Origin IGS: tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgtttttttgtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacttatcttttctgagtgtggtcgagcctgtatgctttcctcgaacaaagataattatggagatcactgtatagaatttcaagaccatgaattttgcaagtttgcacgccggacaatctgcattgcagagccgaaatacagatttcccggcgaacaatgacgttttcccgaccaaaaagatctgtcgcgtggctcttggaacagttgaatggaaatggactaatcatcgaataagactgtcgcacgggataaaccatacatctttcatcatttatgtaaggctgcccgttgcacaaaaaaacggctatgccctgtgaaatgagcatagccgttcgggaatgacgaaagctacttggtcgcgcagctatttga Mask Tandem Repeat Region ================================================ tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgtttttttgtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta Find is-nt database================================================ Query_seq: PG0378:PG0380|PG0378:PG0380:elongation factor Ts:excinuclease ABC subunit B:->->:408869..409241 373 tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgtttttttgtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0378:PG0380|PG0378:PG0380:elongation factor Ts:excinuclease ABC subunit B:->->:408869..409241 373 tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgtttttttgtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0378:PG0380|PG0378:PG0380:elongation factor Ts:excinuclease ABC subunit B:->->:408869..409241 373 tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgtttttttgtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgtttttttgtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 157 End: 291 ............................................................................................................................................................ M S I Q L F Q E P R D R S F W S G K R H C S P G N L Y F G S A M Q I V R R A N L Q N S W S .................................................................................. Protein_Len: 60 Strand: + Start: 5 End: 367 .... M A A R P S S F R H S R T A M L I S Q G I A V F L C N G Q P Y I N D E R C M V Y P V R Q S Y S M I S P F P F N C S K S H ...... Protein_Len: 60 Strand: + Start: 192 End: 371 ............................................................................................................................................................................................... M F L V G K T S L F A G K S V F R L C N A D C P A C K L A K F M V L K F Y T V I S I I I F V R G K H T G S T T L R K D K .. Protein_Len: 51 Strand: - Start: 216 End: 368 ....................................................................................................................................................................................................................... Q E G P F R Y K P E A I C I T R R A F K C F E H D Q F E I C H D G Y N D K N S S L M C A R G C E S F M ..... Protein_Len: 47 Strand: - Start: 142 End: 282 ............................................................................................................................................. E I I L G N G N L Q E L L W A V S R K P R S F T M T R R S I Q I E A R C H L N D P T C V Q L M ........................................................................................... Protein_Len: 60 Strand: - Start: 59 End: 286 .......................................................... F S T H N I G H S L R I R H N T W K W E V T G L A V R C I K K T P F V D N N A P F D T N R S Q L A S Q G A H L S A F N M ....................................................................................... tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgtttttttgtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 290 End: 319 .................................................................................................................................................................................................................................................................................................CTTGAAATTCTATACAGTGATCTCCATAAT...................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgtttttttgtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.5 Tail_Score: -5.60993 Start: 42 End: 71 Full_Region: TTCGTCATTCCCGAA CGGCTATGCTC ATTTCACA GGGCATAGCCG TTTTTTTGTGCAACG .........................................CGGCTATGCTCATTTCACAGGGCATAGCCG.............................................................................................................................................................................................................................................................................................................. Find igs database================================================ Query_seq: PG0378:PG0380|PG0378:PG0380:elongation factor Ts:excinuclease ABC subunit B:->->:408869..409241 373 tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgtttttttgtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta Intra-Species Hit: Count: 1 Min: 1 Max: 373 Len: 373 Subject: NC_002950_PG0378_PG0380|elongation factor Ts:excinuclease ABC subunit B|POSITIVE:POSITIVE|[408869,409241]|373 HSP 1 e-value: 0.0 bit: 698.0 Len: 373 Query Start:1 Query End:373 Subject Strand: POSITIVE Subject Start: 1 Subject End: 373 tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgnnnnnnngtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta tcaaatagctgcgcgaccaagtagctttcgtcattcccgaacggctatgctcatttcacagggcatagccgtttttttgtgcaacgggcagccttacataaatgatgaaagatgtatggtttatcccgtgcgacagtcttattcgatgattagtccatttccattcaactgttccaagagccacgcgacagatctttttggtcgggaaaacgtcattgttcgccgggaaatctgtatttcggctctgcaatgcagattgtccggcgtgcaaacttgcaaaattcatggtcttgaaattctatacagtgatctccataattatctttgttcgaggaaagcatacaggctcgaccacactcagaaaagataagta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAUAGCUGCGCGACCAAGUAGCUUUCGUCAUUCCCGAACGGCUAUGCUCAUUUCACAGGGCAUAGCCGUUUUUUUGUGCAACGGGCAGCCUUACAUAAAUGAUGAAAGAUGUAUGGUUUAUCCCGUGCGACAGUCUUAUUCGAUGAUUAGUCCAUUUCCAUUCAACUGUUCCAAGAGCCACGCGACAGAUCUUUUUGGUCGGGAAAACGUCAUUGUUCGCCGGGAAAUCUGUAUUUCGGCUCUGCAAUGCAGAUUGUCCGGCGUGCAAACUUGCAAAAUUCAUGGUCUUGAAAUUCUAUACAGUGAUCUCCAUAAUUAUCUUUGUUCGAGGAAAGCAUACAGGCUCGACCACACUCAGAAAAGAUAAGUA ........