES 1944858-1978401 =================================================================================== 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 ** =================================================================================== NCBI id: NC_002662 Organism: Lactococcus lactis subsp. lactis Il1403 Gnome size: 2365589 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1036642-1071558 1033815-1079175 1033815-1079173 1033815-1079173 502723-513742 502338-520485 502338-520485 498649-520485 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 443651-484066 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 673191-703058 670089-703058 670089-705133 672777-689221 673191-703058 670089-703058 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 2300705-2339162 2300705-2339162 2285933-2339162 353384-372826 353384-374417 353384-378213 353384-378213 428568-450397 427983-450397 427983-450397 427983-450397 =================================================================================== NCBI id: NC_000964 Organism: Bacillus subtilis subsp. subtilis str. 168 Gnome size: 4214630 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2151284-2285604 2144356-2286435 2146013-2288062 2146013-2288062 2055488-2064044 2060009-2065377 2055868-2065377 FN 2666111-2700582 2653064-2701100 2653062-2701098 2653104-2714712 1320640-1347494 1314453-1348182 1314453-1348182 1314453-1348182 FALSE POSITIVES 528129-549873 724913-774196 1899589-1919395 =================================================================================== 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 272736-351522 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 1200228-1241416 1200226-1241416 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 826277-860029 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 FN FN 4006891-4056690 4007651-4076282 4005528-4094743 3997033-4108102 1267570-1617919 FN FN FN 2331853-2466741 2354923-2387906 FN FN 2955621-2991661 FN FN 2973221-2980853 3409531-3537385 3405940-3468149 3397151-3480006 3397151-3480006 3512834-3535879 3517195-3537385 3512834-3537385 10251-29999 10251-32806 10251-32806 10251-32806 132320-180394 FN FN FN FALSE POSITIVES 4080520-4099672 490798-502770 2057383-2065195 1785333-1795520 3954542-3963528 1983763-1993171 ** 5091596-5102153 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 4446021-4491188 4671630-4678034 4666561-4677964 4666559-4677962 4666559-4677962 1928058-1972330 1928058-1972330 1928058-1972330 1928058-1973727 2735202-2754628 2735079-2771942 2734604-2759926 2735077-2771940 1314607-1441766 1408218-1441766 1408218-1441766 1394712-1441766 3501128-3538076 3497233-3538262 3489900-3540712 3489900-3540712 =================================================================================== NCBI id: NC_003143 Organism: Yersinia pestis CO92 Gnome size: 4653728 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 964013-971311 FN FN FN 1392489-1416524 FN FN 1392489-1410182 1233128-1243405 1219764-1253174 1219762-1253172 1219762-1253172 2554373-2563203 FN 2555162-2562034 FN 2363019-2413098 2364324-2376936 2364324-2404493 2364324-2376936 2379304-2404493 2379304-2404493 2115626-2122603 FN 2115553-2124318 2115553-2124318 FALSE POSITIVES 2961771-2991168 =================================================================================== NCBI id: NC_004668 Organism: Enterococcus faecalis V583 Gnome size: 3218031 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1398097-1443843 1398053-1447105 1398051-1447105 1398051-1447105 2817287-2829554 2815980-2832090 2815978-2832090 FN 2004910-2048146 2002278-2020730 2001579-2020730 2023234-2049919 2021650-2049919 2023234-2049919 1245337-1259965 1242193-1259965 1245337-1259965 1245337-1259965 2700666-2736808 2697272-2736808 2697272-2736808 2697272-2741423 1923000-1962485 1933729-1948114 1933729-1948114 1925423-1962485 289354-326185 288968-332966 288966-332964 288966-332964 =================================================================================== 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 1781782-1824226 1797957-1821238 1797957-1821238 2049204-2056036 FN FN FN 3486521-3505550 FN 3479557-3495896 3479557-3495896 2684129-2695788 FN FN FN 1591303-1598986 FN FN FN 879632-939437 879632-899438 883334-899438 