Origin IGS: aatatttttctatagtttaatattttttatagagaaaatcaatatttaaaaaatattaatattttttaccaaatcttaataattactaactataattaaatataaatcaaaagggggaattaaaatgttaaaaaaattatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgaggattatttacattttttgaaatctatattttaagattatttttaaaatagaaaattttaaatat .........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 atatttaaaattttctattttaaaaataatcttaaaatatagatttcaaaaaatgtaaataatcctcatattgttgccatcaatataagaactgtaaaaaagaatgctatcattatttatctaagaaaaattttactttcaactgaactattaacaatttgtttagaaacttcatttttaacaactttactcatttttaaagtttctattcctgcataagtaatcaaaatcaatgaaaatacagataaaaataatttttttaacattttaattcccccttttgatttatatttaattatagttagtaattattaagatttggtaaaaaatattaatattttttaaatattgattttctctataaaaaatattaaactatagaaaaatatt Mask Tandem Repeat Region ================================================ aatatttttctatagtttaatattttttatagagaaaatcaatatttaaaaaatattaatattttttaccaaatcttaataattactaactataattaaatataaatcaaaagggggaattaaaatgttaaaaaaattatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgaggattatttacattttttgaaatctatattttaagattatttttaaaatagaaaattttaaatat Find is-nt database================================================ Query_seq: FN0238:FN0239|FN0238:FN0239:hypothetical protein:hypothetical protein:<-->:863405..863794 390 aatatttttctatagtttaatattttttatagagaaaatcaatatttaaaaaatattaatattttttaccaaatcttaataattactaactataattaaatataaatcaaaagggggaattaaaatgttaaaaaaattatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgaggattatttacattttttgaaatctatattttaagattatttttaaaatagaaaattttaaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0238:FN0239|FN0238:FN0239:hypothetical protein:hypothetical protein:<-->:863405..863794 390 aatatttttctatagtttaatattttttatagagaaaatcaatatttaaaaaatattaatattttttaccaaatcttaataattactaactataattaaatataaatcaaaagggggaattaaaatgttaaaaaaattatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgaggattatttacattttttgaaatctatattttaagattatttttaaaatagaaaattttaaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0238:FN0239|FN0238:FN0239:hypothetical protein:hypothetical protein:<-->:863405..863794 390 aatatttttctatagtttaatattttttatagagaaaatcaatatttaaaaaatattaatattttttaccaaatcttaataattactaactataattaaatataaatcaaaagggggaattaaaatgttaaaaaaattatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgaggattatttacattttttgaaatctatattttaagattatttttaaaatagaaaattttaaatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatatttttctatagtttaatattttttatagagaaaatcaatatttaaaaaatattaatattttttaccaaatcttaataattactaactataattaaatataaatcaaaagggggaattaaaatgttaaaaaaattatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgaggattatttacattttttgaaatctatattttaagattatttttaaaatagaaaattttaaatat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 92 End: 271 ........................................................................................... M I K Y K S K G G I K M L K K L F L S V F S L I L I T Y A G I E T L K M S K V V K N E V S K Q I V N S S V E S K I F L R ....................................................................................................................... Protein_Len: 58 Strand: - Start: 175 End: 348 .............................................................................................................................................................................. A P I S V K F I L L T T L F S T E L C I T L L E T S L L I K R L Y I I I A N K K V T R I N I A V I H P N N V N K S M .......................................... Protein_Len: 30 Strand: - Start: 79 End: 168 .............................................................................. Y N S V I I L Y L D F P P I L I N F F N N K D T N E N I K M .............................................................................................................................................................................................................................. aatatttttctatagtttaatattttttatagagaaaatcaatatttaaaaaatattaatattttttaccaaatcttaataattactaactataattaaatataaatcaaaagggggaattaaaatgttaaaaaaattatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgaggattatttacattttttgaaatctatattttaagattatttttaaaatagaaaattttaaatat 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: 81 Start: 292 End: 321 ...................................................................................................................................................................................................................................................................................................TTTTACAGTTCTTATATTGATGGCAACAAT..................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatatttttctatagtttaatattttttatagagaaaatcaatatttaaaaaatattaatattttttaccaaatcttaataattactaactataattaaatataaatcaaaagggggaattaaaatgttaaaaaaattatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgaggattatttacattttttgaaatctatattttaagattatttttaaaatagaaaattttaaatat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 40 HP_score: -2.4 Tail_Score: -3.30572 Start: 129 End: 145 Full_Region: GGGGAATTAAAATGT TAAAAA AATTA TTTTTA TCTGTATTTTCATTG ................................................................................................................................TAAAAAAATTATTTTTA..................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: FN0238:FN0239|FN0238:FN0239:hypothetical protein:hypothetical protein:<-->:863405..863794 390 aatatttttctatagtttaatattttttatagagaaaatcaatatttaaaaaatattaatattttttaccaaatcttaataattactaactataattaaatataaatcaaaagggggaattaaaatgttaaaaaaattatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgaggattatttacattttttgaaatctatattttaagattatttttaaaatagaaaattttaaatat Intra-Species Hit: Count: 1 Min: 137 Max: 327 Len: 191 Subject: NC_003454_FN0238_FN0239|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[863405,863794]|390 HSP 1 e-value: 1.0E-104 bit: 379.0 Len: 191 Query Start:137 Query End:327 Subject Strand: POSITIVE Subject Start: 137 Subject End: 327 ........................................................................................................................................ttatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgagg............................................................... ........................................................................................................................................ttatttttatctgtattttcattgattttgattacttatgcaggaatagaaactttaaaaatgagtaaagttgttaaaaatgaagtttctaaacaaattgttaatagttcagttgaaagtaaaatttttcttagataaataatgatagcattcttttttacagttcttatattgatggcaacaatatgagg............................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUUUUAUCUGUAUUUUCAUUGAUUUUGAUUACUUAUGCAGGAAUAGAAACUUUAAAAAUGAGUAAAGUUGUUAAAAAUGAAGUUUCUAAACAAAUUGUUAAUAGUUCAGUUGAAAGUAAAAUUUUUCUUAGAUAAAUAAUGAUAGCAUUCUUUUUUACAGUUCUUAUAUUGAUGGCAACAAUAUGAGG (((((((((((((((((((((((((........(((...((((...(((((((((((..((..(......)..)).....)))))))))))......))))....))))))).))))))))..........)))))))).)))))....................(((((((((.......))))))))). (-30.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUCAUAUUGUUGCCAUCAAUAUAAGAACUGUAAAAAAGAAUGCUAUCAUUAUUUAUCUAAGAAAAAUUUUACUUUCAACUGAACUAUUAACAAUUUGUUUAGAAACUUCAUUUUUAACAACUUUACUCAUUUUUAAAGUUUCUAUUCCUGCAUAAGUAAUCAAAAUCAAUGAAAAUACAGAUAAAAAUAA .((.((((((.......)))))).))..(((((...............(((((((((.((.(((...............((((((............))))))................(((((((........)))))))....))).)).)))))))))...............))))).......... (-21.