(((((((........(((.(((((......((((((((((((((........))))))))))))))..(((((((.((((.((((.(((((...(......).))))).))))...))))))).))))........)))))..)))................((((...))))..)))).)))(((((((((((((((.........((((.((((((..((((((((((.((....)).))))))))))..)))))).))))...(((....((((......)))).((((..((((.(((..........))).))))...))))..)))......)))))))).......)))))))..... (-112.71) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACUUAUCUUUUCUGAGUGUGGUCGAGCCUGUAUGCUUUCCUCGAACAAAGAUAAUUAUGGAGAUCACUGUAUAGAAUUUCAAGACCAUGAAUUUUGCAAGUUUGCACGCCGGACAAUCUGCAUUGCAGAGCCGAAAUACAGAUUUCCCGGCGAACAAUGACGUUUUCCCGACCAAAAAGAUCUGUCGCGUGGCUCUUGGAACAGUUGAAUGGAAAUGGACUAAUCAUCGAAUAAGACUGUCGCACGGGAUAAACCAUACAUCUUUCAUCAUUUAUGUAAGGCUGCCCGUUGCACAAAAAAACGGCUAUGCCCUGUGAAAUGAGCAUAGCCGUUCGGGAAUGACGAAAGCUACUUGGUCGCGCAGCUAUUUGA ................(((((..((((.......((((((.((.....................(((.(((...(((((((((((.......))))).))))))...((((((..((((((.(((.(......).))).))))))..)))))).))).)))....(((((((.......(((..(((.(((..((.((.((....)).)).))..))))))..)))............(((.(((((((.....((.(((((............))))).))...)))).)))))).....((((((((((.(........).))))))))))))))))).)).))))))..))))..))))).......... (-100.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 414 220 171 201 156 NC_002950:PG1562|5end_dTDP-4-dehydrorhamnose_3,5-epimerase_1641582..1641812_NEGATIVE 410 47 3 194 135 NC_002950:PG2189|5end_aspartate_kinase_2297151..2297381_NEGATIVE 398 269 222 60 8 NC_002950:PG1946|5end_ABC_3_transporter_family_protein_2032133..2032363_POSITIVE 378 247 203 216 163 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 370 90 42 163 109 NC_002950:PG1342|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_1422585..1422815_POSITIVE 369 90 43 167 128 NC_002950:PG1937|5end_50S_ribosomal_protein_L4_2024136..2024366_NEGATIVE 368 228 181 221 178 NC_002950:PG0027|5end_hypothetical_protein_32681..32911_POSITIVE 365 269 225 53 8 NC_002950:PG1253|5end_DNA_ligase,_NAD-dependent_1331606..1331836_NEGATIVE 365 90 43 215 155 NC_002950:PG0680|5end_efflux_transporter,_MFP_component,_RND_family_730968..731198_POSITIVE 360 54 11 63 12 NC_002950:PG0603|5end_cytidylate_kinase_659570..659800_POSITIVE 355 70 21 74 3 NC_002950:PG2225|5end_hypothetical_protein_2339440..2339670_POSITIVE 355 270 221 229 193 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 353 266 221 38 1 NC_002950:PG0173|5end_transcriptional_regulator,_putative_194741..194971_NEGATIVE 351 279 237 142 97 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 350 267 222 230 187 NC_002950:PG0731|5end_hypothetical_protein_782676..782906_NEGATIVE 350 95 58 48 7 NC_002950:PG0198|5end_hypothetical_protein_236882..237112_POSITIVE 348 269 221 159 114 NC_002950:PG1351|5end_hypothetical_protein_1432744..1432974_NEGATIVE 348 226 181 175 131 NC_002950:PG1226|5end_peptidyl-prolyl_cis-trans_isomerase,_cyclophilin-type_1303264..1303494_POSITIVE 348 245 201 64 19 NC_002950:PG0860|5end_transcriptional_regulator,_putative_918888..919118_POSITIVE 348 243 201 170 125 NC_002950:PG0507|5end_hypothetical_protein_547916..548146_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 935 266 221 144 99 NC_002950:PG1229|3end_hypothetical_protein_1305559..1305709_NEGATIVE 398 269 222 67 15 NC_002950:PG1945|3end_hypothetical_protein_2032220..2032370_POSITIVE 389 98 51 50 1 NC_002950:PG2226|3end_hypothetical_protein_2342091..2342241_POSITIVE 384 73 36 51 3 NC_002950:PG0378|3end_elongation_factor_Ts_408808..408958_POSITIVE 381 266 221 67 3 NC_002950:PG1416|3end_enoyl-(acyl-carrier-protein)_reductase_II_1501078..1501228_POSITIVE 369 269 221 148 102 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE 368 228 181 145 102 NC_002950:PG0026|3end_hypothetical_protein_32685..32835_POSITIVE 365 269 225 65 20 NC_002950:PG1254|3end_acetyltransferase,_GNAT_family_1331594..1331744_NEGATIVE 364 228 184 146 96 NC_002950:PG0369|3end_phosphopantetheine_adenylyltransferase_403751..403901_POSITIVE 362 277 231 137 89 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 351 279 237 129 84 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 350 90 41 146 93 NC_002950:PG0553|3end_extracellular_protease,_putative_608367..608517_NEGATIVE 345 225 184 89 33 NC_002950:PG1073|3end_D-lysine_5,6-aminomutase,_alpha_subunit_1142046..1142196_POSITIVE 339 269 221 90 41 NC_002950:PG0224|3end_hypothetical_protein_257614..257764_NEGATIVE 334 69 24 102 57 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 334 229 184 150 96 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 332 219 176 147 106 NC_002950:PG0037|3end_50S_ribosomal_protein_L19_46964..47114_POSITIVE 329 89 41 151 98 NC_002950:PG1578|3end_quinolinate_synthetase_1656472..1656622_POSITIVE 329 70 25 80 19 NC_002950:PG0171|3end_5'-nucleotidase_family_protein_193576..193726_POSITIVE 326 50 8 58 22 NC_002950:PG2123|3end_hypothetical_protein_2230243..2230393_POSITIVE