Origin IGS: aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaatttttttcctcattgaatttaccctccctgtttctaaacttgaaaactttttatttatgtatttaattgattttgtagattttattagttttttaaattgtaacatataaatatgactttttcaatcatacttatgcttatttttttatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa .........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 ttataacatttttaagaatttagtaaaagaatgtcaaaatttttaaacatttgggataaaaaaataagcataagtatgattgaaaaagtcatatttatatgttacaatttaaaaaactaataaaatctacaaaatcaattaaatacataaataaaaagttttcaagtttagaaacagggagggtaaattcaatgaggaaaaaaattttaaaaagtaaagtaatgttaattgctctagcttccattctatttgtaagttgtggtggaggcggaggaggaggtgggggaggttctagtaacttgccactaaatccaggaacaccaagtataccaagtacaccaagcactccaagtgttccagaggataattttccaactgtagctaatcct Mask Tandem Repeat Region ================================================ aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaatttttttcctcattgaatttaccctccctgtttctaaacttgaaaactttttatttatgtatttaattgattttgtagattttattagttttttaaattgtaacatataaatatgactttttcaatcatacttatgcttatttttttatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa Find is-nt database================================================ Query_seq: FN1426:FN1427|FN1426:FN1427:Serine protease:Phenazine biosynthesis protein phzF:<-->:2095553..2095941 389 aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaatttttttcctcattgaatttaccctccctgtttctaaacttgaaaactttttatttatgtatttaattgattttgtagattttattagttttttaaattgtaacatataaatatgactttttcaatcatacttatgcttatttttttatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1426:FN1427|FN1426:FN1427:Serine protease:Phenazine biosynthesis protein phzF:<-->:2095553..2095941 389 aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaatttttttcctcattgaatttaccctccctgtttctaaacttgaaaactttttatttatgtatttaattgattttgtagattttattagttttttaaattgtaacatataaatatgactttttcaatcatacttatgcttatttttttatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1426:FN1427|FN1426:FN1427:Serine protease:Phenazine biosynthesis protein phzF:<-->:2095553..2095941 389 aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaatttttttcctcattgaatttaccctccctgtttctaaacttgaaaactttttatttatgtatttaattgattttgtagattttattagttttttaaattgtaacatataaatatgactttttcaatcatacttatgcttatttttttatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaatttttttcctcattgaatttaccctccctgtttctaaacttgaaaactttttatttatgtatttaattgattttgtagattttattagttttttaaattgtaacatataaatatgactttttcaatcatacttatgcttatttttttatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 141 End: 248 ............................................................................................................................................ M E W K L E Q L T L L Y F L K F F S S L N L P S L F L N L K T F Y L C I ............................................................................................................................................. Protein_Len: 60 Strand: + Start: 44 End: 292 ........................................... M L G V L G I L G V P G F S G K L L E P P P P P P P P P P Q L T N R M E A R A I N I T L L F K I F F L I E F T L P V S K ................................................................................................. Protein_Len: 60 Strand: - Start: 1 End: 297 G G G G C S V F L I S A L A I L M V K S K L I K K R M S N V R G T E L S S F K K N I Y K I S K T S K I L K K F Q L M Y M ............................................................................................ aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaatttttttcctcattgaatttaccctccctgtttctaaacttgaaaactttttatttatgtatttaattgattttgtagattttattagttttttaaattgtaacatataaatatgactttttcaatcatacttatgcttatttttttatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa 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: 88 Start: 282 End: 311 .........................................................................................................................................................................................................................................................................................ATTGAAAAAGTCATATTTATATGTTACAAT.............................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 352 End: 381 ...............................................................................................................................................................................................................................................................................................................................................................TTTGACATTCTTTTACTAAATTCTTAAAAA........ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaatttttttcctcattgaatttaccctccctgtttctaaacttgaaaactttttatttatgtatttaattgattttgtagattttattagttttttaaattgtaacatataaatatgactttttcaatcatacttatgcttatttttttatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 48 HP_score: -3.9 Tail_Score: -3.1207 Start: 293 End: 319 Full_Region: ataaaaaaataagca taagtatgatt gaaaa agtcatattta tatgttacaatttaa ....................................................................................................................................................................................................................................................................................................taagtatgattgaaaaagtcatattta...................................................................... TransTerm Strand: - Conf: 55 HP_score: -2.5 Tail_Score: -4.21142 Start: 297 End: 315 Full_Region: aaaaataagcataag tatgatt gaaaa agtcata tttatatgttacaat ........................................................................................................................................................................................................................................................................................................tatgattgaaaaagtcata.......................................................................... Find igs database================================================ Query_seq: FN1426:FN1427|FN1426:FN1427:Serine protease:Phenazine biosynthesis protein phzF:<-->:2095553..2095941 389 aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaatttttttcctcattgaatttaccctccctgtttctaaacttgaaaactttttatttatgtatttaattgattttgtagattttattagttttttaaattgtaacatataaatatgactttttcaatcatacttatgcttatttttttatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa Intra-Species Hit: Count: 1 Min: 1 Max: 389 Len: 389 Subject: NC_003454_FN1426_FN1427|Serine protease:Phenazine biosynthesis protein phzF|NEGATIVE:POSITIVE|[2095553,2095941]|389 HSP 1 e-value: 1.0E-116 bit: 418.0 Len: 232 Query Start:1 Query End:232 Subject Strand: POSITIVE Subject Start: 1 Subject End: 232 aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaannnnnnncctcattgaatttaccctccctgtttctaaacttgaaaac............................................................................................................................................................. aggattagctacagttggaaaattatcctctggaacacttggagtgcttggtgtacttggtatacttggtgttcctggatttagtggcaagttactagaacctcccccacctcctcctccgcctccaccacaacttacaaatagaatggaagctagagcaattaacattactttactttttaaaatttttttcctcattgaatttaccctccctgtttctaaacttgaaaac............................................................................................................................................................. HSP 2 e-value: 1.0E-42 bit: 174.0 Len: 109 Query Start:281 Query End:389 Subject Strand: POSITIVE Subject Start: 281 Subject End: 389 ........................................................................................................................................................................................................................................................................................aattgtaacatataaatatgactttttcaatcatacttatgcttannnnnnnatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa ........................................................................................................................................................................................................................................................................................aattgtaacatataaatatgactttttcaatcatacttatgcttatttttttatcccaaatgtttaaaaattttgacattcttttactaaattcttaaaaatgttataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGAUUAGCUACAGUUGGAAAAUUAUCCUCUGGAACACUUGGAGUGCUUGGUGUACUUGGUAUACUUGGUGUUCCUGGAUUUAGUGGCAAGUUACUAGAACCUCCCCCACCUCCUCCUCCGCCUCCACCACAACUUACAAAUAGAAUGGAAGCUAGAGCAAUUAACAUUACUUUACUUUUUAAAAUUUUUUUCCUCAUUGAAUUUACCCUCCCUGUUUCUAAACUUGAAAACUUUUUAUUUAUGUAUUUAAUUGAUUUUGUAGAUUUUAUUAGUUUUUUAAAUUGUAACAUAUAAAUAUGACUUUUUCAAUCAUACUUAUGCUUAUUUUUUUAUCCCAAAUGUUUAAAAAUUUUGACAUUCUUUUACUAAAUUCUUAAAAAUGUUAUAA .(((((((..((((..((.(((((.......((((....(((((.((..(((((((...))))))).((((.....((.((((((((....)))))))).)).....)))).........)))))))...................((((((.(((((.(((....))).))))).))))))........))))......))))).))....))))..)))...(((((((..((.(((((((((.((....((((((...(((((.....)))))...)))))).)).))))))))).))..)))))))......................)))).................(((((((.((.............)).)))))))