889905-918732 =================================================================================== NCBI id: NC_003155 Organism: Streptomyces avermitilis MA-4680 Gnome size: 9025608 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 6670511-6721444 6673473-6695725 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 3069342-3114478 3069340-3114921 3069340-3114921 FALSE POSITIVES 4434240-4452493 =================================================================================== NCBI id: NC_004741 Organism: Shigella flexneri 2a str. 2457T Gnome size: 4599354 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 238511-254700 234959-256034 234959-256034 234959-256034 1177837-1191596 1177792-1192294 1177790-1192292 1177790-1194524 1614219-1620622 1612576-1617991 1612576-1617991 1612576-1623357 1619869-1623357 1619869-1623357 2021895-2044342 2013831-2041709 2003138-2057970 2009447-2054672 313843-327223 309137-339911 309135-339909 309135-339909 1912634-1921793 1872285-1932001 1872283-1931999 1884346-1939440 710297-746123 692891-746123 692891-743892 692891-743892 1901037-1921793 1872285-1932001 1872283-1931999 1884346-1939440 897790-930670 893482-915474 893482-915474 893482-915474 912202-952163 2678519-2687517 2674398-2688968 2674398-2688968 2674398-2688968 1100131-1105919 1084467-1105919 1084465-1105919 FN 692891-709118 692891-746123 692891-743892 692891-743892 FALSE POSITIVES 2201408-2208976 263399-276609 2211660-2219625 2201408-2219625 =================================================================================== NCBI id: NC_004088 Organism: Yersinia pestis KIM Gnome size: 4600755 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2693615-2700576 2691227-2700576 2691227-2700576 2691227-2701262 3389410-3399754 3389138-3410723 3381641-3415033 3371060-3417396 3595228-3601343 FN FN FN 2417129-2456467 2415700-2456467 2415700-2456467 2415700-2456467 3237524-3255252 3237524-3247743 3237524-3247743 3237524-3255252 =================================================================================== NCBI id: NC_004556 Organism: Xylella fastidiosa Temecula1 Gnome size: 2519802 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2005731-2020421 2005731-2022616 2005731-2022616 FN 1847752-1855582 FN FN FN 1161143-1217907 1161143-1180387 1161143-1180387 1161143-1180387 1189753-1221390 1189751-1221388 1189751-1221388 1117952-1142627 1117952-1143372 1128417-1143372 1117952-1143372 454017-467611 450825-469025 450825-469025 450825-469025 1288547-1392763 1288547-1331541 1288023-1331541 1288547-1331541 1361920-1394823 1361918-1394821 1361918-1394821 1550281-1556188 FN FN FN FALSE POSITIVES 941347-956040 941347-956040 =================================================================================== NCBI id: NC_003997 Organism: Bacillus anthracis str. Ames Gnome size: 5227293 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 447387-484339 447158-484420 447156-484418 447156-484418 3745958-3791042 3743583-3795998 3743581-3795996 3743581-3795996 3456916-3505685 3451329-3524720 3451327-3524718 3452750-3491969 3489410-3514488 4842149-4858240 4845037-4858240 4828728-4859679 4828728-4859679 FALSE POSITIVES 1182398-1196378 =================================================================================== NCBI id: NC_004578 Organism: Pseudomonas syringae pv. tomato str. DC3000 Gnome size: 6397126 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 4515380-4530373 4528892-4563495 4505488-4530373 4505488-4530373 4528890-4566113 4528890-4566113 625118-647483 FN 628136-656971 628136-656971 2252628-2264999 2253746-2271122 2253004-2271122 2253004-2271122 3824683-3865352 3824687-3865357 3824685-3865355 3824685-3865355 4543843-4563495 4528892-4563495 4528890-4566113 4528890-4566113 FALSE POSITIVES 4443121-4460297 4443121-4460297 ** =================================================================================== NCBI id: NC_004567 Organism: Lactobacillus plantarum WCFS1 Gnome size: 3308274 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 590128-633804 589964-633123 589608-633123 589962-633123 2161732-2203820 2156168-2225486 2156166-2225484 2156166-2225484 2998563-3007280 2983802-3011139 2983800-3011137 2983800-3011137 2204171-2218342 2156168-2225486 2156166-2225484 2156166-2225484 FALSE POSITIVES 1083489-1105634 =================================================================================== NCBI id: NC_002488 Organism: Xylella fastidiosa 9a5c Gnome size: 2679306 bp ................................................................................... reference PHAST PHASTER PHASTEST (** = likely true positive) ................................................................................... 