Origin IGS: tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattactaaaataaacatcaaagaaaaattattttgaaaaaaataaaaattttaatattatataaagttattccataataatattttaaatttgttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa .........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 ttgtttgtttctcctataaattaacttttaaaaatatttattaaatcaaaatatttaactaattctaccatactttattaattgatacaagaacaaatttaaaatattattatggaataactttatataatattaaaatttttatttttttcaaaataatttttctttgatgtttattttagtaatataataaaaaattactacaataaaaccaaatgtagcaatctgtattttttattagtctattataactttctcattttata Mask Tandem Repeat Region ================================================ tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattactaaaataaacatcaaagaaaaattattttgaaaaaaataaaaattttaatattatataaagttattccataataatattttaaatttgttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa Find is-nt database================================================ Query_seq: FN0677:FN0678|FN0677:FN0678:hypothetical protein:Ser/Thr protein kinase:->->:1333843..1334108 266 tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattactaaaataaacatcaaagaaaaattattttgaaaaaaataaaaattttaatattatataaagttattccataataatattttaaatttgttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0677:FN0678|FN0677:FN0678:hypothetical protein:Ser/Thr protein kinase:->->:1333843..1334108 266 tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattactaaaataaacatcaaagaaaaattattttgaaaaaaataaaaattttaatattatataaagttattccataataatattttaaatttgttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0677:FN0678|FN0677:FN0678:hypothetical protein:Ser/Thr protein kinase:->->:1333843..1334108 266 tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattactaaaataaacatcaaagaaaaattattttgaaaaaaataaaaattttaatattatataaagttattccataataatattttaaatttgttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattactaaaataaacatcaaagaaaaattattttgaaaaaaataaaaattttaatattatataaagttattccataataatattttaaatttgttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa Predict ORF larger than 30AA ================================================ tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattactaaaataaacatcaaagaaaaattattttgaaaaaaataaaaattttaatattatataaagttattccataataatattttaaatttgttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa 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: 157 End: 186 ............................................................................................................................................................ATTGATACAAGAACAAATTTAAAATATTAT................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 176 End: 205 ...............................................................................................................................................................................CTTGTATCAATTAATAAAGTATGGTAGAAT............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattactaaaataaacatcaaagaaaaattattttgaaaaaaataaaaattttaatattatataaagttattccataataatattttaaatttgttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0677:FN0678|FN0677:FN0678:hypothetical protein:Ser/Thr protein kinase:->->:1333843..1334108 266 tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattactaaaataaacatcaaagaaaaattattttgaaaaaaataaaaattttaatattatataaagttattccataataatattttaaatttgttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa Intra-Species Hit: Count: 1 Min: 1 Max: 266 Len: 266 Subject: NC_003454_FN0677_FN0678|hypothetical protein:Ser/Thr protein kinase|POSITIVE:POSITIVE|[1333843,1334108]|266 HSP 1 e-value: 3.0E-46 bit: 186.0 Len: 94 Query Start:173 Query End:266 Subject Strand: POSITIVE Subject Start: 173 Subject End: 266 ............................................................................................................................................................................gttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa ............................................................................................................................................................................gttcttgtatcaattaataaagtatggtagaattagttaaatattttgatttaataaatatttttaaaagttaatttataggagaaacaaacaa HSP 2 e-value: 6.0E-41 bit: 168.0 Len: 85 Query Start:1 Query End:85 Subject Strand: POSITIVE Subject Start: 1 Subject End: 85 tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattac..................................................................................................................................................................................... tataaaatgagaaagttataatagactaataaaaaatacagattgctacatttggttttattgtagtaattttttattatattac..................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAAUGAGAAAGUUAUAAUAGACUAAUAAAAAAUACAGAUUGCUACAUUUGGUUUUAUUGUAGUAAUUUUUUAUUAUAUUACUAAAAUAAACAUCAAAGAAAAAUUAUUUUGAAAAAAAUAAAAAUUUUAAUAUUAUAUAAAGUUAUUCCAUAAUAAUAUUUUAAAUUUGUUCUUGUAUCAAUUAAUAAAGUAUGGUAGAAUUAGUUAAAUAUUUUGAUUUAAUAAAUAUUUUUAAAAGUUAAUUUAUAGGAGAAACAAACAA ..