Origin IGS: ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccctttatttttttattttatatcattaaacttaactaattcaattatatattattttatctaaaaaagcaatagcaacaaatataat .........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 attatatttgttgctattgcttttttagataaaataatatataattgaattagttaagtttaatgatataaaataaaaaaataaagggggatgtgtaatatgtttaagattcgcaataaacaattttctacttatatggcagatgtgcacatctgtcttggcaacatatacttttattctttgacttagataggattaaaattttatattggtaaagggctatttttaataatagttagttttgtagttcaataaaattttaattttaaataagaaggagaataaaa Mask Tandem Repeat Region ================================================ ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccctttatttttttattttatatcattaaacttaactaattcaattatatattattttatctaaaaaagcaatagcaacaaatataat Find is-nt database================================================ Query_seq: FN1890:FN1891|FN1890:FN1891:hypothetical protein:Glycerophosphoryl diester phosphodiesterase:<-<-:373312..373598 287 ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccctttatttttttattttatatcattaaacttaactaattcaattatatattattttatctaaaaaagcaatagcaacaaatataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1890:FN1891|FN1890:FN1891:hypothetical protein:Glycerophosphoryl diester phosphodiesterase:<-<-:373312..373598 287 ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccctttatttttttattttatatcattaaacttaactaattcaattatatattattttatctaaaaaagcaatagcaacaaatataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1890:FN1891|FN1890:FN1891:hypothetical protein:Glycerophosphoryl diester phosphodiesterase:<-<-:373312..373598 287 ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccctttatttttttattttatatcattaaacttaactaattcaattatatattattttatctaaaaaagcaatagcaacaaatataat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccctttatttttttattttatatcattaaacttaactaattcaattatatattattttatctaaaaaagcaatagcaacaaatataat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 65 End: 157 ................................................................ M A L Y Q Y K I L I L S K S K N K S I C C Q D R C A H L P Y K .................................................................................................................................. Protein_Len: 50 Strand: + Start: 111 End: 260 .............................................................................................................. M K V Y V A K T D V H I C H I S R K L F I A N L K H I T H P P L F F Y F I S L N L T N S I I Y Y F I ........................... Protein_Len: 32 Strand: - Start: 102 End: 197 ..................................................................................................... T L S Y F Y I N G L C I H V D A M Y T S F Q K N R I K F M N C M .......................................................................................... Protein_Len: 30 Strand: - Start: 76 End: 165 ........................................................................... W Y L I K I R D L D F F L L I H Q W S L H A C R G Y L Y F M .......................................................................................................................... ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccctttatttttttattttatatcattaaacttaactaattcaattatatattattttatctaaaaaagcaatagcaacaaatataat 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: 83 Start: 243 End: 272 ..................................................................................................................................................................................................................................................ATTGCTTTTTTAGATAAAATAATATATAAT............... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccctttatttttttattttatatcattaaacttaactaattcaattatatattattttatctaaaaaagcaatagcaacaaatataat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1890:FN1891|FN1890:FN1891:hypothetical protein:Glycerophosphoryl diester phosphodiesterase:<-<-:373312..373598 287 ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccctttatttttttattttatatcattaaacttaactaattcaattatatattattttatctaaaaaagcaatagcaacaaatataat Intra-Species Hit: Count: 1 Min: 1 Max: 287 Len: 287 Subject: NC_003454_FN1890_FN1891|hypothetical protein:Glycerophosphoryl diester phosphodiesterase|NEGATIVE:NEGATIVE|[373312,373598]|287 HSP 1 e-value: 1.0E-110 bit: 400.0 Len: 202 Query Start:1 Query End:202 Subject Strand: POSITIVE Subject Start: 1 Subject End: 202 ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccc..................................................................................... ttttattctccttcttatttaaaattaaaattttattgaactacaaaactaactattattaaaaatagccctttaccaatataaaattttaatcctatctaagtcaaagaataaaagtatatgttgccaagacagatgtgcacatctgccatataagtagaaaattgtttattgcgaatcttaaacatattacacatccccc..................................................................................... HSP 2 e-value: 7.0E-7 bit: 56.0 Len: 28 Query Start:260 Query End:287 Subject Strand: POSITIVE Subject Start: 260 Subject End: 287 ...................................................................................................................................................................................................................................................................ctaaaaaagcaatagcaacaaatataat ...................................................................................................................................................................................................................................................................ctaaaaaagcaatagcaacaaatataat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAUUCUCCUUCUUAUUUAAAAUUAAAAUUUUAUUGAACUACAAAACUAACUAUUAUUAAAAAUAGCCCUUUACCAAUAUAAAAUUUUAAUCCUAUCUAAGUCAAAGAAUAAAAGUAUAUGUUGCCAAGACAGAUGUGCACAUCUGCCAUAUAAGUAGAAAAUUGUUUAUUGCGAAUCUUAAACAUAUUACACAUCCCCCUUUAUUUUUUUAUUUUAUAUCAUUAAACUUAACUAAUUCAAUUAUAUAUUAUUUUAUCUAAAAAAGCAAUAGCAACAAAUAUAAU .((((((((....((((..((..(((((((((((((................(((((......)))))............)))))))))))))..))..))))....)))))))).((((.((((((.....((((((....))))))..((((((((((((((.((((((..........))))))....................))))))).)))))))...................................................)))))).))))... (-38.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUAUUUGUUGCUAUUGCUUUUUUAGAUAAAAUAAUAUAUAAUUGAAUUAGUUAAGUUUAAUGAUAUAAAAUAAAAAAAUAAAGGGGGAUGUGUAAUAUGUUUAAGAUUCGCAAUAAACAAUUUUCUACUUAUAUGGCAGAUGUGCACAUCUGUCUUGGCAACAUAUACUUUUAUUCUUUGACUUAGAUAGGAUUAAAAUUUUAUAUUGGUAAAGGGCUAUUUUUAAUAAUAGUUAGUUUUGUAGUUCAAUAAAAUUUUAAUUUUAAAUAAGAAGGAGAAUAAAA ....(((.((((((((.....................(((((.((((((((.....)))))))).)))))..............(((.(((((((((...((((((..........))))))....(((.((.....)).)))..))))))))).))))))))))).)))..((((((((((..((((..(((((((((((((((((((((..((..(((((((......)))))))..))...))))...)))))))))))))))))..))))..)))))))))). (-63.