489619-530138 497039-523687 506050-523687 486956-528481 2008224-2022372 FN 2006087-2024354 2006087-2024354 649115-690375 647732-697035 647732-697033 647732-697033 2361812-2404268 2351906-2408259 2348689-2388777 2351904-2408257 2177071-2183135 2176140-2198391 2157002-2184206 FN 1514347-1541075 1514347-1540790 1514344-1557570 1504154-1558164 1585980-1631056 1585875-1640907 1585873-1640907 1585873-1640907 FALSE POSITIVES 1779582-1788942 1779582-1788942 ** 2638610-2658009 ** =================================================================================== 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 318704-347654 321147-347654 321147-347654 6587513-6595756 FN 6592538-6608727 6572121-6619689 FALSE POSITIVES 4803034-4831740 4872758-4911592 =================================================================================== NCBI id: NC_003210 Organism: Listeria monocytogenes EGD-e Gnome size: 2944528 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2361897-2400243 2360908-2403235 2360908-2403235 2360908-2403235 120654-131380 120654-136290 120654-131380 116972-131380 =================================================================================== NCBI id: NC_002695 Organism: Escherichia coli O157:H7 str. Sakai Gnome size: 5498450 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 2158314-2203914 2156899-2247627 2153413-2253837 2153413-2213713 300072-310238 300014-310600 300052-323524 300052-325376 1161297-1210641 1161098-1210748 1159810-1186416 1159810-1210746 1180157-1209126 5041093-5079469 5041093-5082381 5041814-5082381 5041814-5082381 1245217-1308182 1245905-1316399 1245903-1316397 1245903-1316397 1921472-1970014 1921443-1972369 1921441-1972367 1921441-1972367 2896151-2943747 2888774-2947429 2888774-2947429 2892298-2946279 3480256-3505039 3476233-3500191 3474905-3498417 3452715-3498417 310806-324405 310756-324405 300052-323524 300052-325376 892240-929292 892240-928363 892240-928363 892240-928363 1594751-1609184 1586046-1623577 1586046-1623575 1586046-1623575 1541626-1589842 1538645-1591832 1538645-1591830 1528081-1582022 1586046-1623577 1586046-1623575 1575357-1581511 3193144-3200085 3192962-3201514 3190520-3204375 3190520-3204375 2593128-2612026 2592961-2614081 2592106-2614079 2592106-2614079 2667460-2713016 2668009-2712038 2668007-2712036 2668007-2712036 1618212-1665394 1586046-1623577 1586046-1623575 1586046-1623575 1609998-1656531 1615552-1666524 1615552-1666524 1756865-1804219 1743558-1811658 1743556-1811656 1743639-1800570 1801541-1811612 2211826-2254161 2156899-2247627 2153413-2253837 2153413-2213713 2217597-2253837 FALSE POSITIVES 1437802-1446999 =================================================================================== NCBI id: NC_004307 Organism: Bifidobacterium longum NCC2705 Gnome size: 2256640 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1298692-1312867 1288884-1312867 1288882-1312867 1288882-1312867 =================================================================================== NCBI id: NC_004310 Organism: Brucella suis 1330 Gnome size: 2107794 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 578085-584879 578578-587942 578578-588373 578578-588373 =================================================================================== 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 1245851-1297054 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 ................................................................................... 