(((((((....((((((((((((..............(((((((((((...........))))))))))))))))))))..)))...............(((...(((((((....))))))).(((((((........))))))).)))........)))))))..(((((((((.(((.((((((((((((((....(((((((.........))))))).....))))))).....))))))).))).))).))))))... (-36.53) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUUGUUUCUCCUAUAAAUUAACUUUUAAAAAUAUUUAUUAAAUCAAAAUAUUUAACUAAUUCUACCAUACUUUAUUAAUUGAUACAAGAACAAAUUUAAAAUAUUAUUAUGGAAUAACUUUAUAUAAUAUUAAAAUUUUUAUUUUUUUCAAAAUAAUUUUUCUUUGAUGUUUAUUUUAGUAAUAUAAUAAAAAAUUACUACAAUAAAACCAAAUGUAGCAAUCUGUAUUUUUUAUUAGUCUAUUAUAACUUUCUCAUUUUAUA ..(((((((.((..(((.((((((...........(((..((((((......))))))..)))..............)))))).)))..)))))))))........((((.(((((...(((......(((((((((....(((((((....)))))))......)))))))))......)))....(((((((((((..(((((...........)))))........))))))))))).))))).))))............... (-24.71) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 233 128 81 214 163 NC_003454:FN0455|5end_Rubrerythrin_1101194..1101424_POSITIVE 212 90 43 68 18 NC_003454:FN0243|5end_Poly(A)_polymerase_866599..866829_POSITIVE 191 76 45 223 191 NC_003454:FN1516|5end_hypothetical_protein_20858..21088_NEGATIVE 189 85 41 99 45 NC_003454:FN0170|5end_GTP-binding_protein_795211..795441_POSITIVE 188 182 141 198 145 NC_003454:FN1146|5end_Hypothetical_exported_24-amino_acid_repeat_protein_1796466..1796696_NEGATIVE 187 184 141 72 33 NC_003454:FN1694|5end_UDP-N-acetyl-D-quinovosamine_4-epimerase_190169..190399_NEGATIVE 185 86 45 110 74 NC_003454:FN1180|5end_hypothetical_protein_1842588..1842818_NEGATIVE 185 219 171 221 175 NC_003454:FN0503|5end_Transcriptional_regulatory_protein,_LYSR_family_1153572..1153802_NEGATIVE 185 206 175 223 195 NC_003454:FN0109|5end_hypothetical_protein_744809..745039_NEGATIVE 182 65 21 117 69 NC_003454:FN1917|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_413756..413986_NEGATIVE 179 223 194 161 130 NC_003454:FN0018|5end_hypothetical_protein_656448..656678_NEGATIVE 175 48 4 72 22 NC_003454:FN2002|5end_Permease_503563..503793_NEGATIVE 174 57 28 212 179 NC_003454:FN0802|5end_Amino_acid_transport_system_permease_protein_1462136..1462366_NEGATIVE 174 88 43 209 154 NC_003454:FN0252|5end_hypothetical_protein_874193..874423_POSITIVE 174 88 43 209 154 NC_003454:FN2060|5end_hypothetical_protein_573649..573879_NEGATIVE 174 88 43 209 154 NC_003454:FN2049|5end_hypothetical_protein_559573..559803_NEGATIVE 168 66 23 230 181 NC_003454:FN1362|5end_Dipeptide_transport_ATP-binding_protein_dppD_2013818..2014048_POSITIVE 168 257 211 229 180 NC_003454:FN1313|5end_Oligopeptide-binding_protein_oppA_1967053..1967283_POSITIVE 168 48 8 153 116 NC_003454:FN1046|5end_hypothetical_protein_1696371..1696601_POSITIVE 167 178 133 222 173 NC_003454:FN2105|5end_Integral_membrane_protein_614701..614931_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 212 90 43 55 5 NC_003454:FN0242|3end_Trk_system_potassium_uptake_protein_trkA_866666..866816_POSITIVE 190 90 43 78 34 NC_003454:FN1881|3end_Esterase_368250..368400_NEGATIVE 188 182 141 70 17 NC_003454:FN1147|3end_hypothetical_protein_1796594..1796744_NEGATIVE 187 184 141 72 33 NC_003454:FN1695|3end_Probable_quinovosaminephosphotransferae_190169..190319_NEGATIVE 185 219 171 145 99 NC_003454:FN0504|3end_Arginine_permease_1153648..1153798_NEGATIVE 182 65 21 133 85 NC_003454:FN1918|3end_SPO0B-associated_GTP-binding_protein_413740..413890_NEGATIVE 178 79 40 67 23 NC_003454:FN1859|3end_Major_outer_membrane_protein_348549..348699_NEGATIVE 176 88 43 101 52 NC_003454:FN1800|3end_Peptidyl-prolyl_cis-trans_isomerase_282534..282684_POSITIVE 166 181 145 63 23 NC_003454:FN0075|3end_Ethanolamine_utilization_protein_eutP_714216..714366_POSITIVE 165 59 23 44 1 NC_003454:FN1032|3end_hypothetical_protein_1685809..1685959_NEGATIVE 164 86 46 114 74 NC_003454:FN0293|3end_Hemolysin_activator_protein_precursor_926023..926173_NEGATIVE 163 78 40 95 50 NC_003454:FN0436|3end_Urea_carboxylase_1077851..1078001_NEGATIVE 162 66 39 39 10 NC_003454:FN0051|3end_hypothetical_protein_688783..688933_NEGATIVE 161 91 57 45 9 NC_003454:FN1853|3end_methylaspartate_mutase_subunit_S_342607..342757_POSITIVE 159 50 10 61 27 NC_003454:FN0853|3end_Glycogen_synthase_1510922..1511072_NEGATIVE 158 84 41 93 57 NC_003454:FN0720|3end_elongation_factor_P_1377619..1377769_POSITIVE 156 89 45 109 66 NC_003454:FN1453|3end_hypothetical_protein_2134073..2134223_NEGATIVE 155 249 207 147 109 NC_003454:FN1684|3end_N-acetylneuraminate_synthase_179083..179233_NEGATIVE 153 260 216 43 5 NC_003454:FN0763|3end_Transporter,_LysE_family_1420440..1420590_POSITIVE 153 223 191 78 49 NC_003454:FN2076|3end_MunI_regulatory_protein_587536..587686_NEGATIVE