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 789 140 91 231 182 NC_003454:FN1890|5end_hypothetical_protein_373221..373451_NEGATIVE 281 234 191 145 94 NC_003454:FN0832|5end_hypothetical_protein_1494305..1494535_POSITIVE 277 211 175 114 76 NC_003454:FN1897|5end_ABC_transporter_integral_membrane_protein_384984..385214_NEGATIVE 257 174 133 63 31 NC_003454:FN0833|5end_hypothetical_protein_1494853..1495083_POSITIVE 237 159 113 56 4 NC_003454:FN0034|5end_hypothetical_protein_676089..676319_NEGATIVE 228 128 83 59 19 NC_003454:FN0087|5end_Ethanolamine_utilization_protein_eutN_724626..724856_POSITIVE 228 162 125 193 157 NC_003454:FN2041|5end_Transcription_antitermination_protein_nusG_549659..549889_NEGATIVE 215 220 179 125 77 NC_003454:FN2071|5end_hypothetical_protein_582375..582605_NEGATIVE 211 217 171 113 62 NC_003454:FN1831|5end_Nitrogen_assimilation_regulatory_protein_321423..321653_NEGATIVE 210 159 116 168 126 NC_003454:FN0332|5end_Magnesium_and_cobalt_transport_protein_corA_967230..967460_NEGATIVE 209 46 1 138 86 NC_003454:FN0829|5end_hypothetical_protein_1489873..1490103_NEGATIVE 209 161 122 164 121 NC_003454:FN0082|5end_Ethanolamine_utilization_protein_eutM_720699..720929_POSITIVE 209 144 102 107 64 NC_003454:FN1905|5end_168_kDa_surface-layer_protein_precursor_398116..398346_NEGATIVE 206 133 93 42 10 NC_003454:FN1232|5end_Transcriptional_regulator,_MarR_family_1889341..1889571_NEGATIVE 205 160 116 64 17 NC_003454:FN0201|5end_Glutaconyl-COA_decarboxylase_beta_subunit_826542..826772_POSITIVE 205 35 1 123 86 NC_003454:FN1984|5end_Glutaredoxin-like_protein_485487..485717_POSITIVE 200 140 92 150 105 NC_003454:FN1618|5end_hypothetical_protein_127205..127435_NEGATIVE 198 183 143 78 35 NC_003454:FN0116|5end_Chaperone_protein_dnaK_748253..748483_POSITIVE 198 277 231 156 107 NC_003454:FN1559|5end_cell_volume_regulation_protein_CvrA_80827..81057_POSITIVE 195 100 51 93 47 NC_003454:FN0936|5end_CapC_protein_1589107..1589337_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 211 175 112 74 NC_003454:FN1898|3end_Sugar_transport_ATP-binding_protein_384986..385136_NEGATIVE 228 128 83 57 17 NC_003454:FN0086|3end_hypothetical_protein_724704..724854_POSITIVE 211 217 171 96 45 NC_003454:FN1832|3end_TonB_protein_321440..321590_NEGATIVE 210 159 116 151 109 NC_003454:FN0333|3end_Glycerol_uptake_operon_antiterminator_regulatory_protein_967247..967397_NEGATIVE 205 160 116 49 2 NC_003454:FN0200|3end_Biotin_carboxyl_carrier_protein_of_glutaconyl-COA_decarboxylase_826607..826757_POSITIVE 200 140 92 79 34 NC_003454:FN1619|3end_Hypothetical_cytosolic_protein_127276..127426_NEGATIVE 198 183 143 47 4 NC_003454:FN0114|3end_GrpE_protein_748302..748452_POSITIVE 198 209 164 115 69 NC_003454:FN1687|3end_Gluconate_5-dehydrogenase_182900..183050_NEGATIVE 195 100 51 103 57 NC_003454:FN0937|3end_Gamma-polyglutamic_acid_synthetase_1589097..1589247_NEGATIVE 195 214 172 101 57 NC_003454:FN1868|3end_Hypothetical_cytosolic_protein_359615..359765_NEGATIVE 190 220 172 123 78 NC_003454:FN0969|3end_hypothetical_protein_1621806..1621956_NEGATIVE 189 174 134 63 14 NC_003454:FN0205|3end_Sodium/glutamate_symport_carrier_protein_832808..832958_POSITIVE 188 218 196 97 70 NC_003454:FN1979|3end_SSU_ribosomal_protein_S15P_482073..482223_POSITIVE 187 50 1 117 66 NC_003454:FN1269|3end_Hypothetical_lipoprotein_1925613..1925763_NEGATIVE 187 220 195 104 73 NC_003454:FN1067|3end_Tetratricopeptide_repeat_family_protein_1713879..1714029_POSITIVE 187 34 5 47 15 NC_003454:FN1858|3end_Short-chain_fatty_acids_transporter_346896..347046_NEGATIVE 186 240 196 96 57 NC_003454:FN0963|3end_hypothetical_protein_1617130..1617280_NEGATIVE 185 222 196 109 80 NC_003454:FN0021|3end_4-diphosphocytidyl-2-C-methyl-D-erythritol_kinase_660854..661004_POSITIVE 183 209 165 92 43 NC_003454:FN1247|3end_LOS_biosynthesis_enzyme_LBGB_1903205..1903355_NEGATIVE 181 177 133 131 85 NC_003454:FN0594|3end_(3R)-hydroxymyristoyl-[acyl_carrier_protein]_dehydratase_1249290..1249440_POSITIVE