... (-60.84) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUAACAUUUUUAAGAAUUUAGUAAAAGAAUGUCAAAAUUUUUAAACAUUUGGGAUAAAAAAAUAAGCAUAAGUAUGAUUGAAAAAGUCAUAUUUAUAUGUUACAAUUUAAAAAACUAAUAAAAUCUACAAAAUCAAUUAAAUACAUAAAUAAAAAGUUUUCAAGUUUAGAAACAGGGAGGGUAAAUUCAAUGAGGAAAAAAAUUUUAAAAAGUAAAGUAAUGUUAAUUGCUCUAGCUUCCAUUCUAUUUGUAAGUUGUGGUGGAGGCGGAGGAGGAGGUGGGGGAGGUUCUAGUAACUUGCCACUAAAUCCAGGAACACCAAGUAUACCAAGUACACCAAGCACUCCAAGUGUUCCAGAGGAUAAUUUUCCAACUGUAGCUAAUCCU ..........(((((((((((.(...........).))))))))))).....(((((............((((((((((((.....))))))))))))..((((((...................(((((.....(((((...((((..........(((((........)))))..(((((.((..(((......)))..................((((((....)))))).)).)))))........)))))))))..)))))...(((((((((..(((((.(((((.....))))).)).)))..))).(((((((...((((.....)))).....(.....)..))))))).........))))))...))))))..))))) (-75.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1086 130 81 221 172 NC_003454:FN1426|5end_Serine_protease_2095462..2095692_NEGATIVE 404 159 116 163 118 NC_003454:FN1126|5end_Acetyltransferase_1770287..1770517_NEGATIVE 346 87 41 199 147 NC_003454:FN1950|5end_Serine_protease_457855..458085_NEGATIVE 307 159 118 97 53 NC_003454:FN1886|5end_hypothetical_protein_371399..371629_POSITIVE 306 117 71 92 39 NC_003454:FN1560|5end_hypothetical_protein_82982..83212_NEGATIVE 297 130 83 173 112 NC_003454:FN2042|5end_Protein_translocase_subunit_SecE_549832..550062_NEGATIVE 286 130 84 71 39 NC_003454:FN1903|5end_Coenzyme_A_disulfide_reductase/_disulfide_bond_regulator_domain_393104..393334_NEGATIVE 283 129 81 117 72 NC_003454:FN1580|5end_2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase_90919..91149_NEGATIVE 282 226 195 120 88 NC_003454:FN1056|5end_hypothetical_protein_1703693..1703923_POSITIVE 280 49 6 63 22 NC_003454:FN1547|5end_PTS_permease_for_N-acetylglucosamine_and_glucose_63270..63500_NEGATIVE 272 110 67 173 139 NC_003454:FN1968|5end_Hemin_transport_system_ATP-binding_protein_hmuV_467189..467419_NEGATIVE 260 120 71 100 42 NC_003454:FN1070|5end_glucose-inhibited_division_protein_A_1717121..1717351_POSITIVE 257 130 81 229 183 NC_003454:FN1104|5end_Holliday_junction_DNA_helicase_ruvA_1749453..1749683_POSITIVE 254 77 39 64 25 NC_003454:FN1937|5end_hypothetical_protein_437932..438162_NEGATIVE 253 122 84 215 179 NC_003454:FN0639|5end_hypothetical_protein_1297427..1297657_NEGATIVE 246 110 64 106 56 NC_003454:FN1994|5end_hypothetical_protein_497577..497807_POSITIVE 244 140 92 69 16 NC_003454:FN1825|5end_hypothetical_protein_313994..314224_POSITIVE 240 219 174 114 67 NC_003454:FN0067|5end_Isoleucyl-tRNA_synthetase_704537..704767_POSITIVE 239 118 71 107 51 NC_003454:FN0832|5end_hypothetical_protein_1494305..1494535_POSITIVE 237 127 102 197 169 NC_003454:FN1381|5end_hypothetical_protein_2032434..2032664_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 159 116 143 98 NC_003454:FN1127|3end_Hypothetical_membrane-spanning_protein_1770307..1770457_NEGATIVE 305 157 111 72 23 NC_003454:FN1561|3end_Hypothetical_cytosolic_protein_83032..83182_NEGATIVE 283 129 81 141 96 NC_003454:FN1581|3end_DNA_mismatch_repair_protein_mutS_90895..91045_NEGATIVE 280 89 41 50 3 NC_003454:FN1267|3end_hypothetical_protein_1923054..1923204_NEGATIVE 273 127 90 151 115 NC_003454:FN1253|3end_hypothetical_protein_1910229..1910379_NEGATIVE 266 145 114 146 100 NC_003454:FN0682|3end_Fibronectin-binding_protein-like_protein_A_1338499..1338649_POSITIVE 254 77 39 47 8 NC_003454:FN1938|3end_hypothetical_protein_437949..438099_NEGATIVE 246 110 64 99 49 NC_003454:FN1993|3end_SUA5_protein_497650..497800_POSITIVE 240 219 174 117 70 NC_003454:FN0066|3end_Two_component_system_histidine_kinase_704620..704770_POSITIVE 236 118 71 87 42 NC_003454:FN1830|3end_DNA_polymerase_III_subunits_gamma_and_tau_318571..318721_NEGATIVE 235 159 120 135 100 NC_003454:FN1626|3end_LSU_ribosomal_protein_L30P_132864..133014_NEGATIVE 229 358 315 105 52 NC_003454:FN1729|3end_4-amino-4-deoxychorismate_lyase_228338..228488_NEGATIVE 228 52 19 119 87 NC_003454:FN1745|3end_Cystathionine_gamma-synthase_242953..243103_NEGATIVE 227 109 61 61 18 NC_003454:FN1505|3end_6,7-dimethyl-8-ribityllumazine_synthase_10949..11099_POSITIVE 218 154 112 151 121 NC_003454:FN0495|3end_Acetyl-CoA_acetyltransferase_1140855..1141005_POSITIVE 214 230 186 127 71 NC_003454:FN1553|3end_Transporter_67150..67300_NEGATIVE 213 118 72 54 1 NC_003454:FN0527|3end_Alanyl-tRNA_synthetase_1182977..1183127_NEGATIVE 213 119 71 122 75 NC_003454:FN0254|3end_Fusobacterium_outer_membrane_protein_family_881390..881540_POSITIVE 211 366 322 122 82 NC_003454:FN0933|3end_3-phosphoshikimate_1-carboxyvinyltransferase_1586536..1586686_POSITIVE 210 228 186 144 110 NC_003454:FN0252|3end_hypothetical_protein_874521..874671_POSITIVE