2728976-2776816 2728976-2776892 2728976-2780003 2728976-2780003 962612-1006517 961043-1004271 961043-1006517 961043-1002017 2042050-2059909 FN FN FN 2844427-2879233 2836644-2885744 2836642-2885742 2836642-2885742 2330961-2345217 2327474-2345217 FN 2330961-2345217 4417918-4438335 4417918-4438335 4417918-4438335 4417918-4438335 1098228-1143714 1098181-1144022 1098179-1144020 1096831-1144020 =================================================================================== NCBI id: NC_004557 Organism: Clostridium tetani E88 Gnome size: 2799251 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1138054-1181003 1137516-1171268 1137516-1192459 1137516-1192459 1663821-1696302 1657698-1693073 1657696-1693071 1657696-1693071 2242455-2281387 2245647-2282092 2248862-2282092 2244315-2282092 =================================================================================== NCBI id: NC_000907 Organism: Haemophilus influenzae Rd KW20 Gnome size: 1830138 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1559962-1594275 1558774-1597183 1558774-1597183 1558774-1597183 1499076-1513073 1495051-1513073 1495049-1513073 1495049-1513073 =================================================================================== 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 3617737-3655581 3617736-3658248 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 742914-788640 1137743-1171867 1131000-1172231 1130998-1172231 1130998-1174569 1410725-1450458 1398708-1455522 1398706-1455520 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 3655939-3668825 3655937-3668825 3650539-3690237 FALSE POSITIVES 5089874-5096357 =================================================================================== NCBI id: NC_002978 Organism: Wolbachia endosymbiont of Drosophila melanogaster Gnome size: 1267782 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 567453-582561 560258-580671 560258-573485 548107-573485 245829-275225 253155-278902 253153-278900 253153-278900 551654-558625 548107-556883 548107-556883 548107-573485 623343-634537 622819-636172 614233-650482 614233-650482 =================================================================================== NCBI id: NC_002655 Organism: Escherichia coli O157:H7 EDL933 Gnome size: 5528445 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 1879335-1897622 1835962-1931572 1835960-1935058 1835960-1935058 3551577-3565707 3546082-3567481 3544754-3565707 3522564-3565707 2966382-3015014 2959005-3018696 2959005-3018696 2959005-3017546 2668339-2688870 2668172-2689292 2667317-2692188 2667317-2692188 2285976-2330172 2272363-2331832 2272753-2342415 2272753-2342415 300073-310251 300055-324556 300053-323525 300053-325377 1897625-1908911 1835962-1931572 1835960-1935058 1835960-1935058 1702185-1725748 1693971-1748316 1670022-1705963 1670022-1705963 1693969-1748314 1684856-1725748 310756-323112 300055-324556 300053-323525 300053-325377 1250521-1295458 1250321-1295565 1249033-1295563 1249033-1295563 1330857-1391923 1330722-1400171 1330720-1400169 1330720-1400169 1678706-1693737 1678682-1693909 1670022-1705963 1670022-1705963 1684856-1725748 1849488-1879269 1835962-1931572 1835960-1935058 1835960-1935058 1909139-1930250 1835962-1931572 1835960-1935058 1835960-1935058 892845-930943 892759-931347 892757-931345 892757-931345 1730065-1756006 1693971-1748316 1693969-1748314 1730065-1756006 1748352-1756006 1626722-1673485 1623741-1675808 1623741-1675806 1623741-1675806 1670022-1705963 1670022-1705963 2743223-2788348 2743226-2797853 2743224-2788401 2742785-2802369 2118738-2165694 2107529-2165694 2116354-2148177 2116354-2148177 2142480-2177204 2142480-2177204 3263064-3270404 3262918-3271470 3260476-3274334 3260476-3274334 =================================================================================== 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 441338-498168 441336-498166 441336-498166 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 2082982-2129322 2069951-2129411 2069951-2129411 2124924-2152937 2124922-2150747 2124922-2150747 FALSE POSITIVES 1936945-1959426 854223-895164 854223-895164 ** 865041-882822 =================================================================================== NCBI id: NC_003919 Organism: Xanthomonas axonopodis pv. citri str. 306 Gnome size: 5175554 bp ................................................................................... reference PHAST PHASTER PHASTEST ................................................................................... 3105263-3115868 3081511-3128919 3081509-3127792 3081509-3127792 1211424-1228677 1220880-1228677 1209301-1229038 1209301-1229038 ===================================================================================