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 148 105 121 77 NC_003454:FN0939|5end_Hypothetical_membrane-spanning_protein_1592919..1593149_NEGATIVE 256 76 40 54 21 NC_003454:FN1726|5end_Na+_driven_multidrug_efflux_pump_226059..226289_NEGATIVE 218 187 142 82 34 NC_003454:FN0684|5end_hydroxylamine_reductase_1338891..1339121_POSITIVE 215 57 19 171 117 NC_003454:FN0827|5end_ABC_transporter_ATP-binding_protein_1487540..1487770_POSITIVE 203 53 11 210 159 NC_003454:FN0363|5end_ATP_synthase_C_chain,_sodium_ion_specific_993703..993933_NEGATIVE 202 72 31 131 80 NC_003454:FN0803|5end_trifunctional_thioredoxin/methionine_sulfoxide_reductase_A/B_protein_1463871..1464101_NEGATIVE 200 139 91 173 123 NC_003454:FN0567|5end_hypothetical_protein_1218389..1218619_POSITIVE 196 168 123 205 160 NC_003454:FN1209|5end_Hypothetical_RNA_binding_protein_1868914..1869144_NEGATIVE 190 186 143 214 172 NC_003454:FN1379|5end_Citrate_lyase_beta_chain_2026355..2026585_POSITIVE 189 178 131 52 3 NC_003454:FN1174|5end_hypothetical_protein_1835446..1835676_POSITIVE 186 168 129 229 181 NC_003454:FN1627|5end_SSU_ribosomal_protein_S5P_133556..133786_NEGATIVE 186 78 32 151 105 NC_003454:FN1588|5end_hypothetical_protein_99556..99786_POSITIVE 185 67 26 72 32 NC_003454:FN1924|5end_Arsenical_pump_membrane_protein_422993..423223_NEGATIVE 183 189 150 61 28 NC_003454:FN1368|5end_COMF_operon_protein_3_2018771..2019001_NEGATIVE 183 180 144 53 1 NC_003454:FN0021|5end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_659890..660120_POSITIVE 179 180 141 176 134 NC_003454:FN0088|5end_hypothetical_protein_724887..725117_POSITIVE 177 154 123 142 111 NC_003454:FN0995|5end_hypothetical_protein_1649966..1650196_POSITIVE 176 179 147 228 198 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 175 115 71 60 10 NC_003454:FN1533|5end_Electron_transfer_flavoprotein_alpha-subunit_46321..46551_NEGATIVE 174 190 142 151 81 NC_003454:FN0214|5end_Crossover_junction_endodeoxyribonuclease_ruvC_839240..839470_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 148 105 65 21 NC_003454:FN0940|3end_hypothetical_protein_1592975..1593125_NEGATIVE 256 76 40 51 18 NC_003454:FN1727|3end_Chloride_channel_protein_226062..226212_NEGATIVE 224 180 132 72 5 NC_003454:FN0020|3end_Heat_shock_protein_15_659989..660139_POSITIVE 215 57 19 142 88 NC_003454:FN0826|3end_periplasmic_component_of_efflux_system_1487591..1487741_POSITIVE 198 72 39 49 13 NC_003454:FN0804|3end_Cytochrome_C-type_biogenesis_protein_ccdA_1463953..1464103_NEGATIVE 198 164 125 136 103 NC_003454:FN0509|3end_Transposase_1158884..1159034_NEGATIVE 198 164 125 136 103 NC_003454:FN1883|3end_Transposase_370118..370268_POSITIVE 197 50 10 145 104 NC_003454:FN0364|3end_ATP_synthase_A_chain,_sodium_ion_specific_993757..993907_NEGATIVE 194 39 1 148 110 NC_003454:FN1795|3end_hypothetical_protein_275739..275889_NEGATIVE 189 53 11 47 13 NC_003454:FN1378|3end_Citrate_lyase_acyl_carrier_protein_2026426..2026576_POSITIVE 189 178 131 55 6 NC_003454:FN1173|3end_hypothetical_protein_1835529..1835679_POSITIVE 187 42 10 142 99 NC_003454:FN0422|3end_carbamoyl-phosphate_synthase_large_subunit_1066283..1066433_POSITIVE 183 189 150 53 20 NC_003454:FN1369|3end_Zinc_finger_protein_2018779..2018929_NEGATIVE 181 65 28 37 3 NC_003454:FN1382|3end_ATPase_2034437..2034587_POSITIVE 178 140 108 137 102 NC_003454:FN1762|3end_Protein_yaaA_255258..255408_NEGATIVE 177 154 123 124 93 NC_003454:FN0994|3end_hypothetical_protein_1650028..1650178_POSITIVE 176 179 147 67 37 NC_003454:FN1741|3end_ATP_synthase_subunit_I_238561..238711_NEGATIVE 174 190 142 151 81 NC_003454:FN0215|3end_MGTC/SAPB_Family_membrane_protein_839240..839390_NEGATIVE 171 120 78 58 23 NC_003454:FN0512|3end_Flavoprotein_1161386..1161536_NEGATIVE 171 185 143 108 67 NC_003454:FN1702|3end_undecaprenyl_pyrophosphate_phosphatase_197164..197314_NEGATIVE